research article absence of cospeciation between the
TRANSCRIPT
Research ArticleAbsence of Cospeciation between the Uncultured FrankiaMicrosymbionts and the Disjunct Actinorhizal Coriaria Species
Imen Nouioui1 Faten Ghodhbane-Gtari1 Maria P Fernandez2
Abdellatif Boudabous1 Philippe Normand2 and Maher Gtari13
1 Laboratoire Microorganismes et Biomolecules Actives Universite de Tunis El Manar (FST) et Universite Carthage (INSAT)2092 Tunis Tunisia
2 Ecologie Microbienne Centre National de la Recherche Scientifique UMR 5557 Universite Lyon I 69622 Villeurbanne Cedex France3 Laboratoire Microorganismes et Biomolecules Actives Faculte des Sciences de Tunis Campus Universitaire 2092 Tunis Tunisia
Correspondence should be addressed to Maher Gtari mahergtarifstrnutn
Received 4 March 2014 Revised 25 March 2014 Accepted 27 March 2014 Published 22 April 2014
Academic Editor Ameur Cherif
Copyright copy 2014 Imen Nouioui et al This is an open access article distributed under the Creative Commons Attribution Licensewhich permits unrestricted use distribution and reproduction in any medium provided the original work is properly cited
Coriaria is an actinorhizal plant that forms root nodules in symbiosis with nitrogen-fixing actinobacteria of the genus FrankiaThissymbiotic association has drawn interest because of the disjunct geographical distribution of Coriaria in four separate areas of theworld and in the context of evolutionary relationships between host plants and their uncultured microsymbionts The evolutionof Frankia-Coriaria symbioses was examined from a phylogenetic viewpoint using multiple genetic markers in both bacteria andhost-plant partners Total DNA extracted from root nodules collected from five species C myrtifolia C arborea C nepalensis Cjaponica andCmicrophylla growing in theMediterranean area (Morocco and France) New Zealand Pakistan Japan andMexicorespectively was used to amplify glnA gene (glutamine synthetase) dnaA gene (chromosome replication initiator) and the nifDK IGS (intergenic spacer between nifD and nifK genes) in Frankia and the matK gene (chloroplast-encoded maturase K) andthe intergenic transcribed spacers (18S rRNA-ITS1-58S rRNA-ITS2-28S rRNA) in Coriaria species Phylogenetic reconstructionindicated that the radiations of Frankia strains and Coriaria species are not congruent The lack of cospeciation between the twosymbiotic partners may be explained by host shift at high taxonomic rank together with wind dispersal andor survival in nonhostrhizosphere
1 Introduction
The genus Frankia comprises nitrogen-fixing actinobac-teria that are able to induce perennial root nodules onwoody dicotyledonous plants called actinorhizals [1] Theactinorhizal plant families belong to three dicotyledonousorders Fagales (BetulaceaeCasuarinaceae and Myricaceae)Rosales (Elaeagnaceae Rhamnaceae and Rosaceae) andCucurbitales (Coriariaceae and Datiscaceae) [2] Analysis ofthe molecular phylogeny of members of Frankia genus con-sistently identifies four main clusters regardless of the typinglocus used [3] Three symbiotic Frankia clusters containingstrains able to establish effective nodules and fulfill Kochrsquospostulates and one atypical with strains unable to establisheffective nodulation on their host plants have been definedamong Frankia genera Cluster 1 includes Frankia strains in
association with Betulaceae Myricaceae and CasuarinaceaeCluster 2 contains Frankia nodulating species from theCoriariaceae Datiscaceae and Rosaceae families as well asCeanothus of the Rhamnaceae Frankia strains in cluster 3form effective root nodules on plants from members of theMyricaceae Rhamnaceae Elaeagnaceae andGymnostoma ofthe Casuarinaceae
Symbiotic Frankia strains have been only isolated fromFagales (Frankia cluster 1) and the families Elaeagnaceaeand Rhamnaceae (Frankia cluster 3) of the Rosales whileFrankia of cluster 2 have still not yet been isolated in culturedespite repeated attempts [2] The position in the Frankiaphylogenetic tree of cluster 2 relative to the other clusters hasvaried depending on the marker used It was proposed at thebase using glnA and 16S rRNA genes [4 5] derived with ITS16Sndash23S rRNA genes [6] and concatenated gyrB nifH and
Hindawi Publishing CorporationBioMed Research InternationalVolume 2014 Article ID 924235 9 pageshttpdxdoiorg1011552014924235
2 BioMed Research International
glnII genes [7] and should be clarified by the upcoming wholegenome phylogeny Nevertheless a position at the base of allsymbiotic lineages has been retained in the latest treatment ofBergeyrsquos manual [8]
Cross-inoculation studies using crushed nodules suggestthat cluster 2 strains form a separate and unique hostspecificity group [9ndash11] even though provenances from thefull geographical range have not yet been tested Despitethe high taxonomic diversity of host plants belonging tothe cross-inoculation group of cluster 2 and its disjunctrange uncultured Frankia in root nodules of several hostplants have so far shown a low level of diversity regardlessof the typing locus used [6 7 11ndash16] suggesting a recentemergence a strong and recent evolutionary bottleneck ora nonrepresentative sampling The time of emergence of allFrankia lineages is poorly documented as no convincingfossil remains An equivalence between 16S rRNA sequencesdistance and time of emergence has been proposed byOchman andWilson [17] where 1 is equivalent to 50millionyears and since 4 divergence exists between Frankia cluster2 and the other clusters one would conclude that Frankiaemerged 200 million years ago [5] which would mean thatthere is missing diversity either due to a recent evolutionarybottleneck or due to a lack of sampling [16] A possibility thusexists that the missing variability in cluster 2 strains is due tothe fact that sampling has so far been limited essentially toNorth American and Mediterranean areas
Evidence for cospeciation has been found so far only inthe case of Casuarina species growing in Australia and theirFrankia [18] that are in their immense majority resistant togrowth in pure culture Among actinorhizal plants of theCucurbitales subclade the family Coriariaceae with only onegenus Coriaria contains about 17 species [19] that occur infour disjunct areas of theworld theMediterranean SoutheastAsia Central and South America and the Pacific islands ofNew Zealand and Papua New Guinea [20ndash24] Yokoyama etal [19] considered that the Eurasian species are basal and haveemerged some 60million years agoThis date is in agreementwith the 65 million years proposed by Bell et al [25] based onmultiple genes (rbcL 18S rDNA atpB) phylogeny while thesame authors propose an emergence of the Casuarinaceae atabout 30 million years
The present study was aimed at testing the hypothesisof cospeciation between uncultured Frankiamicrosymbiontsand their Coriaria host species sampled from sites coveringthe full geographical range of the genus Coriaria myrtifolia(Morocco and France) C nepalensis (Pakistan) C arborea(New Zealand) C japonica (Japan) and C microphylla(Mexico)
2 Materials and Methods
21 DNA Extraction PCR Amplification and SequencingRoot nodules from naturally occurring Coriaria species(Table 1) were kindly provided by Dr Marıa Valdes (EscuelaNacional de Ciencias Biologicas Mexico DF Mexico) DrSajjad Mirza (National Institute for Biotechnology GeneticEngineering Faisalabad Pakistan) Dr Warwick Silvester(University of Waikato Waikato New Zealand) Dr Kawther
Benbrahim (University of Fes Fes Morocco) Dr TakashiYamanaka (Forest and Forestry Products Research InstituteIbaraki Japan) and Dr Jean-Claude Cleyet-Marel (INRA-IRD Montpellier France) Individual lobes were selectedsurface-sterilized in 30 (volvol) H
2O2 and rinsed several
times with distilled sterile water The DNA extraction fromsingle nodule lobes was performed as previously describedby Rouvier et al [26] Nodule lobes were crushed with sterileplastic mortars and pestles in 300 120583L of extraction buffer(100mMTris (pH 8) 20mM EDTA 14MNaCl 2 (wtvol)CTAB (cetyltrimethyl ammonium bromide) and 1 (wtvol)PVPP (polyvinyl polypyrrolidone)) The homogenates wereincubated at 65∘C for 60min extracted with chloroform-isoamyl alcohol (24 1 volvol) and the resulting DNA wasethanol-precipitated and resolubilized The extracted DNAwas used for PCR amplification of both bacterial and plantDNA regions using the primers listed in Table 2 The ampli-cons were then cycle-sequenced in both directions usingan ABI cycle sequencing kit (Applied Biosystem 3130) Thenucleotide sequences obtained in this studywere deposited inthe NCBI nucleotide sequence database under the accessionnumbers given in Table 1
22 Phylogenetic Analysis Frankia strainCcI3 andCasuarinaequisetifolia were used as outgroups in this study becausethey are physiologically distinct from the group studied yetphylogenetically close The data sets were completed withhomologous sequences present in the databases (Table 1)Alignments of Frankia glnA dnaA and IGS nifD-K andCori-aria matK and 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNAwere generated with ClustalW [27] manually edited withMEGA50 [28] Bacterial and plant sequenceswere separatelyconcatenated and thenused to examinemaximum-likelihoodcladogram evolutionary relationships of each symbiotic part-ner using 1000 bootstraps by following the GTR + G basesubstitution model The distance between the sequences wascalculated using Kimurarsquos two-parameter model [29] Phy-logenetic trees were constructed using the Neighbor-Joiningmethod [30] with 1000 bootstraps [31] as implemented inMEGA 50 In parallel a Bayesian inference was realizedwith MrBayes [32] using the GTR + G model and 1000000generations
A statistical test for the presence of congruence betweenCoriaria and Frankia phylogenies was evaluated throughglobal distance-based fitting in ParaFit program [33] asimplemented in CopyCat [34] and tests of random associa-tion were performed with 9999 permutations globally acrossboth phylogenies for each association
An additional statistical test for correlation betweengeographical distances (obtained using httpwwwdaftlogiccomprojects-google-maps-distance-calculatorhtm) andphylogenetic distanceswasmade using Pearsonrsquos r correlationimplemented in the R software [35]
3 Results
To avoid taxonomic ambiguities DNAs from both Coriariahosts and Frankiamicrosymbionts were characterized on thesame root nodule tissuesThemethod of DNA isolation from
BioMed Research International 3
Table1Listof
Coria
riaroot
nodu
lesa
ndsequ
encesu
sedin
thisstu
dy
Species
Localitycoordinatesaltitud
e(asl)
Nod
ule
labels
Plantsequencea
ccessio
nnu
mberBa
cterialsequencea
ccessio
nnu
mberRe
ferences
ITS1-ITS
2matK
glnA
dnaA
IGSnifD
-K
Cmyrtifolia
Morocco
OuedEl
Koub
Ouezzane
35∘011015840879N
05∘201015840565E
140m
CmMs1
KC796592
KC7966
01KC
796522
KC796582
KC796555
Thisstu
dyCm
Ms2
CmMs3
CmMs4
KC796523
KC796524
KC796525
KC796583
KC796584
KC796585
KC796556
KC796557
KC796558
Thisstu
dyTh
isstu
dyTh
isstu
dy
BabBe
rredC
hefchaou
en
35∘001015840979N
04∘58101584009210158401015840E1290
m
CmM1a
KC796590
KC796599
KC796517
KC796578
KC796550
Thisstu
dyCm
M1b
KC796518
KC796579
KC796551
Thisstu
dyCm
M1c
KC796519
KC796580
KC796552
Thisstu
dyCm
M2a
KC796591
KC7966
00KC
796520
mdashKC
796553
Thisstu
dyCm
M2b
KC796521
KC796581
KC796554
Thisstu
dyFrance
Nyons44∘21101584046
5010158401015840N5∘081015840218210158401015840E259m
CmNy1
KC796598
KC7966
03KC
796531
KC796591
KC796564
Thisstu
dyCm
Ny2
CmNy3
CmNy4
CmNy5
KC796532
KC796533
KC796534
KC796535
KC796592
KC796593
KC796594
KC796595
KC796565
mdashKC
796566
KC796567
Thisstu
dyTh
isstu
dyTh
isstu
dyTh
isstu
dy
Mon
tpellier43∘361015840514810158401015840N3∘521015840239710158401015840E41
m
CmF1
KC796526
KC796586
KC796559
Thisstu
dyCm
F2KC
796593
KC7966
02KC
796527
KC796587
KC796560
Thisstu
dyCm
F3Cm
F4Cm
F5
KC796528
KC796529
KC796530
KC796588
KC796589
KC796590
KC796561
KC796562
KC796563
Thisstu
dyTh
isstu
dyTh
isstu
dyAF280102
Yang
etalun
publish
edAB0
16459
(Yokoyam
aetal2000
[19])
Cjaponica
Japan
Tosa
distr
ict+3
3∘451015840391810158401015840+
133∘27101584042891015840101584010
m
CjJA
KC7966
05KC
796536
KC796503
KC796576
Thisstu
dyCjJB
KC796594
KC796537
KC796504
KC796577
Thisstu
dyCjJC
CjJD
CjJE
KC796538
KC796539
KC796540
KC796505
KC796506
KC796507
KC796578
KC796579
KC796580
Thisstu
dyTh
isstu
dyTh
isstu
dyAF280101
Yang
etalun
publish
edAB0
16456
(Yokoyam
aetal2000
[19])
Cnepalen
sis
Pakista
n
Murree+3
3∘5410158401510158401015840N73∘2310158402510158401015840E33904
2∘N
7339
03∘E22912m
CnP1
KC796597
KC7966
07KC
796544
KC796508
KC796584
Thisstu
dyCn
P2KC
796545
KC796509
KC796585
Thisstu
dyCn
P3KC
796546
KC796510
KC796586
Thisstu
dyCn
P4AF280103
Yang
etalun
publish
ed
4 BioMed Research International
Table1Con
tinued
Species
Localitycoordinatesaltitud
e(asl)
Nod
ule
labels
Plantsequencea
ccessio
nnu
mberBa
cterialsequencea
ccessio
nnu
mberRe
ferences
ITS1-ITS
2matK
glnA
dnaA
IGSnifD
-K
Carborea
NewZealand
Hapuk
uriv
erN
orth
Canterbu
rySou
thisland
minus42∘231015840422410158401015840+
173∘41101584018071015840101584064m
CaNZ1
KC796595
KC7966
04KC
796542
KC796511
KC796581
Thisstu
dyCa
NZ2
KC796543
KC796512
KC796582
Thisstu
dyCa
NZ3
KC796544
KC796513
KC796583
Thisstu
dyAB164
54(Yokoyam
aetal2000
[19])
EF635457
Rotherham
etalun
publish
edEF
635475
Rotherham
etalun
publish
edAF277293
Yang
etalun
publish
ed
Cmicrophylla
Mexico
Morelo
s99∘30101584019∘301015840240
0m
CmicMx1
KC796596
KC7966
06KC
796547
KC796514
KC796587
Thisstu
dyCm
icMx2
KC796548
KC796515
KC796588
Thisstu
dyCm
icMx3
KC796549
KC796516
KC796589
Thisstu
dyAY
091813
Yang
etalun
publish
edAB0
16458
(Yokoyam
aetal2000
[19])
Cinterm
edia
AF280100
Yang
etalun
publish
edAB0
16455
(Yokoyam
aetal2000
[19])
Cterm
inalis
AY091817
Yang
etalun
publish
ed
Cruscifolia
AY091815
Yang
etalun
publish
edAY
091814
Yang
etalun
publish
edAF280104
Yang
etalun
publish
edAB0
16462
(Yokoyam
aetal2000
[19])
Csarm
entosa
AY091816
Yang
etalun
publish
edAB0
1646
4(Yokoyam
aetal2000
[19])
Cpapu
ana
AB0
16461
(Yokoyam
aetal2000
[19])
Datisca
glomerata
CP002801
CP002801
CP002801
(Persson
etal2011[50])
AY968449
Zhangetalun
publish
edAF4
85250
Forrestand
Hollin
gsworth
unpu
blish
ed
Casuarina
equisetifolia
CP00
0249
CP00
0249
CP00
0249
(Normandetal2007
[51])
AB0
15462
Sogo
etalun
publish
edAY
8640
57Herbertetalun
publish
ed
BioMed Research International 5
Table 2 Primers used for PCR amplification and DNA sequencing
