dave lunt presentation to nottingham ukngs 2013
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TRANSCRIPT
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
Dave Lunt
JD Eisenback
JD Eisenback
juveniles enter root tip
Evolutionary Biology Group, University of Hull
Institute of Evolutionary Biology, University of Edinburgh
Georgios KoutsovoulosMark Blaxter
Sujai Kumar
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
Dave Lunt
JD Eisenback
JD Eisenback
juveniles enter root tip
davelunt.net
@davelunt
@EvoHull +EvoHull
+davelunt
Institute of Evolutionary Biology, University of EdinburghMark Blaxter
nematodes.org
Evolutionary Biology Group, University of Hull
http://www.slideshare.net/davelunt/lunt-nottingham
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
Acknowledgements
JD Eisenback
JD Eisenback
juveniles enter root tip
Africa Gómez, Richard Ennos, Amir Szitenberg, Karim Gharbi, Chris Mitchell, Steve Moss, Tom Powers, Janete Brito, Etienne Danchin, Marian
Thomson & GenePool
FundingNERC, BBSRC, Yorkshire Agricultural Society,
Nuffield Foundation, University of Hull, University of Edinburgh
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
JD Eisenback
JD Eisenback
juveniles enter root tip
WHAT’S IN A GENOME & WHY?
mostly transposons, repeats, & sequences of incertae sedis
In eukaryotes its
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
JD Eisenback
JD Eisenback
juveniles enter root tip
WHAT’S IN A GENOME & WHY?
mostly transposons, repeats, & sequences of incertae sedis
In eukaryotes its
But Why?
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
JD Eisenback
JD Eisenback
juveniles enter root tip
WHAT’S IN A GENOME & WHY?
Evolutionary Forces:Selection
Gene FlowMutation
Drift Recombination
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
JD Eisenback
JD Eisenback
juveniles enter root tip
WHAT’S IN A GENOME & WHY?
Evolutionary Forces:Selection
Gene FlowMutation
Drift
Recombination
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
Recombination and asexuality• Recombination shapes the genome
•We can study its action in species that have lost meiotic recombination- asexuals
• Reproduction solely by mitosis has consequences for the genome e.g.• Extreme ‘Allelic’ Sequence Divergence• Decay of genes specific to meiosis,
gametes, sexual dimorphism
A B C D E Fsexualasexual
origin of asexuality
asexual
RECOMBINATION AND ASEXUALITY
Extreme Allelic Sequence Divergence
• "If we suppose an ameiotic form evolving for a very long period of time we might imagine its two chromosome sets becoming completely unlike, so that it could no longer be considered as a diploid either in a genetical or cytological sense."
• Sometimes called Meselson effect, similar to paralogous loci
A B C D E Fsexualasexual
origin of asexuality
asexual
MJD White ‘Animal Cytology and Evolution’ 1st ed 1945, p283
RECOMBINATION AND ASEXUALITY
Extreme Allelic Sequence Divergence
A B C D E Fsexualasexual
origin of asexuality
asexual
RECOMBINATION AND ASEXUALITY
loss of meiosis
A B C D E F
Extreme Allelic Sequence Divergence
alleles
taxon
Recent
Ancient
1 2 3
asexual sexualasexual
Redrawn after Birky 1996
Divergence between sexual species alleles
Divergence between asexual ‘alleles’
allele
s by r
ecom
binati
on
meiosis
homog
enize
s
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne Root Knot Nematodes• Globally important agricultural species
• ~5% loss of world agriculture JD Eisenback
RKN juveniles enter root tip
infected uninfected
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne Reproduction•Wide variety of reproductive modes in a
single genus
•Mitotic parthenogens (apomics)
•Meiotic parthenogens (automicts)
• Sexual (amphimicts)
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne Reproduction•Wide variety of reproductive modes in a
single genus
•Many species are mitotic parthenogens without chromosome pairs• Incapable of meiosis
• Could be ‘ancient’ asexuals• 17 million years without meiosis?
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne Reproduction•Wide variety of reproductive modes in a
single genus•Many species are mitotic parthenogens
without chromosome pairs
•Other species are meiotic parthenogens or sexual• automixis or amphimixis
• undergo meiosis and syngamy
THE MELOIDOGYNE RKN SYSTEM
Meloidogyne Reproduction• Wide variety of reproductive modes in a single genus
MELOIDOGYNE REPRODUCTION
Previous Single Gene Sequencing
• I can reject ancient asexuality on basis of interspecific allele sharing and identical molecular evolution of sperm protein genes
• Although meet ASD expectations of ancient asexuality, other explanations fit better -- ie interspecific hybrid origins
Lunt DH 2008 BMC Evolutionary Biology 8:194
MELOIDOGYNE REPRODUCTION
Hybrid Speciation•Once thought that hybrid speciation was
rare and inconsequential in animals
• Genome biology is revealing a different view
•We have investigated the origins of Meloidogyne asexuals in this context
SEM Meloidogyne female
JD Eisenback
JD Eisenback
RKN juveniles enter root tip
Comparative genomics of hybrid origins•We have a phylogenetic design for
investigations
• Can map breeding system onto tree
•Origins of hybrid genomes can be investigated with whole genome sequences
MELOIDOGYNE HYBRIDIZATION GENOMICS
Is M. floridensis the parent of the asexuals?