Gene primers Sequence (51015840-31015840) Amplicons approximate size (bp) ReferencesglnA
DB41 TTCTTCATCCACGACCCG 500 (Clawson et al 2004 [4])DB44 GGCTTCGGCATGAAGGT
dnaAF7154 dnaAF GAGGARTTCACCAACGACTTCAT 700 Bautista et al unpublishedF7155 dnaAR CRGAAGTGCTGGCCGATCTT
IGS nifD-KF9372 nifD1 5 GTCATGCTCGCCGTCGGNG 700 This studyF9374 nifK1 5 GTTCTTCTCCCGGTAyTCCCA
F9373 nifD2 5 ACCGGCTACGAGTTCGCNCA 700 This studyF9375 nifK2 5 TGCGAGCCGTGCACCAGNG
18S-ITS1-58S-ITS2-28SITS1 TCCGTAGGTGAACCTGCGG 700 (White et al 1990 [52])ITS4 TCCTCCGCTTATTGATATGC
F9030-CJ-ITSF AGCCGGACCCGCGACGAGTTT 400 This studyF9031-CJ-ITSR CGACGTTGCGTGACGACGCCCA
matKF9249-matKF ACATTTAAATTATGTGTCAG 700 This studyF9250-matkR TGCATATACGCACAAATC
root nodules used in this study yielded PCR-amplifiable DNAfor both bacterial and plant PCR target sequences in all casesHowever in several instances it was easier to amplify Frankiathan Coriaria DNA which may have been mostly due to thespecificity of the primer sets used Thus in this study newprimers were designed (Table 2)
For the bacterial microsymbionts the average uncorrec-ted p-distances (proportion of differences between sequen-ces) were computed for each region and were found to berelatively small for dnaA (119901 = 00378) intermediate for glnA(119901 = 00625) and high for IGS nifD-K region (119901 = 00833)Blast analyses of the individual genes permitted assigningthem all to Frankia cluster 2 Nearly 3000 nucleotides wereobtained by concatenating sequences of the three DNAregions
Sequences variation for Coriaria species was small basedonmatKgene (119901 = 00205) compared to ITS1-ITS2 sequences(119901 = 00423) By concatenatingmatK and ITS1- ITS2 regiona composite sequence of 1500 nt was used for phylogeneticinference
All studied sequenceswere analyzed independently to testfor incongruence between the data sets for each symbioticpartner Similar topologies have been generally observedbetween phylogenetic trees inferred from glnA dnaA andIGS nifD-K sequences for Frankia and from matK and ITSsequences for Coriaria regardless of the used phylogeneticmethods (not shown)
The topologies of the trees obtained for the two symbioticpartners were not congruent (Figure 1) Moreover globaldistance-based ParaFit analysis recovered mostly randomassociations between Frankia and Coriaria host plant species(119901 = 033) and rejected cospeciation hypothesis On the
microbial side the New Zealand microsymbionts were atthe root (Group A) then three groups emerged groupB comprising the Pakistani Mexican and Mediterraneansymbionts from France group C comprising microsym-bionts from Morocco and then group D comprising Frenchand Japanese microsymbionts as well as the Dg1 referencesequence obtained initially from a Pakistani soil On thehost plant side group 1 at the root comprises New Zealandand South American sequences while group 2 comprises theJapanese Mediterranean and Pakistani sequences
On the other hand no significant correlations were foundfor Frankia symbionts (1199032 = 0772 Fgeneticdist = (geogdist times5830Eminus06) + 2541Eminus02) nor for the Coriaria host plants (1199032= 0883 Fgeneticdist = (geogdist times 2023Eminus06) + 6460Eminus03)(data not shown)
4 Discussion
Cospeciation has been postulated to have occurred insome Frankia actinorhizal host plants in particular in theCasuarina-Frankia cluster 1b [18] but not in Alnus-infectiveand Elaeagnus-infective Frankia strains where many isolatesable to fulfill Kochrsquos postulates have been obtained Totest if cospeciation was general or an exception it wasdecided to study uncultured Frankia microsymbionts andrepresentative Coriaria hosts a lineage where no Frankiaisolate exists and where geographic discontinuities may havelimited dispersion DNA sequences were obtained from rootnodules collected from New Zealand (C arborea) Pakistan(C nepalensis) Japan (C japonica) Mexico (C microphylla)and France and Morocco (C myrtifolia) and multiple molec-ular markers were analyzed for phylogenetic inference
6 BioMed Research International
Dg1
FCjJBFCjJA
FCmF1FCmF2FCmMs2FCmMs4FCmMs1FCmM1aFCmM1cFCmM1bFCmNy4FCmMs3FCmM2bFCmNy1FCmNy5FCnP1FCnP2FCmMx1FCmMx2FCaNZ2FCaNZ1100
99
99
69
100
8980
92
68
91
100
99
97
99
7581
OceaniaAsia
EuropeN AfricaAmerica
Gro
up A
G
roup
BG
roup
CG
roup
D
CmM1aCmM2aCmMs1
CmF2CmNy5
C myrtifolia C myrtifolia
CnP1
C nepalensisC terminalis C intermedia C japonica
CmicMx1C microphylla
C papuanaCaNZ1C arborea
C ruscifolia C sarmentosa
C lurida
8676
7590
7096
54
90
7083
7351
90
87
CjJA
Gro
up 2
Gro
up 1
Frankia Coriaria
Figure 1 Phylogenetic trees of the Frankiamicrosymbionts (left) and the Coriaria host plants (right)The Frankia tree was constructed usingthe glnA dnaA and the nifD-K intergenic spacer while the Coriaria tree was done using thematK and the 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNA with ML method using strain CcI3 and Casuarina as outgroups respectively for Frankia and hot plant phylogenetic trees Thenumbers at branches indicate bootstrap results above 50 Lines are drawn between the microsymbionts and their hosts The color codeindicates the place of origin of the leave or of the set when homogenousThe groups numbers 1 and 2 on the right are according to Yokoyamaet al [19]
Paleontological data based on macrofossils and pollenfossils have brought several authors [36ndash40] to conclude thatthe Coriariaceae had a Laurasian origin (North Americaand Eurasia) There have been a few dissenting opinions inparticular those of Croizat [41] and Schuster [42] who con-sidered that Coriaria originated in Gondwana and migratedto the Northern Hemisphere However such paleontologicalstudies are not very convincing as it is recognizably hardto ascribe fossils to a given family and even more so to agiven genus Thus several authors have been surprised bythe results of molecular phylogeny positioning Coriariaceaeclose to the Datiscaceae Molecular approaches would thusgive support to a Gondwanan origin
Yokoyama et al [19] proposed that Coriaria species hademerged 59ndash63 million years ago which is coherent withthe date of 70 million years proposed by Bell et al [25]considerably older than that proposed (30million years) bythe same authors for the Casuarinaceae
Topology and clustering of Coriaria phylogeny obtainedin the current study are similar to those obtained byYokoyama et al [19] while the position at the base of thehost plant species from New Zealand C arborea and the
South American C ruscifolia and C microphylla species wascontrary to that of Yokoyama et al [19] who found theEurasian species at the base using rbcL (a large subunit ofribulose 15-bisphosphate carboxylaseoxygenase) and matK(maturase K) genes The present study suggests that theCoriaria ancestor may have emerged between Asia and NZand then dispersed worldwide and that the Asian lineagemay have given rise relatively recently to the Mediterraneanspecies while theNZ lineage gave rise to theNorth Americanspecies (Figure 2)
Previous studies had concluded that Frankia cluster 2 hada low genetic diversity [6 7 16] but these studies had beenfocused on only part of the full diversity of the symbioticCoriaria-Frankia essentially in North America and Mediter-ranean In this work we aimed to expand the scope of thestudy to the worldwide diversity and phylogeny ofmicrosym-bionts of Coriaria species Four microbial subgroups wereidentified that did not fit to the geographic range of the hostplants while two host plant subgroups were identified Theposition of subgroup A containing microsymbionts of NewZealand C arborea at the base of Frankia cluster 2 is inagreement with previous study [16] In view of previously
BioMed Research International 7
C ruscifolia
C nepalensis
Coriaria agustissima
C kingiana
C plumosaC lurida
C pteroidesC pottsiana
C sarmentosa
C papuana
C sarmentosa
CmNy1-2-3-4-5CmF1-2-3-4-5Coriaria myrtifoliaCmM1a-b-cCmM2a-bCmMs1-2-3-4-5 CnP1-2-3
Coriaria sp
C arborea
C microphyllaCmicMx1-2-3
CaNZ1-2-3
C japonicaCjJA-B-C-D-E
C terminalisC intermedia
Figure 2 Distribution of Coriaria species Root nodules have been sampled from C myrtifolia C arborea C nepalensis C japonica and Cmicrophylla growing in Mediterranean areas (Morocco and France) New Zealand Pakistan Japan and Mexico respectively Short arrowsindicate sampling sites for this study while long arrows indicate possible routes of dispersal as discussed
reported data members of cluster 2 Frankia studied herewere found to have relatively higher sequences variation (p-distance = 00625) than those reported by Vanden Heuvel etal [16] (119901 = 000454) based on the same 460 nt of the glnAgene
Molecular clock dating suggests that Frankia genus hasemerged much earlier 125Myr bp before the appearance ofangiosperm fossils in the Cretaceous period and the extantactinorhizal plants [4] Normand et al [5] using the 4divergence in the 16S rRNA between cluster 2 and otherFrankia lineages as equivalent to 50MY1 distance [17]concluded that the genus Frankia had emerged long beforethe extant dicotyledonous lineages These authors proposedFrankia cluster 2 as the proto-Frankia as nonsymbioticancestor of 62ndash130Myr bp [43] and 100ndash200Myr bp [5] Sincethe distance in the 16S rRNA gene between cluster 1a (Frankiaalni) and cluster 1b is less than 1 the date of emergence of theCasuarina-infective lineage has been proposed to be less than50 million years [5]Thus the CasuarinaFrankia 1b lineage isconsiderably younger than the CoriariaFrankia lineage andwould have had less time to migrate out of its cradle andmingle with other hosts in its new territories and lose thecospeciation signal
Symbiotic partnership often tends to become obligatoryas in the case of Casuarina host plants where Frankia is onlypresent in soils close to the host plant [44] which means thatthe bacterium loses autonomy and becomes dependent on itshost Speciation of the host could then lead to synchronousspeciation of its microsymbiont unless dispersal throughlong-distance carriers such as winds or migratory birds
occurred or if there is survival of Frankia cluster 2 in therhizosphere of nonhosts as was recently demonstrated forAlnus glutinosa in Tunisia [45] The numerous transitionsseen in the Frankia phylogenetic tree from one continent toanother would reinforce the idea
Yokoyama et al [19] concluded from their study of theCoriaria species phylogeny that the Eurasian species haddiverged earlier and are more diverse than other groups butthat nevertheless the origin of the genus could have been inNorth America whence the South America and the Pacificspecies could have originated Our study brings us to suggesta third possibility Oceania which could also be the originof this actinorhizal symbiosis which can be concluded fromphylogenetic inferences positioning both bacterial and hostplant partners as at the base to Frankia-Coriaria symbiosisAnother element that would support this hypothesis is thelarge number of extant species there according to Yokoyamaet al [19] New Zealand would be home to 8 of the 17 existingspecies A similar argument has often been made to establishSub-Saharan Africa as the cradle of humankind [46] orMexico for maize [47]
Comparison of both the plant and the microbe phyloge-netic topologies did not show any evidence for cospeciationof Frankia microsymbiontsand their Coriaria host speciesThe results obtained in this study suggest that Frankiamicrosymbionts hosted currently by Coriaria species hadprobably dispersed globally as a proto-Frankia a free livingand nonsymbiotic ancestor In parallel the proto-Coriariathen diversified into the extantCoriaria species that appear tohave been retreating given their scattered distribution a trend
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
2 BioMed Research International
glnII genes [7] and should be clarified by the upcoming wholegenome phylogeny Nevertheless a position at the base of allsymbiotic lineages has been retained in the latest treatment ofBergeyrsquos manual [8]
Cross-inoculation studies using crushed nodules suggestthat cluster 2 strains form a separate and unique hostspecificity group [9ndash11] even though provenances from thefull geographical range have not yet been tested Despitethe high taxonomic diversity of host plants belonging tothe cross-inoculation group of cluster 2 and its disjunctrange uncultured Frankia in root nodules of several hostplants have so far shown a low level of diversity regardlessof the typing locus used [6 7 11ndash16] suggesting a recentemergence a strong and recent evolutionary bottleneck ora nonrepresentative sampling The time of emergence of allFrankia lineages is poorly documented as no convincingfossil remains An equivalence between 16S rRNA sequencesdistance and time of emergence has been proposed byOchman andWilson [17] where 1 is equivalent to 50millionyears and since 4 divergence exists between Frankia cluster2 and the other clusters one would conclude that Frankiaemerged 200 million years ago [5] which would mean thatthere is missing diversity either due to a recent evolutionarybottleneck or due to a lack of sampling [16] A possibility thusexists that the missing variability in cluster 2 strains is due tothe fact that sampling has so far been limited essentially toNorth American and Mediterranean areas
Evidence for cospeciation has been found so far only inthe case of Casuarina species growing in Australia and theirFrankia [18] that are in their immense majority resistant togrowth in pure culture Among actinorhizal plants of theCucurbitales subclade the family Coriariaceae with only onegenus Coriaria contains about 17 species [19] that occur infour disjunct areas of theworld theMediterranean SoutheastAsia Central and South America and the Pacific islands ofNew Zealand and Papua New Guinea [20ndash24] Yokoyama etal [19] considered that the Eurasian species are basal and haveemerged some 60million years agoThis date is in agreementwith the 65 million years proposed by Bell et al [25] based onmultiple genes (rbcL 18S rDNA atpB) phylogeny while thesame authors propose an emergence of the Casuarinaceae atabout 30 million years
The present study was aimed at testing the hypothesisof cospeciation between uncultured Frankiamicrosymbiontsand their Coriaria host species sampled from sites coveringthe full geographical range of the genus Coriaria myrtifolia(Morocco and France) C nepalensis (Pakistan) C arborea(New Zealand) C japonica (Japan) and C microphylla(Mexico)
2 Materials and Methods
21 DNA Extraction PCR Amplification and SequencingRoot nodules from naturally occurring Coriaria species(Table 1) were kindly provided by Dr Marıa Valdes (EscuelaNacional de Ciencias Biologicas Mexico DF Mexico) DrSajjad Mirza (National Institute for Biotechnology GeneticEngineering Faisalabad Pakistan) Dr Warwick Silvester(University of Waikato Waikato New Zealand) Dr Kawther
Benbrahim (University of Fes Fes Morocco) Dr TakashiYamanaka (Forest and Forestry Products Research InstituteIbaraki Japan) and Dr Jean-Claude Cleyet-Marel (INRA-IRD Montpellier France) Individual lobes were selectedsurface-sterilized in 30 (volvol) H
2O2 and rinsed several
times with distilled sterile water The DNA extraction fromsingle nodule lobes was performed as previously describedby Rouvier et al [26] Nodule lobes were crushed with sterileplastic mortars and pestles in 300 120583L of extraction buffer(100mMTris (pH 8) 20mM EDTA 14MNaCl 2 (wtvol)CTAB (cetyltrimethyl ammonium bromide) and 1 (wtvol)PVPP (polyvinyl polypyrrolidone)) The homogenates wereincubated at 65∘C for 60min extracted with chloroform-isoamyl alcohol (24 1 volvol) and the resulting DNA wasethanol-precipitated and resolubilized The extracted DNAwas used for PCR amplification of both bacterial and plantDNA regions using the primers listed in Table 2 The ampli-cons were then cycle-sequenced in both directions usingan ABI cycle sequencing kit (Applied Biosystem 3130) Thenucleotide sequences obtained in this studywere deposited inthe NCBI nucleotide sequence database under the accessionnumbers given in Table 1
22 Phylogenetic Analysis Frankia strainCcI3 andCasuarinaequisetifolia were used as outgroups in this study becausethey are physiologically distinct from the group studied yetphylogenetically close The data sets were completed withhomologous sequences present in the databases (Table 1)Alignments of Frankia glnA dnaA and IGS nifD-K andCori-aria matK and 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNAwere generated with ClustalW [27] manually edited withMEGA50 [28] Bacterial and plant sequenceswere separatelyconcatenated and thenused to examinemaximum-likelihoodcladogram evolutionary relationships of each symbiotic part-ner using 1000 bootstraps by following the GTR + G basesubstitution model The distance between the sequences wascalculated using Kimurarsquos two-parameter model [29] Phy-logenetic trees were constructed using the Neighbor-Joiningmethod [30] with 1000 bootstraps [31] as implemented inMEGA 50 In parallel a Bayesian inference was realizedwith MrBayes [32] using the GTR + G model and 1000000generations
A statistical test for the presence of congruence betweenCoriaria and Frankia phylogenies was evaluated throughglobal distance-based fitting in ParaFit program [33] asimplemented in CopyCat [34] and tests of random associa-tion were performed with 9999 permutations globally acrossboth phylogenies for each association
An additional statistical test for correlation betweengeographical distances (obtained using httpwwwdaftlogiccomprojects-google-maps-distance-calculatorhtm) andphylogenetic distanceswasmade using Pearsonrsquos r correlationimplemented in the R software [35]
3 Results
To avoid taxonomic ambiguities DNAs from both Coriariahosts and Frankiamicrosymbionts were characterized on thesame root nodule tissuesThemethod of DNA isolation from
BioMed Research International 3
Table1Listof
Coria
riaroot
nodu
lesa
ndsequ
encesu
sedin
thisstu
dy
Species
Localitycoordinatesaltitud
e(asl)
Nod
ule
labels
Plantsequencea
ccessio
nnu
mberBa
cterialsequencea
ccessio
nnu
mberRe
ferences
ITS1-ITS
2matK
glnA
dnaA
IGSnifD
-K
Cmyrtifolia
Morocco
OuedEl
Koub
Ouezzane
35∘011015840879N
05∘201015840565E
140m
CmMs1
KC796592
KC7966
01KC
796522
KC796582
KC796555
Thisstu
dyCm
Ms2
CmMs3
CmMs4
KC796523
KC796524
KC796525
KC796583
KC796584
KC796585
KC796556
KC796557
KC796558
Thisstu
dyTh
isstu
dyTh
isstu
dy
BabBe
rredC
hefchaou
en
35∘001015840979N
04∘58101584009210158401015840E1290
m
CmM1a
KC796590
KC796599
KC796517
KC796578
KC796550
Thisstu
dyCm
M1b
KC796518
KC796579
KC796551
Thisstu
dyCm
M1c
KC796519
KC796580
KC796552
Thisstu
dyCm
M2a
KC796591
KC7966
00KC
796520
mdashKC
796553
Thisstu
dyCm
M2b
KC796521
KC796581
KC796554
Thisstu
dyFrance
Nyons44∘21101584046
5010158401015840N5∘081015840218210158401015840E259m
CmNy1
KC796598
KC7966
03KC
796531
KC796591
KC796564
Thisstu
dyCm
Ny2
CmNy3
CmNy4
CmNy5
KC796532
KC796533
KC796534
KC796535
KC796592
KC796593
KC796594
KC796595
KC796565
mdashKC
796566
KC796567
Thisstu
dyTh
isstu
dyTh
isstu
dyTh
isstu
dy
Mon
tpellier43∘361015840514810158401015840N3∘521015840239710158401015840E41
m
CmF1
KC796526
KC796586
KC796559
Thisstu
dyCm
F2KC
796593
KC7966
02KC
796527
KC796587
KC796560
Thisstu
dyCm
F3Cm
F4Cm
F5
KC796528
KC796529
KC796530
KC796588
KC796589
KC796590
KC796561
KC796562
KC796563
Thisstu
dyTh
isstu
dyTh
isstu
dyAF280102
Yang
etalun
publish
edAB0
16459
(Yokoyam
aetal2000
[19])
Cjaponica
Japan
Tosa
distr
ict+3
3∘451015840391810158401015840+
133∘27101584042891015840101584010
m
CjJA
KC7966
05KC
796536
KC796503
KC796576
Thisstu
dyCjJB
KC796594
KC796537
KC796504
KC796577
Thisstu
dyCjJC
CjJD
CjJE
KC796538
KC796539
KC796540
KC796505
KC796506
KC796507
KC796578
KC796579
KC796580
Thisstu
dyTh
isstu
dyTh
isstu
dyAF280101
Yang
etalun
publish
edAB0
16456
(Yokoyam
aetal2000
[19])
Cnepalen
sis
Pakista
n
Murree+3
3∘5410158401510158401015840N73∘2310158402510158401015840E33904
2∘N
7339
03∘E22912m
CnP1
KC796597
KC7966
07KC
796544
KC796508
KC796584
Thisstu
dyCn
P2KC
796545
KC796509
KC796585
Thisstu
dyCn
P3KC
796546
KC796510
KC796586
Thisstu
dyCn
P4AF280103
Yang
etalun
publish
ed
4 BioMed Research International
Table1Con
tinued
Species
Localitycoordinatesaltitud
e(asl)
Nod
ule
labels
Plantsequencea
ccessio
nnu
mberBa
cterialsequencea
ccessio
nnu
mberRe
ferences
ITS1-ITS
2matK
glnA
dnaA
IGSnifD
-K
Carborea
NewZealand
Hapuk
uriv
erN
orth
Canterbu
rySou
thisland
minus42∘231015840422410158401015840+
173∘41101584018071015840101584064m
CaNZ1
KC796595
KC7966
04KC
796542
KC796511
KC796581
Thisstu
dyCa
NZ2
KC796543
KC796512
KC796582
Thisstu
dyCa
NZ3
KC796544
KC796513
KC796583
Thisstu
dyAB164
54(Yokoyam
aetal2000
[19])
EF635457
Rotherham
etalun
publish
edEF
635475
Rotherham
etalun
publish
edAF277293
Yang
etalun
publish
ed
Cmicrophylla
Mexico
Morelo
s99∘30101584019∘301015840240
0m
CmicMx1
KC796596
KC7966
06KC
796547
KC796514
KC796587
Thisstu
dyCm
icMx2
KC796548
KC796515
KC796588
Thisstu
dyCm
icMx3
KC796549
KC796516
KC796589
Thisstu
dyAY
091813
Yang
etalun
publish
edAB0
16458
(Yokoyam
aetal2000
[19])
Cinterm
edia
AF280100
Yang
etalun
publish
edAB0
16455
(Yokoyam
aetal2000
[19])
Cterm
inalis
AY091817
Yang
etalun
publish
ed
Cruscifolia
AY091815
Yang
etalun
publish
edAY
091814
Yang
etalun
publish
edAF280104
Yang
etalun
publish
edAB0
16462
(Yokoyam
aetal2000
[19])
Csarm
entosa
AY091816
Yang
etalun
publish
edAB0
1646
4(Yokoyam
aetal2000
[19])
Cpapu
ana
AB0
16461
(Yokoyam
aetal2000
[19])
Datisca
glomerata
CP002801
CP002801
CP002801
(Persson
etal2011[50])
AY968449
Zhangetalun
publish
edAF4
85250
Forrestand
Hollin
gsworth
unpu
blish
ed
Casuarina
equisetifolia
CP00
0249
CP00
0249
CP00
0249
(Normandetal2007
[51])
AB0
15462
Sogo
etalun
publish
edAY
8640
57Herbertetalun
publish
ed
BioMed Research International 5
Table 2 Primers used for PCR amplification and DNA sequencing
Gene primers Sequence (51015840-31015840) Amplicons approximate size (bp) ReferencesglnA
DB41 TTCTTCATCCACGACCCG 500 (Clawson et al 2004 [4])DB44 GGCTTCGGCATGAAGGT
dnaAF7154 dnaAF GAGGARTTCACCAACGACTTCAT 700 Bautista et al unpublishedF7155 dnaAR CRGAAGTGCTGGCCGATCTT
IGS nifD-KF9372 nifD1 5 GTCATGCTCGCCGTCGGNG 700 This studyF9374 nifK1 5 GTTCTTCTCCCGGTAyTCCCA
F9373 nifD2 5 ACCGGCTACGAGTTCGCNCA 700 This studyF9375 nifK2 5 TGCGAGCCGTGCACCAGNG
18S-ITS1-58S-ITS2-28SITS1 TCCGTAGGTGAACCTGCGG 700 (White et al 1990 [52])ITS4 TCCTCCGCTTATTGATATGC
F9030-CJ-ITSF AGCCGGACCCGCGACGAGTTT 400 This studyF9031-CJ-ITSR CGACGTTGCGTGACGACGCCCA
matKF9249-matKF ACATTTAAATTATGTGTCAG 700 This studyF9250-matkR TGCATATACGCACAAATC
root nodules used in this study yielded PCR-amplifiable DNAfor both bacterial and plant PCR target sequences in all casesHowever in several instances it was easier to amplify Frankiathan Coriaria DNA which may have been mostly due to thespecificity of the primer sets used Thus in this study newprimers were designed (Table 2)
For the bacterial microsymbionts the average uncorrec-ted p-distances (proportion of differences between sequen-ces) were computed for each region and were found to berelatively small for dnaA (119901 = 00378) intermediate for glnA(119901 = 00625) and high for IGS nifD-K region (119901 = 00833)Blast analyses of the individual genes permitted assigningthem all to Frankia cluster 2 Nearly 3000 nucleotides wereobtained by concatenating sequences of the three DNAregions
Sequences variation for Coriaria species was small basedonmatKgene (119901 = 00205) compared to ITS1-ITS2 sequences(119901 = 00423) By concatenatingmatK and ITS1- ITS2 regiona composite sequence of 1500 nt was used for phylogeneticinference
All studied sequenceswere analyzed independently to testfor incongruence between the data sets for each symbioticpartner Similar topologies have been generally observedbetween phylogenetic trees inferred from glnA dnaA andIGS nifD-K sequences for Frankia and from matK and ITSsequences for Coriaria regardless of the used phylogeneticmethods (not shown)
The topologies of the trees obtained for the two symbioticpartners were not congruent (Figure 1) Moreover globaldistance-based ParaFit analysis recovered mostly randomassociations between Frankia and Coriaria host plant species(119901 = 033) and rejected cospeciation hypothesis On the
microbial side the New Zealand microsymbionts were atthe root (Group A) then three groups emerged groupB comprising the Pakistani Mexican and Mediterraneansymbionts from France group C comprising microsym-bionts from Morocco and then group D comprising Frenchand Japanese microsymbionts as well as the Dg1 referencesequence obtained initially from a Pakistani soil On thehost plant side group 1 at the root comprises New Zealandand South American sequences while group 2 comprises theJapanese Mediterranean and Pakistani sequences
On the other hand no significant correlations were foundfor Frankia symbionts (1199032 = 0772 Fgeneticdist = (geogdist times5830Eminus06) + 2541Eminus02) nor for the Coriaria host plants (1199032= 0883 Fgeneticdist = (geogdist times 2023Eminus06) + 6460Eminus03)(data not shown)
4 Discussion
Cospeciation has been postulated to have occurred insome Frankia actinorhizal host plants in particular in theCasuarina-Frankia cluster 1b [18] but not in Alnus-infectiveand Elaeagnus-infective Frankia strains where many isolatesable to fulfill Kochrsquos postulates have been obtained Totest if cospeciation was general or an exception it wasdecided to study uncultured Frankia microsymbionts andrepresentative Coriaria hosts a lineage where no Frankiaisolate exists and where geographic discontinuities may havelimited dispersion DNA sequences were obtained from rootnodules collected from New Zealand (C arborea) Pakistan(C nepalensis) Japan (C japonica) Mexico (C microphylla)and France and Morocco (C myrtifolia) and multiple molec-ular markers were analyzed for phylogenetic inference
6 BioMed Research International
Dg1
FCjJBFCjJA
FCmF1FCmF2FCmMs2FCmMs4FCmMs1FCmM1aFCmM1cFCmM1bFCmNy4FCmMs3FCmM2bFCmNy1FCmNy5FCnP1FCnP2FCmMx1FCmMx2FCaNZ2FCaNZ1100
99
99
69
100
8980
92
68
91
100
99
97
99
7581
OceaniaAsia
EuropeN AfricaAmerica
Gro
up A
G
roup
BG
roup
CG
roup
D
CmM1aCmM2aCmMs1
CmF2CmNy5
C myrtifolia C myrtifolia
CnP1
C nepalensisC terminalis C intermedia C japonica
CmicMx1C microphylla
C papuanaCaNZ1C arborea
C ruscifolia C sarmentosa
C lurida
8676
7590
7096
54
90
7083
7351
90
87
CjJA
Gro
up 2
Gro
up 1
Frankia Coriaria
Figure 1 Phylogenetic trees of the Frankiamicrosymbionts (left) and the Coriaria host plants (right)The Frankia tree was constructed usingthe glnA dnaA and the nifD-K intergenic spacer while the Coriaria tree was done using thematK and the 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNA with ML method using strain CcI3 and Casuarina as outgroups respectively for Frankia and hot plant phylogenetic trees Thenumbers at branches indicate bootstrap results above 50 Lines are drawn between the microsymbionts and their hosts The color codeindicates the place of origin of the leave or of the set when homogenousThe groups numbers 1 and 2 on the right are according to Yokoyamaet al [19]
Paleontological data based on macrofossils and pollenfossils have brought several authors [36ndash40] to conclude thatthe Coriariaceae had a Laurasian origin (North Americaand Eurasia) There have been a few dissenting opinions inparticular those of Croizat [41] and Schuster [42] who con-sidered that Coriaria originated in Gondwana and migratedto the Northern Hemisphere However such paleontologicalstudies are not very convincing as it is recognizably hardto ascribe fossils to a given family and even more so to agiven genus Thus several authors have been surprised bythe results of molecular phylogeny positioning Coriariaceaeclose to the Datiscaceae Molecular approaches would thusgive support to a Gondwanan origin
Yokoyama et al [19] proposed that Coriaria species hademerged 59ndash63 million years ago which is coherent withthe date of 70 million years proposed by Bell et al [25]considerably older than that proposed (30million years) bythe same authors for the Casuarinaceae
Topology and clustering of Coriaria phylogeny obtainedin the current study are similar to those obtained byYokoyama et al [19] while the position at the base of thehost plant species from New Zealand C arborea and the
South American C ruscifolia and C microphylla species wascontrary to that of Yokoyama et al [19] who found theEurasian species at the base using rbcL (a large subunit ofribulose 15-bisphosphate carboxylaseoxygenase) and matK(maturase K) genes The present study suggests that theCoriaria ancestor may have emerged between Asia and NZand then dispersed worldwide and that the Asian lineagemay have given rise relatively recently to the Mediterraneanspecies while theNZ lineage gave rise to theNorth Americanspecies (Figure 2)