We can investigate this using genome sequences;
--look at the within-genome patterns of diversity
--look at phylogenetic relationships of all genes
MELOIDOGYNE HYBRIDIZATION GENOMICS
M.floridensis M. ???
M. incognita
M. javanica
M. arenaria
x
apomicts
parental species
automict
MELOIDOGYNE HYBRIDIZATION GENOMICS
Meloidogyne comparative genomics
We have sequenced M. floridensis genome and are able to compare to 2 other Meloidogyne genomes published by other groups
M.floridensis M. ???
M. incognita
M. javanica
M. arenaria
x
apomicts
parental species
automict
asexual hybrid?
sexual parental?
sexual outgroup
MELOIDOGYNE COMPARATIVE GENOMICS
The Meloidogyne floridensis genome
• Illumina HiSeq2000 v2 reagents• 100bp paired end • 250bp fragments• 81k scaffolds• N50 3.5k• 30% GC
M. floridensis draft genome raw data SRA ERP001338
Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
MELOIDOGYNE COMPARATIVE GENOMICS
The Meloidogyne floridensis genome
M. floridensis draft genome raw data SRA ERP001338Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• DNA isolated from nematodes on plant roots will include many microbial ‘contaminants’
• preliminary assembly of trimmed reads ignoring pairing information
• annotate 10k random sampled contigs with taxonomic info determined by megablast
• Scatterplot of %GC and read coverage coloured by taxonomy
Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
24
Methodology:Kumar S, Blaxter ML (2012) Simultaneous genome sequencing of symbionts and their hosts. Symbiosis 55: 119–126. doi:10.1007/s13199-012-0154-6
nematodes
MELOIDOGYNE COMPARATIVE GENOMICS
The Meloidogyne floridensis genome• Stringent removal of bacterial
sequences
• Clusters of bacterial orders Bacillales, Burkholderiales, Pseudomonadales and Rhizobiales
• lower coverage and higher %GC clusters excluded
• Second round of megablast and hits to bacteria removed
Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
MELOIDOGYNE COMPARATIVE GENOMICS
The Meloidogyne floridensis genome• 100Mb assembly ~100x genomic
coverage
• 15.3k predicted proteins
• similar to published Meloidogyne genomes
• Suitable for comparative analyses
Lunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
MELOIDOGYNE COMPARATIVE GENOMICS
Comparative genomics questionsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• Is there evidence of hybrid origins of asexual species?
• Is M. floridensis a parental?
• How do offspring and parental genomes differ?
•What was the other parent?
• Broader implications?
INTRA-GENOMIC ANALYSES
ID of duplicated protein-coding regionsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• Coding sequences from each of the three target genomes (M. hapla, M. incognita and M. floridensis) were compared to the set of genes from the same species
• The percent identity of the best matching (non-self) coding sequence was calculated, and is plotted as a frequency histogram
• Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
Self identity comparisons
INTRA-GENOMIC ANALYSES
ID of duplicated protein-coding regionsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• Coding sequences from each of the three target genomes (M. hapla, M. incognita and M. floridensis) were compared to the set of genes from the same species
• The percent identity of the best matching (non-self) coding sequence was calculated, and is plotted as a frequency histogram
• Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
Self identity comparisons
INTRA-GENOMIC ANALYSES
ID of duplicated protein-coding regionsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• Coding sequences from each of the three target genomes (M. hapla, M. incognita and M. floridensis) were compared to the set of genes from the same species
• The percent identity of the best matching (non-self) coding sequence was calculated, and is plotted as a frequency histogram
• Both M. incognita and M. floridensis show evidence of presence of many duplicates, while M. hapla does not
Self identity comparisons
INTRA-GENOMIC ANALYSES
ID of duplicated protein-coding regionsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
Self identity comparisons•We have strong evidence that both M. incognita and M. floridensis contain diverged gene copies. • These loci duplicated at
approximately the same point in time. • A ploidy change is not
involved. • This is expected pattern for
hybrid genomes
COMPARATIVE GENOMICS
M. floridensis Genome SizeLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• Assembly size is not haploid genome size for hybrid species
•Divergence (4-8%) between homeologous (hybrid) copies will preclude assembly
•Our assembly of 100Mb is ~2x 50-54Mb genome size of M. hapla
HYBRIDIZATION HYPOTHESES
Hybridization HypothesesLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• There are very many ways species could hybridize, duplicate genes, lose genes