Previous studies had concluded that Frankia cluster 2 hada low genetic diversity [6 7 16] but these studies had beenfocused on only part of the full diversity of the symbioticCoriaria-Frankia essentially in North America and Mediter-ranean In this work we aimed to expand the scope of thestudy to the worldwide diversity and phylogeny ofmicrosym-bionts of Coriaria species Four microbial subgroups wereidentified that did not fit to the geographic range of the hostplants while two host plant subgroups were identified Theposition of subgroup A containing microsymbionts of NewZealand C arborea at the base of Frankia cluster 2 is inagreement with previous study [16] In view of previously
BioMed Research International 7
C ruscifolia
C nepalensis
Coriaria agustissima
C kingiana
C plumosaC lurida
C pteroidesC pottsiana
C sarmentosa
C papuana
C sarmentosa
CmNy1-2-3-4-5CmF1-2-3-4-5Coriaria myrtifoliaCmM1a-b-cCmM2a-bCmMs1-2-3-4-5 CnP1-2-3
Coriaria sp
C arborea
C microphyllaCmicMx1-2-3
CaNZ1-2-3
C japonicaCjJA-B-C-D-E
C terminalisC intermedia
Figure 2 Distribution of Coriaria species Root nodules have been sampled from C myrtifolia C arborea C nepalensis C japonica and Cmicrophylla growing in Mediterranean areas (Morocco and France) New Zealand Pakistan Japan and Mexico respectively Short arrowsindicate sampling sites for this study while long arrows indicate possible routes of dispersal as discussed
reported data members of cluster 2 Frankia studied herewere found to have relatively higher sequences variation (p-distance = 00625) than those reported by Vanden Heuvel etal [16] (119901 = 000454) based on the same 460 nt of the glnAgene
Molecular clock dating suggests that Frankia genus hasemerged much earlier 125Myr bp before the appearance ofangiosperm fossils in the Cretaceous period and the extantactinorhizal plants [4] Normand et al [5] using the 4divergence in the 16S rRNA between cluster 2 and otherFrankia lineages as equivalent to 50MY1 distance [17]concluded that the genus Frankia had emerged long beforethe extant dicotyledonous lineages These authors proposedFrankia cluster 2 as the proto-Frankia as nonsymbioticancestor of 62ndash130Myr bp [43] and 100ndash200Myr bp [5] Sincethe distance in the 16S rRNA gene between cluster 1a (Frankiaalni) and cluster 1b is less than 1 the date of emergence of theCasuarina-infective lineage has been proposed to be less than50 million years [5]Thus the CasuarinaFrankia 1b lineage isconsiderably younger than the CoriariaFrankia lineage andwould have had less time to migrate out of its cradle andmingle with other hosts in its new territories and lose thecospeciation signal
Symbiotic partnership often tends to become obligatoryas in the case of Casuarina host plants where Frankia is onlypresent in soils close to the host plant [44] which means thatthe bacterium loses autonomy and becomes dependent on itshost Speciation of the host could then lead to synchronousspeciation of its microsymbiont unless dispersal throughlong-distance carriers such as winds or migratory birds
occurred or if there is survival of Frankia cluster 2 in therhizosphere of nonhosts as was recently demonstrated forAlnus glutinosa in Tunisia [45] The numerous transitionsseen in the Frankia phylogenetic tree from one continent toanother would reinforce the idea
Yokoyama et al [19] concluded from their study of theCoriaria species phylogeny that the Eurasian species haddiverged earlier and are more diverse than other groups butthat nevertheless the origin of the genus could have been inNorth America whence the South America and the Pacificspecies could have originated Our study brings us to suggesta third possibility Oceania which could also be the originof this actinorhizal symbiosis which can be concluded fromphylogenetic inferences positioning both bacterial and hostplant partners as at the base to Frankia-Coriaria symbiosisAnother element that would support this hypothesis is thelarge number of extant species there according to Yokoyamaet al [19] New Zealand would be home to 8 of the 17 existingspecies A similar argument has often been made to establishSub-Saharan Africa as the cradle of humankind [46] orMexico for maize [47]
Comparison of both the plant and the microbe phyloge-netic topologies did not show any evidence for cospeciationof Frankia microsymbiontsand their Coriaria host speciesThe results obtained in this study suggest that Frankiamicrosymbionts hosted currently by Coriaria species hadprobably dispersed globally as a proto-Frankia a free livingand nonsymbiotic ancestor In parallel the proto-Coriariathen diversified into the extantCoriaria species that appear tohave been retreating given their scattered distribution a trend
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
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Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
BioMed Research International 3
Table1Listof
Coria
riaroot
nodu
lesa
ndsequ
encesu
sedin
thisstu
dy
Species
Localitycoordinatesaltitud
e(asl)
Nod
ule
labels
Plantsequencea
ccessio
nnu
mberBa
cterialsequencea
ccessio
nnu
mberRe
ferences
ITS1-ITS
2matK
glnA
dnaA
IGSnifD
-K
Cmyrtifolia
Morocco
OuedEl
Koub
Ouezzane
35∘011015840879N
05∘201015840565E
140m
CmMs1
KC796592
KC7966
01KC
796522
KC796582
KC796555
Thisstu
dyCm
Ms2
CmMs3
CmMs4
KC796523
KC796524
KC796525
KC796583
KC796584
KC796585
KC796556
KC796557
KC796558
Thisstu
dyTh
isstu
dyTh
isstu
dy
BabBe
rredC
hefchaou
en
35∘001015840979N
04∘58101584009210158401015840E1290
m
CmM1a
KC796590
KC796599
KC796517
KC796578
KC796550
Thisstu
dyCm
M1b
KC796518
KC796579
KC796551
Thisstu
dyCm
M1c
KC796519
KC796580
KC796552
Thisstu
dyCm
M2a
KC796591
KC7966
00KC
796520
mdashKC
796553
Thisstu
dyCm
M2b
KC796521
KC796581
KC796554
Thisstu
dyFrance
Nyons44∘21101584046
5010158401015840N5∘081015840218210158401015840E259m
CmNy1
KC796598
KC7966
03KC
796531
KC796591
KC796564
Thisstu
dyCm
Ny2
CmNy3
CmNy4
CmNy5
KC796532
KC796533
KC796534
KC796535
KC796592
KC796593
KC796594
KC796595
KC796565
mdashKC
796566
KC796567
Thisstu
dyTh
isstu
dyTh
isstu
dyTh
isstu
dy
Mon
tpellier43∘361015840514810158401015840N3∘521015840239710158401015840E41
m
CmF1
KC796526
KC796586
KC796559
Thisstu
dyCm
F2KC
796593
KC7966
02KC
796527
KC796587
KC796560
Thisstu
dyCm
F3Cm
F4Cm
F5
KC796528
KC796529
KC796530
KC796588
KC796589
KC796590
KC796561
KC796562
KC796563
Thisstu
dyTh
isstu
dyTh
isstu
dyAF280102
Yang
etalun
publish
edAB0
16459
(Yokoyam
aetal2000
[19])
Cjaponica
Japan
Tosa
distr
ict+3
3∘451015840391810158401015840+
133∘27101584042891015840101584010
m
CjJA
KC7966
05KC
796536
KC796503
KC796576
Thisstu
dyCjJB
KC796594
KC796537
KC796504
KC796577
Thisstu
dyCjJC
CjJD
CjJE
KC796538
KC796539
KC796540
KC796505
KC796506
KC796507
KC796578
KC796579
KC796580
Thisstu
dyTh
isstu
dyTh
isstu
dyAF280101
Yang
etalun
publish
edAB0
16456
(Yokoyam
aetal2000
[19])
Cnepalen
sis
Pakista
n
Murree+3
3∘5410158401510158401015840N73∘2310158402510158401015840E33904
2∘N
7339
03∘E22912m
CnP1
KC796597
KC7966
07KC
796544
KC796508
KC796584
Thisstu
dyCn
P2KC
796545
KC796509
KC796585
Thisstu
dyCn
P3KC
796546
KC796510
KC796586
Thisstu
dyCn
P4AF280103
Yang
etalun
publish
ed
4 BioMed Research International
Table1Con
tinued
Species
Localitycoordinatesaltitud
e(asl)
Nod
ule
labels
Plantsequencea
ccessio
nnu
mberBa
cterialsequencea
ccessio
nnu
mberRe
ferences
ITS1-ITS
2matK
glnA
dnaA
IGSnifD
-K
Carborea
NewZealand
Hapuk
uriv
erN
orth
Canterbu
rySou
thisland
minus42∘231015840422410158401015840+
173∘41101584018071015840101584064m
CaNZ1
KC796595
KC7966
04KC
796542
KC796511
KC796581
Thisstu
dyCa
NZ2
KC796543
KC796512
KC796582
Thisstu
dyCa
NZ3
KC796544
KC796513
KC796583
Thisstu
dyAB164
54(Yokoyam
aetal2000
[19])
EF635457
Rotherham
etalun
publish
edEF
635475
Rotherham
etalun
publish
edAF277293
Yang
etalun
publish
ed
Cmicrophylla
Mexico
Morelo
s99∘30101584019∘301015840240
0m
CmicMx1
KC796596
KC7966
06KC
796547
KC796514
KC796587
Thisstu
dyCm
icMx2
KC796548
KC796515
KC796588
Thisstu
dyCm
icMx3
KC796549
KC796516
KC796589
Thisstu
dyAY
091813
Yang
etalun
publish
edAB0
16458
(Yokoyam
aetal2000
[19])
Cinterm
edia
AF280100
Yang
etalun
publish
edAB0
16455
(Yokoyam
aetal2000
[19])
Cterm
inalis
AY091817
Yang
etalun
publish
ed
Cruscifolia
AY091815
Yang
etalun
publish
edAY
091814
Yang
etalun
publish
edAF280104
Yang
etalun
publish
edAB0
16462
(Yokoyam
aetal2000
[19])
Csarm
entosa
AY091816
Yang
etalun
publish
edAB0
1646
4(Yokoyam
aetal2000
[19])
Cpapu
ana
AB0
16461
(Yokoyam
aetal2000
[19])
Datisca
glomerata
CP002801
CP002801
CP002801
(Persson
etal2011[50])
AY968449
Zhangetalun
publish
edAF4
85250
Forrestand
Hollin
gsworth
unpu
blish
ed
Casuarina
equisetifolia
CP00
0249
CP00
0249
CP00
0249
(Normandetal2007
[51])
AB0
15462
Sogo
etalun
publish
edAY
8640
57Herbertetalun
publish
ed
BioMed Research International 5
Table 2 Primers used for PCR amplification and DNA sequencing
Gene primers Sequence (51015840-31015840) Amplicons approximate size (bp) ReferencesglnA
DB41 TTCTTCATCCACGACCCG 500 (Clawson et al 2004 [4])DB44 GGCTTCGGCATGAAGGT
dnaAF7154 dnaAF GAGGARTTCACCAACGACTTCAT 700 Bautista et al unpublishedF7155 dnaAR CRGAAGTGCTGGCCGATCTT
IGS nifD-KF9372 nifD1 5 GTCATGCTCGCCGTCGGNG 700 This studyF9374 nifK1 5 GTTCTTCTCCCGGTAyTCCCA
F9373 nifD2 5 ACCGGCTACGAGTTCGCNCA 700 This studyF9375 nifK2 5 TGCGAGCCGTGCACCAGNG
18S-ITS1-58S-ITS2-28SITS1 TCCGTAGGTGAACCTGCGG 700 (White et al 1990 [52])ITS4 TCCTCCGCTTATTGATATGC
F9030-CJ-ITSF AGCCGGACCCGCGACGAGTTT 400 This studyF9031-CJ-ITSR CGACGTTGCGTGACGACGCCCA
matKF9249-matKF ACATTTAAATTATGTGTCAG 700 This studyF9250-matkR TGCATATACGCACAAATC
root nodules used in this study yielded PCR-amplifiable DNAfor both bacterial and plant PCR target sequences in all casesHowever in several instances it was easier to amplify Frankiathan Coriaria DNA which may have been mostly due to thespecificity of the primer sets used Thus in this study newprimers were designed (Table 2)
For the bacterial microsymbionts the average uncorrec-ted p-distances (proportion of differences between sequen-ces) were computed for each region and were found to berelatively small for dnaA (119901 = 00378) intermediate for glnA(119901 = 00625) and high for IGS nifD-K region (119901 = 00833)Blast analyses of the individual genes permitted assigningthem all to Frankia cluster 2 Nearly 3000 nucleotides wereobtained by concatenating sequences of the three DNAregions
Sequences variation for Coriaria species was small basedonmatKgene (119901 = 00205) compared to ITS1-ITS2 sequences(119901 = 00423) By concatenatingmatK and ITS1- ITS2 regiona composite sequence of 1500 nt was used for phylogeneticinference
All studied sequenceswere analyzed independently to testfor incongruence between the data sets for each symbioticpartner Similar topologies have been generally observedbetween phylogenetic trees inferred from glnA dnaA andIGS nifD-K sequences for Frankia and from matK and ITSsequences for Coriaria regardless of the used phylogeneticmethods (not shown)
The topologies of the trees obtained for the two symbioticpartners were not congruent (Figure 1) Moreover globaldistance-based ParaFit analysis recovered mostly randomassociations between Frankia and Coriaria host plant species(119901 = 033) and rejected cospeciation hypothesis On the
microbial side the New Zealand microsymbionts were atthe root (Group A) then three groups emerged groupB comprising the Pakistani Mexican and Mediterraneansymbionts from France group C comprising microsym-bionts from Morocco and then group D comprising Frenchand Japanese microsymbionts as well as the Dg1 referencesequence obtained initially from a Pakistani soil On thehost plant side group 1 at the root comprises New Zealandand South American sequences while group 2 comprises theJapanese Mediterranean and Pakistani sequences
On the other hand no significant correlations were foundfor Frankia symbionts (1199032 = 0772 Fgeneticdist = (geogdist times5830Eminus06) + 2541Eminus02) nor for the Coriaria host plants (1199032= 0883 Fgeneticdist = (geogdist times 2023Eminus06) + 6460Eminus03)(data not shown)
4 Discussion
Cospeciation has been postulated to have occurred insome Frankia actinorhizal host plants in particular in theCasuarina-Frankia cluster 1b [18] but not in Alnus-infectiveand Elaeagnus-infective Frankia strains where many isolatesable to fulfill Kochrsquos postulates have been obtained Totest if cospeciation was general or an exception it wasdecided to study uncultured Frankia microsymbionts andrepresentative Coriaria hosts a lineage where no Frankiaisolate exists and where geographic discontinuities may havelimited dispersion DNA sequences were obtained from rootnodules collected from New Zealand (C arborea) Pakistan(C nepalensis) Japan (C japonica) Mexico (C microphylla)and France and Morocco (C myrtifolia) and multiple molec-ular markers were analyzed for phylogenetic inference
6 BioMed Research International
Dg1
FCjJBFCjJA
FCmF1FCmF2FCmMs2FCmMs4FCmMs1FCmM1aFCmM1cFCmM1bFCmNy4FCmMs3FCmM2bFCmNy1FCmNy5FCnP1FCnP2FCmMx1FCmMx2FCaNZ2FCaNZ1100
99
99
69
100
8980
92
68
91
100
99
97
99
7581
OceaniaAsia
EuropeN AfricaAmerica
Gro
up A
G
roup
BG
roup
CG
roup
D
CmM1aCmM2aCmMs1
CmF2CmNy5
C myrtifolia C myrtifolia
CnP1
C nepalensisC terminalis C intermedia C japonica
CmicMx1C microphylla
C papuanaCaNZ1C arborea
C ruscifolia C sarmentosa
C lurida
8676
7590
7096
54
90
7083
7351
90
87
CjJA
Gro
up 2
Gro
up 1
Frankia Coriaria
Figure 1 Phylogenetic trees of the Frankiamicrosymbionts (left) and the Coriaria host plants (right)The Frankia tree was constructed usingthe glnA dnaA and the nifD-K intergenic spacer while the Coriaria tree was done using thematK and the 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNA with ML method using strain CcI3 and Casuarina as outgroups respectively for Frankia and hot plant phylogenetic trees Thenumbers at branches indicate bootstrap results above 50 Lines are drawn between the microsymbionts and their hosts The color codeindicates the place of origin of the leave or of the set when homogenousThe groups numbers 1 and 2 on the right are according to Yokoyamaet al [19]
Paleontological data based on macrofossils and pollenfossils have brought several authors [36ndash40] to conclude thatthe Coriariaceae had a Laurasian origin (North Americaand Eurasia) There have been a few dissenting opinions inparticular those of Croizat [41] and Schuster [42] who con-sidered that Coriaria originated in Gondwana and migratedto the Northern Hemisphere However such paleontologicalstudies are not very convincing as it is recognizably hardto ascribe fossils to a given family and even more so to agiven genus Thus several authors have been surprised bythe results of molecular phylogeny positioning Coriariaceaeclose to the Datiscaceae Molecular approaches would thusgive support to a Gondwanan origin
Yokoyama et al [19] proposed that Coriaria species hademerged 59ndash63 million years ago which is coherent withthe date of 70 million years proposed by Bell et al [25]considerably older than that proposed (30million years) bythe same authors for the Casuarinaceae
Topology and clustering of Coriaria phylogeny obtainedin the current study are similar to those obtained byYokoyama et al [19] while the position at the base of thehost plant species from New Zealand C arborea and the
South American C ruscifolia and C microphylla species wascontrary to that of Yokoyama et al [19] who found theEurasian species at the base using rbcL (a large subunit ofribulose 15-bisphosphate carboxylaseoxygenase) and matK(maturase K) genes The present study suggests that theCoriaria ancestor may have emerged between Asia and NZand then dispersed worldwide and that the Asian lineagemay have given rise relatively recently to the Mediterraneanspecies while theNZ lineage gave rise to theNorth Americanspecies (Figure 2)
Previous studies had concluded that Frankia cluster 2 hada low genetic diversity [6 7 16] but these studies had beenfocused on only part of the full diversity of the symbioticCoriaria-Frankia essentially in North America and Mediter-ranean In this work we aimed to expand the scope of thestudy to the worldwide diversity and phylogeny ofmicrosym-bionts of Coriaria species Four microbial subgroups wereidentified that did not fit to the geographic range of the hostplants while two host plant subgroups were identified Theposition of subgroup A containing microsymbionts of NewZealand C arborea at the base of Frankia cluster 2 is inagreement with previous study [16] In view of previously
BioMed Research International 7
C ruscifolia
C nepalensis
Coriaria agustissima
C kingiana
C plumosaC lurida
C pteroidesC pottsiana
C sarmentosa
C papuana
C sarmentosa
CmNy1-2-3-4-5CmF1-2-3-4-5Coriaria myrtifoliaCmM1a-b-cCmM2a-bCmMs1-2-3-4-5 CnP1-2-3
Coriaria sp
C arborea
C microphyllaCmicMx1-2-3
CaNZ1-2-3
C japonicaCjJA-B-C-D-E
C terminalisC intermedia
Figure 2 Distribution of Coriaria species Root nodules have been sampled from C myrtifolia C arborea C nepalensis C japonica and Cmicrophylla growing in Mediterranean areas (Morocco and France) New Zealand Pakistan Japan and Mexico respectively Short arrowsindicate sampling sites for this study while long arrows indicate possible routes of dispersal as discussed
reported data members of cluster 2 Frankia studied herewere found to have relatively higher sequences variation (p-distance = 00625) than those reported by Vanden Heuvel etal [16] (119901 = 000454) based on the same 460 nt of the glnAgene
Molecular clock dating suggests that Frankia genus hasemerged much earlier 125Myr bp before the appearance ofangiosperm fossils in the Cretaceous period and the extantactinorhizal plants [4] Normand et al [5] using the 4divergence in the 16S rRNA between cluster 2 and otherFrankia lineages as equivalent to 50MY1 distance [17]concluded that the genus Frankia had emerged long beforethe extant dicotyledonous lineages These authors proposedFrankia cluster 2 as the proto-Frankia as nonsymbioticancestor of 62ndash130Myr bp [43] and 100ndash200Myr bp [5] Sincethe distance in the 16S rRNA gene between cluster 1a (Frankiaalni) and cluster 1b is less than 1 the date of emergence of theCasuarina-infective lineage has been proposed to be less than50 million years [5]Thus the CasuarinaFrankia 1b lineage isconsiderably younger than the CoriariaFrankia lineage andwould have had less time to migrate out of its cradle andmingle with other hosts in its new territories and lose thecospeciation signal
Symbiotic partnership often tends to become obligatoryas in the case of Casuarina host plants where Frankia is onlypresent in soils close to the host plant [44] which means thatthe bacterium loses autonomy and becomes dependent on itshost Speciation of the host could then lead to synchronousspeciation of its microsymbiont unless dispersal throughlong-distance carriers such as winds or migratory birds
occurred or if there is survival of Frankia cluster 2 in therhizosphere of nonhosts as was recently demonstrated forAlnus glutinosa in Tunisia [45] The numerous transitionsseen in the Frankia phylogenetic tree from one continent toanother would reinforce the idea
Yokoyama et al [19] concluded from their study of theCoriaria species phylogeny that the Eurasian species haddiverged earlier and are more diverse than other groups butthat nevertheless the origin of the genus could have been inNorth America whence the South America and the Pacificspecies could have originated Our study brings us to suggesta third possibility Oceania which could also be the originof this actinorhizal symbiosis which can be concluded fromphylogenetic inferences positioning both bacterial and hostplant partners as at the base to Frankia-Coriaria symbiosisAnother element that would support this hypothesis is thelarge number of extant species there according to Yokoyamaet al [19] New Zealand would be home to 8 of the 17 existingspecies A similar argument has often been made to establishSub-Saharan Africa as the cradle of humankind [46] orMexico for maize [47]
Comparison of both the plant and the microbe phyloge-netic topologies did not show any evidence for cospeciationof Frankia microsymbiontsand their Coriaria host speciesThe results obtained in this study suggest that Frankiamicrosymbionts hosted currently by Coriaria species hadprobably dispersed globally as a proto-Frankia a free livingand nonsymbiotic ancestor In parallel the proto-Coriariathen diversified into the extantCoriaria species that appear tohave been retreating given their scattered distribution a trend
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Volume 2014
Zoology
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Molecular Biology International
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Signal TransductionJournal of
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BioMed Research International
Evolutionary BiologyInternational Journal of
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Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
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Virolog y
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Volume 2014
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International Journal of
Microbiology
4 BioMed Research International
Table1Con
tinued
Species
Localitycoordinatesaltitud
e(asl)
Nod
ule
labels
Plantsequencea
ccessio
nnu
mberBa
cterialsequencea
ccessio
nnu
mberRe
ferences
ITS1-ITS
2matK
glnA
dnaA
IGSnifD
-K
Carborea
NewZealand
Hapuk
uriv
erN
orth
Canterbu
rySou
thisland
minus42∘231015840422410158401015840+
173∘41101584018071015840101584064m
CaNZ1
KC796595
KC7966
04KC
796542
KC796511
KC796581
Thisstu
dyCa
NZ2
KC796543
KC796512
KC796582
Thisstu
dyCa
NZ3
KC796544
KC796513
KC796583
Thisstu
dyAB164
54(Yokoyam
aetal2000
[19])
EF635457
Rotherham
etalun
publish
edEF
635475
Rotherham
etalun
publish
edAF277293
Yang
etalun
publish
ed
Cmicrophylla
Mexico
Morelo
s99∘30101584019∘301015840240
0m
CmicMx1
KC796596
KC7966
06KC
796547
KC796514
KC796587
Thisstu
dyCm
icMx2
KC796548
KC796515
KC796588
Thisstu
dyCm
icMx3
KC796549
KC796516
KC796589
Thisstu
dyAY
091813
Yang
etalun
publish
edAB0
16458
(Yokoyam
aetal2000
[19])
Cinterm
edia
AF280100
Yang
etalun
publish
edAB0
16455
(Yokoyam
aetal2000
[19])
Cterm
inalis
AY091817
Yang
etalun
publish
ed
Cruscifolia
AY091815
Yang
etalun
publish
edAY
091814
Yang
etalun
publish
edAF280104
Yang
etalun
publish
edAB0
16462
(Yokoyam
aetal2000
[19])
Csarm
entosa
AY091816
Yang
etalun
publish
edAB0
1646
4(Yokoyam
aetal2000
[19])
Cpapu
ana
AB0
16461
(Yokoyam
aetal2000
[19])
Datisca
glomerata
CP002801
CP002801
CP002801
(Persson
etal2011[50])
AY968449
Zhangetalun
publish
edAF4
85250
Forrestand
Hollin
gsworth
unpu
blish
ed
Casuarina
equisetifolia
CP00
0249
CP00
0249
CP00
0249
(Normandetal2007
[51])
AB0
15462
Sogo
etalun
publish
edAY
8640
57Herbertetalun
publish
ed
BioMed Research International 5
Table 2 Primers used for PCR amplification and DNA sequencing
Gene primers Sequence (51015840-31015840) Amplicons approximate size (bp) ReferencesglnA
DB41 TTCTTCATCCACGACCCG 500 (Clawson et al 2004 [4])DB44 GGCTTCGGCATGAAGGT
dnaAF7154 dnaAF GAGGARTTCACCAACGACTTCAT 700 Bautista et al unpublishedF7155 dnaAR CRGAAGTGCTGGCCGATCTT
IGS nifD-KF9372 nifD1 5 GTCATGCTCGCCGTCGGNG 700 This studyF9374 nifK1 5 GTTCTTCTCCCGGTAyTCCCA
F9373 nifD2 5 ACCGGCTACGAGTTCGCNCA 700 This studyF9375 nifK2 5 TGCGAGCCGTGCACCAGNG
18S-ITS1-58S-ITS2-28SITS1 TCCGTAGGTGAACCTGCGG 700 (White et al 1990 [52])ITS4 TCCTCCGCTTATTGATATGC
F9030-CJ-ITSF AGCCGGACCCGCGACGAGTTT 400 This studyF9031-CJ-ITSR CGACGTTGCGTGACGACGCCCA
matKF9249-matKF ACATTTAAATTATGTGTCAG 700 This studyF9250-matkR TGCATATACGCACAAATC
root nodules used in this study yielded PCR-amplifiable DNAfor both bacterial and plant PCR target sequences in all casesHowever in several instances it was easier to amplify Frankiathan Coriaria DNA which may have been mostly due to thespecificity of the primer sets used Thus in this study newprimers were designed (Table 2)
For the bacterial microsymbionts the average uncorrec-ted p-distances (proportion of differences between sequen-ces) were computed for each region and were found to berelatively small for dnaA (119901 = 00378) intermediate for glnA(119901 = 00625) and high for IGS nifD-K region (119901 = 00833)Blast analyses of the individual genes permitted assigningthem all to Frankia cluster 2 Nearly 3000 nucleotides wereobtained by concatenating sequences of the three DNAregions
Sequences variation for Coriaria species was small basedonmatKgene (119901 = 00205) compared to ITS1-ITS2 sequences(119901 = 00423) By concatenatingmatK and ITS1- ITS2 regiona composite sequence of 1500 nt was used for phylogeneticinference
All studied sequenceswere analyzed independently to testfor incongruence between the data sets for each symbioticpartner Similar topologies have been generally observedbetween phylogenetic trees inferred from glnA dnaA andIGS nifD-K sequences for Frankia and from matK and ITSsequences for Coriaria regardless of the used phylogeneticmethods (not shown)
The topologies of the trees obtained for the two symbioticpartners were not congruent (Figure 1) Moreover globaldistance-based ParaFit analysis recovered mostly randomassociations between Frankia and Coriaria host plant species(119901 = 033) and rejected cospeciation hypothesis On the
microbial side the New Zealand microsymbionts were atthe root (Group A) then three groups emerged groupB comprising the Pakistani Mexican and Mediterraneansymbionts from France group C comprising microsym-bionts from Morocco and then group D comprising Frenchand Japanese microsymbionts as well as the Dg1 referencesequence obtained initially from a Pakistani soil On thehost plant side group 1 at the root comprises New Zealandand South American sequences while group 2 comprises theJapanese Mediterranean and Pakistani sequences
On the other hand no significant correlations were foundfor Frankia symbionts (1199032 = 0772 Fgeneticdist = (geogdist times5830Eminus06) + 2541Eminus02) nor for the Coriaria host plants (1199032= 0883 Fgeneticdist = (geogdist times 2023Eminus06) + 6460Eminus03)(data not shown)
4 Discussion
Cospeciation has been postulated to have occurred insome Frankia actinorhizal host plants in particular in theCasuarina-Frankia cluster 1b [18] but not in Alnus-infectiveand Elaeagnus-infective Frankia strains where many isolatesable to fulfill Kochrsquos postulates have been obtained Totest if cospeciation was general or an exception it wasdecided to study uncultured Frankia microsymbionts andrepresentative Coriaria hosts a lineage where no Frankiaisolate exists and where geographic discontinuities may havelimited dispersion DNA sequences were obtained from rootnodules collected from New Zealand (C arborea) Pakistan(C nepalensis) Japan (C japonica) Mexico (C microphylla)and France and Morocco (C myrtifolia) and multiple molec-ular markers were analyzed for phylogenetic inference
6 BioMed Research International
Dg1
FCjJBFCjJA
FCmF1FCmF2FCmMs2FCmMs4FCmMs1FCmM1aFCmM1cFCmM1bFCmNy4FCmMs3FCmM2bFCmNy1FCmNy5FCnP1FCnP2FCmMx1FCmMx2FCaNZ2FCaNZ1100
99
99
69
100
8980
92
68
91
100
99
97
99
7581
OceaniaAsia
EuropeN AfricaAmerica
Gro
up A
G
roup
BG
roup
CG
roup
D
CmM1aCmM2aCmMs1
CmF2CmNy5
C myrtifolia C myrtifolia
CnP1
C nepalensisC terminalis C intermedia C japonica
CmicMx1C microphylla
C papuanaCaNZ1C arborea
C ruscifolia C sarmentosa
C lurida
8676
7590
7096
54
90
7083
7351
90
87
CjJA
Gro
up 2
Gro
up 1
Frankia Coriaria
Figure 1 Phylogenetic trees of the Frankiamicrosymbionts (left) and the Coriaria host plants (right)The Frankia tree was constructed usingthe glnA dnaA and the nifD-K intergenic spacer while the Coriaria tree was done using thematK and the 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNA with ML method using strain CcI3 and Casuarina as outgroups respectively for Frankia and hot plant phylogenetic trees Thenumbers at branches indicate bootstrap results above 50 Lines are drawn between the microsymbionts and their hosts The color codeindicates the place of origin of the leave or of the set when homogenousThe groups numbers 1 and 2 on the right are according to Yokoyamaet al [19]
Paleontological data based on macrofossils and pollenfossils have brought several authors [36ndash40] to conclude thatthe Coriariaceae had a Laurasian origin (North Americaand Eurasia) There have been a few dissenting opinions inparticular those of Croizat [41] and Schuster [42] who con-sidered that Coriaria originated in Gondwana and migratedto the Northern Hemisphere However such paleontologicalstudies are not very convincing as it is recognizably hardto ascribe fossils to a given family and even more so to agiven genus Thus several authors have been surprised bythe results of molecular phylogeny positioning Coriariaceaeclose to the Datiscaceae Molecular approaches would thusgive support to a Gondwanan origin
Yokoyama et al [19] proposed that Coriaria species hademerged 59ndash63 million years ago which is coherent withthe date of 70 million years proposed by Bell et al [25]considerably older than that proposed (30million years) bythe same authors for the Casuarinaceae