•We have selected a broad range of possibilities informed by prior knowledge
•We have tested their predictions phylogenetically
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(A)Whole genome duplication(s)
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(B)M. incognita is an
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(D)M. floridensis is a hybrid
and M. incognita is a secondary hybrid
between M. floridensis and a 3rd parent
HYBRIDIZATION HYPOTHESES
Testing by PhylogenomicsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
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• Coding sequences from 3 genomes were placed into orthologous groups and trees constructed• InParanoid algorithm, ML trees constructed
with RAxML• Found 4018 clusters of orthologs that included
all 3 species•We retained just those that had a single copy
in the outgroup M. hapla and resolved the relationships between Mi and Mf gene copies• Trees were parsed and pooled to represent
frequencies of different relationships
40
Each tree contains a single M. hapla sequence as outgroup (black square)
Grey square indicates relative
frequency of those
topologies
Trees are pooled within squares into different patterns of relationships
Grid squares represent different numbers of gene copies
HYBRIDIZATION HYPOTHESES
Testing by PhylogenomicsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
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M. i
ncog
nita
X+Y Y+Z
C Scenario 4
M. h
apla
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y
(X+Y)+Z
D Scenario 5
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X X+Z
B Scenario 3
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X Z+Z
A Scenario 1 & 2
X+Y
D
•We assess the fit of the tree topologies to our hypotheses• Five out of seven cluster sets, and 95% of all
trees, support hybrid origins for both M. floridensis and M. incognita
• ie exclude hypotheses A and B• Hypothesis C best explains 17 trees• Hypothesis D best explains 1335 trees
HYBRIDIZATION HYPOTHESES
Testing by PhylogenomicsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
M. h
apla
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y Y+Z
C Scenario 4
M. h
apla
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y
(X+Y)+Z
D Scenario 5
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X X+Z
B Scenario 3
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X Z+Z
A Scenario 1 & 2
X+Y
A
M. h
apla
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y Y+Z
C Scenario 4
M. h
apla
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y
(X+Y)+Z
D Scenario 5
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X X+Z
B Scenario 3
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X Z+Z
A Scenario 1 & 2
X+Y
B
M. h
apla
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y Y+Z
C Scenario 4
M. h
apla
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y
(X+Y)+Z
D Scenario 5
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X X+Z
B Scenario 3
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X Z+Z
A Scenario 1 & 2
X+Y
C
• The genome data supports both M. incognita and M. floridensis as interspecific hybrids
•M. floridensis is a parental species of M. incognita with other parent unknown
• Complex hybridization may be a feature of this genus?
M. h
apla
X Y ZM
. flo
riden
sis
M. i
ncog
nita
X+Y Y+Z
C Scenario 4M
. hap
la
X Y Z
M. f
lorid
ensi
s
M. i
ncog
nita
X+Y
(X+Y)+Z
D Scenario 5
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X X+Z
B Scenario 3
M. h
apla
X Z
M. f
lorid
ensi
s
M. i
ncog
nita
X Z+Z
A Scenario 1 & 2
X+Y
Hypothesis D
MELOIDOGYNE COMPARATIVE GENOMICS
Comparative genomics questionsLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• Is there evidence of hybrid origins of asexual species?• Yes, complex hybrid origins are clear• Is M. floridensis a parental?• Yes, identified by phylogenomics and
sequence identity• How do offspring and parental genomes
differ?• Broader implications?
MELOIDOGYNE COMPARATIVE GENOMICS
Ongoing WorkLunt et al arXiv 2013 http://arxiv.org/abs/1306.6163
• 19 genomes in a phylogenetic design
• Testing effect of breeding system on genome change
• hybrids, inbred, outbred, loss of meiosis
• TEs, mutational patterns, gene families
Current NERC grant on breeding system and Meloidogyne genome evolution
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
Dave Lunt
JD Eisenback
JD Eisenback
juveniles enter root tip
Evolutionary Biology Group, University of Hull
Institute of Evolutionary Biology, University of Edinburgh
Georgios KoutsovoulosMark Blaxter
Sujai Kumar
COMPLEX HYBRID ORIGINS OF ROOT KNOT NEMATODES
SEM Meloidogyne female
Dave Lunt
JD Eisenback
JD Eisenback
juveniles enter root tip
davelunt.net
@davelunt
@EvoHull +EvoHull
+davelunt
Institute of Evolutionary Biology, University of EdinburghMark Blaxter
nematodes.org
Evolutionary Biology Group, University of Hull
http://www.slideshare.net/davelunt/lunt-nottingham