Topology and clustering of Coriaria phylogeny obtainedin the current study are similar to those obtained byYokoyama et al [19] while the position at the base of thehost plant species from New Zealand C arborea and the
South American C ruscifolia and C microphylla species wascontrary to that of Yokoyama et al [19] who found theEurasian species at the base using rbcL (a large subunit ofribulose 15-bisphosphate carboxylaseoxygenase) and matK(maturase K) genes The present study suggests that theCoriaria ancestor may have emerged between Asia and NZand then dispersed worldwide and that the Asian lineagemay have given rise relatively recently to the Mediterraneanspecies while theNZ lineage gave rise to theNorth Americanspecies (Figure 2)
Previous studies had concluded that Frankia cluster 2 hada low genetic diversity [6 7 16] but these studies had beenfocused on only part of the full diversity of the symbioticCoriaria-Frankia essentially in North America and Mediter-ranean In this work we aimed to expand the scope of thestudy to the worldwide diversity and phylogeny ofmicrosym-bionts of Coriaria species Four microbial subgroups wereidentified that did not fit to the geographic range of the hostplants while two host plant subgroups were identified Theposition of subgroup A containing microsymbionts of NewZealand C arborea at the base of Frankia cluster 2 is inagreement with previous study [16] In view of previously
BioMed Research International 7
C ruscifolia
C nepalensis
Coriaria agustissima
C kingiana
C plumosaC lurida
C pteroidesC pottsiana
C sarmentosa
C papuana
C sarmentosa
CmNy1-2-3-4-5CmF1-2-3-4-5Coriaria myrtifoliaCmM1a-b-cCmM2a-bCmMs1-2-3-4-5 CnP1-2-3
Coriaria sp
C arborea
C microphyllaCmicMx1-2-3
CaNZ1-2-3
C japonicaCjJA-B-C-D-E
C terminalisC intermedia
Figure 2 Distribution of Coriaria species Root nodules have been sampled from C myrtifolia C arborea C nepalensis C japonica and Cmicrophylla growing in Mediterranean areas (Morocco and France) New Zealand Pakistan Japan and Mexico respectively Short arrowsindicate sampling sites for this study while long arrows indicate possible routes of dispersal as discussed
reported data members of cluster 2 Frankia studied herewere found to have relatively higher sequences variation (p-distance = 00625) than those reported by Vanden Heuvel etal [16] (119901 = 000454) based on the same 460 nt of the glnAgene
Molecular clock dating suggests that Frankia genus hasemerged much earlier 125Myr bp before the appearance ofangiosperm fossils in the Cretaceous period and the extantactinorhizal plants [4] Normand et al [5] using the 4divergence in the 16S rRNA between cluster 2 and otherFrankia lineages as equivalent to 50MY1 distance [17]concluded that the genus Frankia had emerged long beforethe extant dicotyledonous lineages These authors proposedFrankia cluster 2 as the proto-Frankia as nonsymbioticancestor of 62ndash130Myr bp [43] and 100ndash200Myr bp [5] Sincethe distance in the 16S rRNA gene between cluster 1a (Frankiaalni) and cluster 1b is less than 1 the date of emergence of theCasuarina-infective lineage has been proposed to be less than50 million years [5]Thus the CasuarinaFrankia 1b lineage isconsiderably younger than the CoriariaFrankia lineage andwould have had less time to migrate out of its cradle andmingle with other hosts in its new territories and lose thecospeciation signal
Symbiotic partnership often tends to become obligatoryas in the case of Casuarina host plants where Frankia is onlypresent in soils close to the host plant [44] which means thatthe bacterium loses autonomy and becomes dependent on itshost Speciation of the host could then lead to synchronousspeciation of its microsymbiont unless dispersal throughlong-distance carriers such as winds or migratory birds
occurred or if there is survival of Frankia cluster 2 in therhizosphere of nonhosts as was recently demonstrated forAlnus glutinosa in Tunisia [45] The numerous transitionsseen in the Frankia phylogenetic tree from one continent toanother would reinforce the idea
Yokoyama et al [19] concluded from their study of theCoriaria species phylogeny that the Eurasian species haddiverged earlier and are more diverse than other groups butthat nevertheless the origin of the genus could have been inNorth America whence the South America and the Pacificspecies could have originated Our study brings us to suggesta third possibility Oceania which could also be the originof this actinorhizal symbiosis which can be concluded fromphylogenetic inferences positioning both bacterial and hostplant partners as at the base to Frankia-Coriaria symbiosisAnother element that would support this hypothesis is thelarge number of extant species there according to Yokoyamaet al [19] New Zealand would be home to 8 of the 17 existingspecies A similar argument has often been made to establishSub-Saharan Africa as the cradle of humankind [46] orMexico for maize [47]
Comparison of both the plant and the microbe phyloge-netic topologies did not show any evidence for cospeciationof Frankia microsymbiontsand their Coriaria host speciesThe results obtained in this study suggest that Frankiamicrosymbionts hosted currently by Coriaria species hadprobably dispersed globally as a proto-Frankia a free livingand nonsymbiotic ancestor In parallel the proto-Coriariathen diversified into the extantCoriaria species that appear tohave been retreating given their scattered distribution a trend
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
BioMed Research International 5
Table 2 Primers used for PCR amplification and DNA sequencing
Gene primers Sequence (51015840-31015840) Amplicons approximate size (bp) ReferencesglnA
DB41 TTCTTCATCCACGACCCG 500 (Clawson et al 2004 [4])DB44 GGCTTCGGCATGAAGGT
dnaAF7154 dnaAF GAGGARTTCACCAACGACTTCAT 700 Bautista et al unpublishedF7155 dnaAR CRGAAGTGCTGGCCGATCTT
IGS nifD-KF9372 nifD1 5 GTCATGCTCGCCGTCGGNG 700 This studyF9374 nifK1 5 GTTCTTCTCCCGGTAyTCCCA
F9373 nifD2 5 ACCGGCTACGAGTTCGCNCA 700 This studyF9375 nifK2 5 TGCGAGCCGTGCACCAGNG
18S-ITS1-58S-ITS2-28SITS1 TCCGTAGGTGAACCTGCGG 700 (White et al 1990 [52])ITS4 TCCTCCGCTTATTGATATGC
F9030-CJ-ITSF AGCCGGACCCGCGACGAGTTT 400 This studyF9031-CJ-ITSR CGACGTTGCGTGACGACGCCCA
matKF9249-matKF ACATTTAAATTATGTGTCAG 700 This studyF9250-matkR TGCATATACGCACAAATC
root nodules used in this study yielded PCR-amplifiable DNAfor both bacterial and plant PCR target sequences in all casesHowever in several instances it was easier to amplify Frankiathan Coriaria DNA which may have been mostly due to thespecificity of the primer sets used Thus in this study newprimers were designed (Table 2)
For the bacterial microsymbionts the average uncorrec-ted p-distances (proportion of differences between sequen-ces) were computed for each region and were found to berelatively small for dnaA (119901 = 00378) intermediate for glnA(119901 = 00625) and high for IGS nifD-K region (119901 = 00833)Blast analyses of the individual genes permitted assigningthem all to Frankia cluster 2 Nearly 3000 nucleotides wereobtained by concatenating sequences of the three DNAregions
Sequences variation for Coriaria species was small basedonmatKgene (119901 = 00205) compared to ITS1-ITS2 sequences(119901 = 00423) By concatenatingmatK and ITS1- ITS2 regiona composite sequence of 1500 nt was used for phylogeneticinference
All studied sequenceswere analyzed independently to testfor incongruence between the data sets for each symbioticpartner Similar topologies have been generally observedbetween phylogenetic trees inferred from glnA dnaA andIGS nifD-K sequences for Frankia and from matK and ITSsequences for Coriaria regardless of the used phylogeneticmethods (not shown)
The topologies of the trees obtained for the two symbioticpartners were not congruent (Figure 1) Moreover globaldistance-based ParaFit analysis recovered mostly randomassociations between Frankia and Coriaria host plant species(119901 = 033) and rejected cospeciation hypothesis On the
microbial side the New Zealand microsymbionts were atthe root (Group A) then three groups emerged groupB comprising the Pakistani Mexican and Mediterraneansymbionts from France group C comprising microsym-bionts from Morocco and then group D comprising Frenchand Japanese microsymbionts as well as the Dg1 referencesequence obtained initially from a Pakistani soil On thehost plant side group 1 at the root comprises New Zealandand South American sequences while group 2 comprises theJapanese Mediterranean and Pakistani sequences
On the other hand no significant correlations were foundfor Frankia symbionts (1199032 = 0772 Fgeneticdist = (geogdist times5830Eminus06) + 2541Eminus02) nor for the Coriaria host plants (1199032= 0883 Fgeneticdist = (geogdist times 2023Eminus06) + 6460Eminus03)(data not shown)
4 Discussion
Cospeciation has been postulated to have occurred insome Frankia actinorhizal host plants in particular in theCasuarina-Frankia cluster 1b [18] but not in Alnus-infectiveand Elaeagnus-infective Frankia strains where many isolatesable to fulfill Kochrsquos postulates have been obtained Totest if cospeciation was general or an exception it wasdecided to study uncultured Frankia microsymbionts andrepresentative Coriaria hosts a lineage where no Frankiaisolate exists and where geographic discontinuities may havelimited dispersion DNA sequences were obtained from rootnodules collected from New Zealand (C arborea) Pakistan(C nepalensis) Japan (C japonica) Mexico (C microphylla)and France and Morocco (C myrtifolia) and multiple molec-ular markers were analyzed for phylogenetic inference
6 BioMed Research International
Dg1
FCjJBFCjJA
FCmF1FCmF2FCmMs2FCmMs4FCmMs1FCmM1aFCmM1cFCmM1bFCmNy4FCmMs3FCmM2bFCmNy1FCmNy5FCnP1FCnP2FCmMx1FCmMx2FCaNZ2FCaNZ1100
99
99
69
100
8980
92
68
91
100
99
97
99
7581
OceaniaAsia
EuropeN AfricaAmerica
Gro
up A
G
roup
BG
roup
CG
roup
D
CmM1aCmM2aCmMs1
CmF2CmNy5
C myrtifolia C myrtifolia
CnP1
C nepalensisC terminalis C intermedia C japonica
CmicMx1C microphylla
C papuanaCaNZ1C arborea
C ruscifolia C sarmentosa
C lurida
8676
7590
7096
54
90
7083
7351
90
87
CjJA
Gro
up 2
Gro
up 1
Frankia Coriaria
Figure 1 Phylogenetic trees of the Frankiamicrosymbionts (left) and the Coriaria host plants (right)The Frankia tree was constructed usingthe glnA dnaA and the nifD-K intergenic spacer while the Coriaria tree was done using thematK and the 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNA with ML method using strain CcI3 and Casuarina as outgroups respectively for Frankia and hot plant phylogenetic trees Thenumbers at branches indicate bootstrap results above 50 Lines are drawn between the microsymbionts and their hosts The color codeindicates the place of origin of the leave or of the set when homogenousThe groups numbers 1 and 2 on the right are according to Yokoyamaet al [19]
Paleontological data based on macrofossils and pollenfossils have brought several authors [36ndash40] to conclude thatthe Coriariaceae had a Laurasian origin (North Americaand Eurasia) There have been a few dissenting opinions inparticular those of Croizat [41] and Schuster [42] who con-sidered that Coriaria originated in Gondwana and migratedto the Northern Hemisphere However such paleontologicalstudies are not very convincing as it is recognizably hardto ascribe fossils to a given family and even more so to agiven genus Thus several authors have been surprised bythe results of molecular phylogeny positioning Coriariaceaeclose to the Datiscaceae Molecular approaches would thusgive support to a Gondwanan origin
Yokoyama et al [19] proposed that Coriaria species hademerged 59ndash63 million years ago which is coherent withthe date of 70 million years proposed by Bell et al [25]considerably older than that proposed (30million years) bythe same authors for the Casuarinaceae
Topology and clustering of Coriaria phylogeny obtainedin the current study are similar to those obtained byYokoyama et al [19] while the position at the base of thehost plant species from New Zealand C arborea and the
South American C ruscifolia and C microphylla species wascontrary to that of Yokoyama et al [19] who found theEurasian species at the base using rbcL (a large subunit ofribulose 15-bisphosphate carboxylaseoxygenase) and matK(maturase K) genes The present study suggests that theCoriaria ancestor may have emerged between Asia and NZand then dispersed worldwide and that the Asian lineagemay have given rise relatively recently to the Mediterraneanspecies while theNZ lineage gave rise to theNorth Americanspecies (Figure 2)
Previous studies had concluded that Frankia cluster 2 hada low genetic diversity [6 7 16] but these studies had beenfocused on only part of the full diversity of the symbioticCoriaria-Frankia essentially in North America and Mediter-ranean In this work we aimed to expand the scope of thestudy to the worldwide diversity and phylogeny ofmicrosym-bionts of Coriaria species Four microbial subgroups wereidentified that did not fit to the geographic range of the hostplants while two host plant subgroups were identified Theposition of subgroup A containing microsymbionts of NewZealand C arborea at the base of Frankia cluster 2 is inagreement with previous study [16] In view of previously
BioMed Research International 7
C ruscifolia
C nepalensis
Coriaria agustissima
C kingiana
C plumosaC lurida
C pteroidesC pottsiana
C sarmentosa
C papuana
C sarmentosa
CmNy1-2-3-4-5CmF1-2-3-4-5Coriaria myrtifoliaCmM1a-b-cCmM2a-bCmMs1-2-3-4-5 CnP1-2-3
Coriaria sp
C arborea
C microphyllaCmicMx1-2-3
CaNZ1-2-3
C japonicaCjJA-B-C-D-E
C terminalisC intermedia
Figure 2 Distribution of Coriaria species Root nodules have been sampled from C myrtifolia C arborea C nepalensis C japonica and Cmicrophylla growing in Mediterranean areas (Morocco and France) New Zealand Pakistan Japan and Mexico respectively Short arrowsindicate sampling sites for this study while long arrows indicate possible routes of dispersal as discussed
reported data members of cluster 2 Frankia studied herewere found to have relatively higher sequences variation (p-distance = 00625) than those reported by Vanden Heuvel etal [16] (119901 = 000454) based on the same 460 nt of the glnAgene
Molecular clock dating suggests that Frankia genus hasemerged much earlier 125Myr bp before the appearance ofangiosperm fossils in the Cretaceous period and the extantactinorhizal plants [4] Normand et al [5] using the 4divergence in the 16S rRNA between cluster 2 and otherFrankia lineages as equivalent to 50MY1 distance [17]concluded that the genus Frankia had emerged long beforethe extant dicotyledonous lineages These authors proposedFrankia cluster 2 as the proto-Frankia as nonsymbioticancestor of 62ndash130Myr bp [43] and 100ndash200Myr bp [5] Sincethe distance in the 16S rRNA gene between cluster 1a (Frankiaalni) and cluster 1b is less than 1 the date of emergence of theCasuarina-infective lineage has been proposed to be less than50 million years [5]Thus the CasuarinaFrankia 1b lineage isconsiderably younger than the CoriariaFrankia lineage andwould have had less time to migrate out of its cradle andmingle with other hosts in its new territories and lose thecospeciation signal
Symbiotic partnership often tends to become obligatoryas in the case of Casuarina host plants where Frankia is onlypresent in soils close to the host plant [44] which means thatthe bacterium loses autonomy and becomes dependent on itshost Speciation of the host could then lead to synchronousspeciation of its microsymbiont unless dispersal throughlong-distance carriers such as winds or migratory birds
occurred or if there is survival of Frankia cluster 2 in therhizosphere of nonhosts as was recently demonstrated forAlnus glutinosa in Tunisia [45] The numerous transitionsseen in the Frankia phylogenetic tree from one continent toanother would reinforce the idea
Yokoyama et al [19] concluded from their study of theCoriaria species phylogeny that the Eurasian species haddiverged earlier and are more diverse than other groups butthat nevertheless the origin of the genus could have been inNorth America whence the South America and the Pacificspecies could have originated Our study brings us to suggesta third possibility Oceania which could also be the originof this actinorhizal symbiosis which can be concluded fromphylogenetic inferences positioning both bacterial and hostplant partners as at the base to Frankia-Coriaria symbiosisAnother element that would support this hypothesis is thelarge number of extant species there according to Yokoyamaet al [19] New Zealand would be home to 8 of the 17 existingspecies A similar argument has often been made to establishSub-Saharan Africa as the cradle of humankind [46] orMexico for maize [47]
Comparison of both the plant and the microbe phyloge-netic topologies did not show any evidence for cospeciationof Frankia microsymbiontsand their Coriaria host speciesThe results obtained in this study suggest that Frankiamicrosymbionts hosted currently by Coriaria species hadprobably dispersed globally as a proto-Frankia a free livingand nonsymbiotic ancestor In parallel the proto-Coriariathen diversified into the extantCoriaria species that appear tohave been retreating given their scattered distribution a trend
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
6 BioMed Research International
Dg1
FCjJBFCjJA
FCmF1FCmF2FCmMs2FCmMs4FCmMs1FCmM1aFCmM1cFCmM1bFCmNy4FCmMs3FCmM2bFCmNy1FCmNy5FCnP1FCnP2FCmMx1FCmMx2FCaNZ2FCaNZ1100
99
99
69
100
8980
92
68
91
100
99
97
99
7581
OceaniaAsia
EuropeN AfricaAmerica
Gro
up A
G
roup
BG
roup
CG
roup
D
CmM1aCmM2aCmMs1
CmF2CmNy5
C myrtifolia C myrtifolia
CnP1
C nepalensisC terminalis C intermedia C japonica
CmicMx1C microphylla
C papuanaCaNZ1C arborea
C ruscifolia C sarmentosa
C lurida
8676
7590
7096
54
90
7083
7351
90
87
CjJA
Gro
up 2
Gro
up 1
Frankia Coriaria
Figure 1 Phylogenetic trees of the Frankiamicrosymbionts (left) and the Coriaria host plants (right)The Frankia tree was constructed usingthe glnA dnaA and the nifD-K intergenic spacer while the Coriaria tree was done using thematK and the 18S rRNA-ITS1-58S rRNA-ITS2-28S rRNA with ML method using strain CcI3 and Casuarina as outgroups respectively for Frankia and hot plant phylogenetic trees Thenumbers at branches indicate bootstrap results above 50 Lines are drawn between the microsymbionts and their hosts The color codeindicates the place of origin of the leave or of the set when homogenousThe groups numbers 1 and 2 on the right are according to Yokoyamaet al [19]
Paleontological data based on macrofossils and pollenfossils have brought several authors [36ndash40] to conclude thatthe Coriariaceae had a Laurasian origin (North Americaand Eurasia) There have been a few dissenting opinions inparticular those of Croizat [41] and Schuster [42] who con-sidered that Coriaria originated in Gondwana and migratedto the Northern Hemisphere However such paleontologicalstudies are not very convincing as it is recognizably hardto ascribe fossils to a given family and even more so to agiven genus Thus several authors have been surprised bythe results of molecular phylogeny positioning Coriariaceaeclose to the Datiscaceae Molecular approaches would thusgive support to a Gondwanan origin
Yokoyama et al [19] proposed that Coriaria species hademerged 59ndash63 million years ago which is coherent withthe date of 70 million years proposed by Bell et al [25]considerably older than that proposed (30million years) bythe same authors for the Casuarinaceae
Topology and clustering of Coriaria phylogeny obtainedin the current study are similar to those obtained byYokoyama et al [19] while the position at the base of thehost plant species from New Zealand C arborea and the
South American C ruscifolia and C microphylla species wascontrary to that of Yokoyama et al [19] who found theEurasian species at the base using rbcL (a large subunit ofribulose 15-bisphosphate carboxylaseoxygenase) and matK(maturase K) genes The present study suggests that theCoriaria ancestor may have emerged between Asia and NZand then dispersed worldwide and that the Asian lineagemay have given rise relatively recently to the Mediterraneanspecies while theNZ lineage gave rise to theNorth Americanspecies (Figure 2)
Previous studies had concluded that Frankia cluster 2 hada low genetic diversity [6 7 16] but these studies had beenfocused on only part of the full diversity of the symbioticCoriaria-Frankia essentially in North America and Mediter-ranean In this work we aimed to expand the scope of thestudy to the worldwide diversity and phylogeny ofmicrosym-bionts of Coriaria species Four microbial subgroups wereidentified that did not fit to the geographic range of the hostplants while two host plant subgroups were identified Theposition of subgroup A containing microsymbionts of NewZealand C arborea at the base of Frankia cluster 2 is inagreement with previous study [16] In view of previously
BioMed Research International 7
C ruscifolia
C nepalensis
Coriaria agustissima
C kingiana
C plumosaC lurida
C pteroidesC pottsiana
C sarmentosa
C papuana
C sarmentosa
CmNy1-2-3-4-5CmF1-2-3-4-5Coriaria myrtifoliaCmM1a-b-cCmM2a-bCmMs1-2-3-4-5 CnP1-2-3
Coriaria sp
C arborea
C microphyllaCmicMx1-2-3
CaNZ1-2-3
C japonicaCjJA-B-C-D-E
C terminalisC intermedia
Figure 2 Distribution of Coriaria species Root nodules have been sampled from C myrtifolia C arborea C nepalensis C japonica and Cmicrophylla growing in Mediterranean areas (Morocco and France) New Zealand Pakistan Japan and Mexico respectively Short arrowsindicate sampling sites for this study while long arrows indicate possible routes of dispersal as discussed
reported data members of cluster 2 Frankia studied herewere found to have relatively higher sequences variation (p-distance = 00625) than those reported by Vanden Heuvel etal [16] (119901 = 000454) based on the same 460 nt of the glnAgene
Molecular clock dating suggests that Frankia genus hasemerged much earlier 125Myr bp before the appearance ofangiosperm fossils in the Cretaceous period and the extantactinorhizal plants [4] Normand et al [5] using the 4divergence in the 16S rRNA between cluster 2 and otherFrankia lineages as equivalent to 50MY1 distance [17]concluded that the genus Frankia had emerged long beforethe extant dicotyledonous lineages These authors proposedFrankia cluster 2 as the proto-Frankia as nonsymbioticancestor of 62ndash130Myr bp [43] and 100ndash200Myr bp [5] Sincethe distance in the 16S rRNA gene between cluster 1a (Frankiaalni) and cluster 1b is less than 1 the date of emergence of theCasuarina-infective lineage has been proposed to be less than50 million years [5]Thus the CasuarinaFrankia 1b lineage isconsiderably younger than the CoriariaFrankia lineage andwould have had less time to migrate out of its cradle andmingle with other hosts in its new territories and lose thecospeciation signal
Symbiotic partnership often tends to become obligatoryas in the case of Casuarina host plants where Frankia is onlypresent in soils close to the host plant [44] which means thatthe bacterium loses autonomy and becomes dependent on itshost Speciation of the host could then lead to synchronousspeciation of its microsymbiont unless dispersal throughlong-distance carriers such as winds or migratory birds
occurred or if there is survival of Frankia cluster 2 in therhizosphere of nonhosts as was recently demonstrated forAlnus glutinosa in Tunisia [45] The numerous transitionsseen in the Frankia phylogenetic tree from one continent toanother would reinforce the idea
Yokoyama et al [19] concluded from their study of theCoriaria species phylogeny that the Eurasian species haddiverged earlier and are more diverse than other groups butthat nevertheless the origin of the genus could have been inNorth America whence the South America and the Pacificspecies could have originated Our study brings us to suggesta third possibility Oceania which could also be the originof this actinorhizal symbiosis which can be concluded fromphylogenetic inferences positioning both bacterial and hostplant partners as at the base to Frankia-Coriaria symbiosisAnother element that would support this hypothesis is thelarge number of extant species there according to Yokoyamaet al [19] New Zealand would be home to 8 of the 17 existingspecies A similar argument has often been made to establishSub-Saharan Africa as the cradle of humankind [46] orMexico for maize [47]
Comparison of both the plant and the microbe phyloge-netic topologies did not show any evidence for cospeciationof Frankia microsymbiontsand their Coriaria host speciesThe results obtained in this study suggest that Frankiamicrosymbionts hosted currently by Coriaria species hadprobably dispersed globally as a proto-Frankia a free livingand nonsymbiotic ancestor In parallel the proto-Coriariathen diversified into the extantCoriaria species that appear tohave been retreating given their scattered distribution a trend
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
BioMed Research International 7
C ruscifolia
C nepalensis
Coriaria agustissima
C kingiana
C plumosaC lurida
C pteroidesC pottsiana
C sarmentosa
C papuana
C sarmentosa
CmNy1-2-3-4-5CmF1-2-3-4-5Coriaria myrtifoliaCmM1a-b-cCmM2a-bCmMs1-2-3-4-5 CnP1-2-3
Coriaria sp
C arborea
C microphyllaCmicMx1-2-3
CaNZ1-2-3
C japonicaCjJA-B-C-D-E
C terminalisC intermedia
Figure 2 Distribution of Coriaria species Root nodules have been sampled from C myrtifolia C arborea C nepalensis C japonica and Cmicrophylla growing in Mediterranean areas (Morocco and France) New Zealand Pakistan Japan and Mexico respectively Short arrowsindicate sampling sites for this study while long arrows indicate possible routes of dispersal as discussed
reported data members of cluster 2 Frankia studied herewere found to have relatively higher sequences variation (p-distance = 00625) than those reported by Vanden Heuvel etal [16] (119901 = 000454) based on the same 460 nt of the glnAgene
Molecular clock dating suggests that Frankia genus hasemerged much earlier 125Myr bp before the appearance ofangiosperm fossils in the Cretaceous period and the extantactinorhizal plants [4] Normand et al [5] using the 4divergence in the 16S rRNA between cluster 2 and otherFrankia lineages as equivalent to 50MY1 distance [17]concluded that the genus Frankia had emerged long beforethe extant dicotyledonous lineages These authors proposedFrankia cluster 2 as the proto-Frankia as nonsymbioticancestor of 62ndash130Myr bp [43] and 100ndash200Myr bp [5] Sincethe distance in the 16S rRNA gene between cluster 1a (Frankiaalni) and cluster 1b is less than 1 the date of emergence of theCasuarina-infective lineage has been proposed to be less than50 million years [5]Thus the CasuarinaFrankia 1b lineage isconsiderably younger than the CoriariaFrankia lineage andwould have had less time to migrate out of its cradle andmingle with other hosts in its new territories and lose thecospeciation signal
Symbiotic partnership often tends to become obligatoryas in the case of Casuarina host plants where Frankia is onlypresent in soils close to the host plant [44] which means thatthe bacterium loses autonomy and becomes dependent on itshost Speciation of the host could then lead to synchronousspeciation of its microsymbiont unless dispersal throughlong-distance carriers such as winds or migratory birds
occurred or if there is survival of Frankia cluster 2 in therhizosphere of nonhosts as was recently demonstrated forAlnus glutinosa in Tunisia [45] The numerous transitionsseen in the Frankia phylogenetic tree from one continent toanother would reinforce the idea
Yokoyama et al [19] concluded from their study of theCoriaria species phylogeny that the Eurasian species haddiverged earlier and are more diverse than other groups butthat nevertheless the origin of the genus could have been inNorth America whence the South America and the Pacificspecies could have originated Our study brings us to suggesta third possibility Oceania which could also be the originof this actinorhizal symbiosis which can be concluded fromphylogenetic inferences positioning both bacterial and hostplant partners as at the base to Frankia-Coriaria symbiosisAnother element that would support this hypothesis is thelarge number of extant species there according to Yokoyamaet al [19] New Zealand would be home to 8 of the 17 existingspecies A similar argument has often been made to establishSub-Saharan Africa as the cradle of humankind [46] orMexico for maize [47]
Comparison of both the plant and the microbe phyloge-netic topologies did not show any evidence for cospeciationof Frankia microsymbiontsand their Coriaria host speciesThe results obtained in this study suggest that Frankiamicrosymbionts hosted currently by Coriaria species hadprobably dispersed globally as a proto-Frankia a free livingand nonsymbiotic ancestor In parallel the proto-Coriariathen diversified into the extantCoriaria species that appear tohave been retreating given their scattered distribution a trend
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
8 BioMed Research International
possibly reinforced recently due to man uprooting becauseof the toxicity of the fruits for mammals [48 49] It canthus be hypothesized that Coriaria appeared in the PacificIslands more than 70 million years ago and presumably wassymbiotic from the start before dispersing over all continentsas they drifted apart The Coriaria species diversified intheir different biotopes as they saw the appearance of otherplants hosting the same microsymbiont of Frankia cluster 2such as Datiscaceae Rosaceae Ceanothus or even nonhostspecies such as Alnus glutinosa that was recently found tohost Frankia cluster 2 in its rhizosphere [45] Members ofthese alternative host plant species cooccur sympatricallywith Coriaria such as Ceanothus and Purshia species inMexico and Datisca cannabina in Pakistan These Frankiacluster 2 host plant species have more extended geographicdistribution and overlap in some instancesCoriariarsquos disjunctarea and as a result can compensate Frankiamicrosymbiontsremoteness which would thus obscure the cospeciationsignal Cospeciation may also occur but subsequently is lostafter bacterial mixing and fitness selection in the presence ofldquoindigenousrdquo and ldquodispersalrdquo symbionts
Conflict of Interests
The authors declare that there is no conflict of interestsregarding the publication of this paper
Acknowledgments
This work is supported by CMCU (Comite Mixte Tuniso-Francais pour la Cooperation Inter-Universitaire No10G0903) The authors are grateful to Dr Marıa Valdes(Escuela Nacional de Ciencias Biologicas Mexico Mexico)Dr Sajjad Mirza (National Institute for BiotechnologyGenetic Engineering Faisalabad Pakistan) Dr WarwickSilvester (University of Waikato Waikato New Zealand)Dr Kawther Benbrahim and Dr A Ennabili (University ofFes Fes Morocco) Mr Spick (Montpellier Botanical gardenFrance) Dr J C Cleyet-Marel (Montpellier INRA France)Mr D Moukouanga (IRD Montpellier France) and DrTakashi Yamanaka (Forest and Forestry Products ResearchInstitute Ibaraki Japan) for providing Coriaria nodules
References
[1] M P Lechevalier ldquoTaxonomy of the genus Frankia (Actinomyc-etales)rdquo International Journal of Systematic Bacteriology vol 44no 1 pp 1ndash8 1994
[2] D R Benson B D VandenHeuvel and D Potter ldquoActinorhizalsymbioses diversity and biogeographyrdquo in Plant MicrobiologyM Gillings Ed pp 97ndash127 BIOS Scientific Publishers OxfordUK 2004
[3] M Gtari L S Tisa and P Normand ldquoDiversity of Frankiastrains actinobacteria symbionts of actinorhizal plantsrdquo inSymbiotic Endophytes Soil Biology R Aroca Ed vol 37Chapter 7 pp 123ndash148 Springer Berlin Germany 2013
[4] M L Clawson A Bourret and D R Benson ldquoAssessing thephylogeny of Frankia-actinorhizal plant nitrogen-fixing root
nodule symbioses with Frankia 16S rRNA and glutamine syn-thetase gene sequencesrdquoMolecular Phylogenetics and Evolutionvol 31 no 1 pp 131ndash138 2004
[5] P Normand S Orso B Cournoyer et al ldquoMolecular phylogenyof the genus Frankia and related genera and emendation ofthe family Frankiaceaerdquo International Journal of SystematicBacteriology vol 46 no 1 pp 1ndash9 1996
[6] F Ghodhbane-Gtari I Nouioui M Chair A Boudabous andM Gtari ldquo16S-23S rRNA intergenic spacer region variability inthe genus Frankiardquo Microbial Ecology vol 60 no 3 pp 487ndash495 2010
[7] I Nouioui F Ghodhbane-Gtari N J Beauchemin L S Tisaand M Gtari ldquoPhylogeny of members of the Frankia genusbased on gyrB nifH and glnII sequencesrdquoAntonie van Leeuwen-hoek vol 100 no 4 pp 579ndash587 2011
[8] P Normand and D R Benson ldquoGenus I Frankia Brunchorst1886 174ALrdquo in Bergeyrsquos Manual of Systematic Bacteriology TheActinobacteria M Goodfellow P Kampfer H-J Busse et alEds vol 5 of Bergeyrsquos Manual Trust pp 512ndash520 Springer NewYork NY USA 2012
[9] J G Torrey ldquoCross-inoculation groups within Frankia andhost-endosymbiont associationsrdquo inThe Biology of Frankia andActinorhizal Plants C R Schwintzer and J D Tjepkema Edspp 83ndash106 Academic Press San Diego Calif USA 1990
[10] S J Kohls J Thimmapuram C A Buschena M W Paschkeand J O Dawson ldquoNodulation patterns of actinorhizal plantsin the family Rosaceaerdquo Plant and Soil vol 162 no 2 pp 229ndash239 1994
[11] M S Mirza K Pawlowski F Y Hafeez A H Chaudharyand A D L Akkermans ldquoUltrastructure of the endophyte andlocalization of nifH transcripts in root nodules of Coriarianepalensis Wall by in situ hybridizationrdquo New Phytologist vol126 no 1 pp 131ndash136 1994
[12] G Nick E Paget P Simonet A Moiroud and P NormandldquoThe nodular endophytes of Coriaria spp form a distinctlineage within the genus FrankiardquoMolecular Ecology vol 1 no3 pp 175ndash181 1992
[13] M Bosco S Jamann C Chapelon and S P Normand ldquoFrankiamicrosymbiont in Dryas drummondii nodules is closely relatedto the microsymbiont of Coriaria and genetically distinct fromother characterized Frankia strainsrdquo in Nitrogen Fixation withNon-Legumes N A Hegazi M Fayez and M Monib Eds pp173ndash183 The American University in Cairo Press 1994
[14] D R Benson D W Stephens M L Clawson and W BSilvester ldquoAmplification of 16S rRNAgenes from Frankia strainsin root nodules of Ceanothus griseus Coriaria arborea Coriariaplumosa Discaria toumatou and Purshia tridentatardquo Appliedand Environmental Microbiology vol 62 no 8 pp 2904ndash29091996
[15] D R Benson andM L Clawson ldquoEvolution of the actinorhizalplant symbiosesrdquo in Prokaryotic Nitrogen Fixation A ModelSystem for Analysis of Biological Process E W Triplett Ed pp207ndash224 Horizon Scientific Press Wymondham UK 2000
[16] B D Vanden Heuvel D R Benson E Bortiri and D PotterldquoLow genetic diversity among Frankia spp strains nodulatingsympatric populations of actinorhizal species of RosaceaeCeanothus (Rhamnaceae) and Datisca glomerata (Datiscaceae)west of the Sierra Nevada (California)rdquo Canadian Journal ofMicrobiology vol 50 no 12 pp 989ndash1000 2004
[17] H Ochman and A C Wilson ldquoEvolution in bacteria evidencefor a universal substitution rate in cellular genomesrdquo Journal ofMolecular Evolution vol 26 no 1-2 pp 74ndash86 1987
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
BioMed Research International 9
[18] P Simonet E Navarro C Rouvier et al ldquoCo-evolutionbetween Frankia populations and host plants in the familyCasuarinaceae and consequent patterns of global dispersalrdquoEnvironmental Microbiology vol 1 no 6 pp 525ndash533 1999
[19] J Yokoyama M Suzuki K Iwatsuki and M Hasebe ldquoMolecu-lar phylogeny ofCoriaria with special emphasis on the disjunctdistributionrdquoMolecular Phylogenetics and Evolution vol 14 no1 pp 11ndash19 2000
[20] R D O Good ldquoThe geography of the genus Coriariardquo NewPhytologist vol 29 pp 170ndash198 1930
[21] H H Allan ldquoCoriariaceaerdquo in Flora of New Zealand L BMoore Ed pp 300ndash305 Government printerWellington NewZealand 1961
[22] R Melville ldquoContinental drift mesozoic continents and themigrations of the angiospermsrdquo Nature vol 211 no 5045 pp116ndash120 1966
[23] L E Skog ldquoThe genus Coriaria Coriariaceae in the WesternHemisphererdquo Rhodora vol 74 pp 242ndash253 1972
[24] R Melville ldquoVicarious plant distributions and paleogeographyof the Pacific regionrdquo inVicariance Biogeography G Nelson andE D Rosen Eds pp 413ndash435 Columbia University Press NewYork NY USA 1981
[25] C D Bell D E Soltis and P S Soltis ldquoThe age and diversi-fication of the angiosperms re-revisitedrdquo American Journal ofBotany vol 97 no 8 pp 1296ndash1303 2010
[26] C Rouvier J Schwenke Y Prin et al ldquoBiologie et diversitegenetique des souches de Frankia associees aux CasuarinaceesrdquoActa Botanica Gallica vol 143 pp 567ndash580 1996
[27] J D Thompson D G Higgins and T J Gibson ldquoCLUSTALW improving the sensitivity of progressive multiple sequencealignment through sequence weighting position-specific gappenalties and weight matrix choicerdquoNucleic Acids Research vol22 no 22 pp 4673ndash4680 1994
[28] K Tamura D Peterson N Peterson G Stecher M Nei andS Kumar ldquoMEGA5 molecular evolutionary genetics analysisusing maximum likelihood evolutionary distance and max-imum parsimony methodsrdquo Molecular Biology and Evolutionvol 28 no 10 pp 2731ndash2739 2011
[29] M Kimura ldquoA simple method for estimating evolutionary ratesof base substitutions through comparative studies of nucleotidesequencesrdquo Journal ofMolecular Evolution vol 16 no 2 pp 111ndash120 1980
[30] N Saitou and M Nei ldquoThe neighbor-joining method a newmethod for reconstructing phylogenetic treesrdquo Molecular Biol-ogy and Evolution vol 4 no 4 pp 406ndash425 1987
[31] J Felsenstein ldquoConfidence limits on phylogenies an approachusing the bootstraprdquo Evolution vol 39 pp 783ndash791 1985
[32] F Ronquist and J P Huelsenbeck ldquoMrBayes 3 bayesian phylo-genetic inference under mixed modelsrdquo Bioinformatics vol 19no 12 pp 1572ndash1574 2003
[33] P Legendre Y Desdevises and E Bazin ldquoA statistical test forhost-parasite coevolutionrdquo Systematic Biology vol 51 no 2 pp217ndash234 2002
[34] J P Meier-Kolthoff A F Auch D H Huson and M GokerldquoCopyCat cophylogenetic analysis toolrdquo Bioinformatics vol 23no 7 pp 898ndash900 2007
[35] R Ihaka and R Gentleman ldquoR a language for data analysis andgraphicsrdquo Journal of Computational andGraphical Statistics vol5 no 3 pp 299ndash314 1996
[36] A N Gladkova ldquoFragments of the history of the Myricaceaefamilyrdquo Pollen and Spore vol 4 p 345 1962
[37] J A Doyle ldquoCretaceous angiosperm pollen of the Atlanticcoastal plain and its evolutionnary significancerdquo Journal of theArnold Arboretum vol 50 pp 1ndash35 1969
[38] P H Raven and D I Axelrod ldquoAngiosperm biogeography andpast continental movementsrdquo Annals of the Missouri BotanicalGarden vol 61 pp 539ndash673 1974
[39] J Muller ldquoFossil pollen records of extant angiospermsrdquo TheBotanical Review vol 47 no 1 pp 1ndash142 1981
[40] O Eriksson and B Bremer ldquoPollination systems dispersalmodes life forms and diversification rates in angiospermfamiliesrdquo Evolution vol 46 pp 258ndash266 1992
[41] L Croizat Manual of Phytogeography An Account of PlantDispersal Throughout the World Junk The Hague 1952
[42] RM Schuster ldquoPlate tectonics and its bearing on the geograph-ical origin and dispersal of angiospermsrdquo in Origin and EarlyEvolution of Angiosperms C B Beck Ed pp 48ndash138 ColumbiaUniversity Press New York 1976
[43] S-C Jeong A Liston and D D Myrold ldquoMolecular phylogenyof the genus Ceanothus (Rhamnaceae) using rbcL and ndhFsequencesrdquoTheoretical and Applied Genetics vol 94 no 6-7 pp852ndash857 1997
[44] J F Zimpfer C A Smyth and J O Dawson ldquoThe capacity ofJamaican mine spoils agricultural and forest soils to nodulateMyrica cerifera Leucaena leucocephala and Casuarina cunning-hamianardquo Physiologia Plantarum vol 99 no 4 pp 664ndash6721997
[45] I Nouioui I Sbissi F Ghodhbane-Gtari K Benbrahim PNormand and M Gtari ldquoFirst report on the occurrence of theuncultivated cluster 2 Frankia microsymbionts in soil outsidethe native actinorhizal host range areardquo Journal of Biosciencesvol 38 pp 695ndash698 2013
[46] S Ramachandran O Deshpande C C Roseman N ARosenberg M W Feldman and L L Cavalli-Sforza ldquoSupportfrom the relationship of genetic and geographic in humanpopulations for a serial founder effect originating in AfricardquoProceedings of the National Academy of Sciences of the UnitedStates of America vol 102 no 44 pp 15942ndash15947 2005
[47] B Prasanna ldquoDiversity in global maize germplasm character-ization and utilizationrdquo Journal of Biosciences vol 37 pp 843ndash855 2012
[48] L DeHaro P Pommier L TichadouMHayek-Lanthois and JArditti ldquoPoisoning by Coriaria myrtifolia Linnaeus a new casereport and review of the literaturerdquo Toxicon vol 46 no 6 pp600ndash603 2005
[49] S F Belcher and T R Morton ldquoTutu toxicity three casereports of Coriaria arborea ingestion review of literature andrecommendations for managementrdquoThe New Zealand MedicalJournal vol 126 pp 103ndash109 2013
[50] T Persson D R Benson P Normand et al ldquoGenomesequence of ldquoCandidatus Frankia datiscaerdquo Dg1 the unculturedmicrosymbiont from nitrogen-fixing root nodules of the dicotDatisca glomeratardquo Journal of Bacteriology vol 193 no 24 pp7017ndash7018 2011
[51] P Normand P Lapierre L S Tisa et al ldquoGenome character-istics of facultatively symbiotic Frankia sp strains reflect hostrange and host plant biogeographyrdquo Genome Research vol 17no 1 pp 7ndash15 2007
[52] T J White T Bruns S Lee and J Taylor ldquoAmplificationand direct sequencing of fungal ribosomal RNA genes forphylogeneticsrdquo in PCR Protocols A Guide to Methods andApplications M A Innis D H Gelfand J J Sninsky and TJ White Eds pp 315ndash322 Academic Press San Diego CalifUSA 1990
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology
Submit your manuscripts athttpwwwhindawicom
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Anatomy Research International
PeptidesInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporation httpwwwhindawicom
International Journal of
Volume 2014
Zoology
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Molecular Biology International
GenomicsInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
The Scientific World JournalHindawi Publishing Corporation httpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioinformaticsAdvances in
Marine BiologyJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Signal TransductionJournal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
BioMed Research International
Evolutionary BiologyInternational Journal of
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Biochemistry Research International
ArchaeaHindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Genetics Research International
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Advances in
Virolog y
Hindawi Publishing Corporationhttpwwwhindawicom
Nucleic AcidsJournal of
Volume 2014
Stem CellsInternational
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
Enzyme Research
Hindawi Publishing Corporationhttpwwwhindawicom Volume 2014
International Journal of
Microbiology