ewald (j.z.) groenewald - opening plenary
DESCRIPTION
Identifying Quarantine Organisms with DNA Barcodes – QBOL and its Contribution to Q-bankTRANSCRIPT
Identifying Quarantine Organisms Identifying Quarantine Organisms
with DNA Barcodes – with DNA Barcodes –
QBOL and its ContributionQBOL and its Contribution
to Q-bankto Q-bank
presented by
Ewald (J.Z.) Groenewald Ewald (J.Z.) Groenewald
[email protected]@cbs.knaw.nl
www.qbol.org
EPPO – EPPO – European and Mediterranean European and Mediterranean
Plant Protection OrganizationPlant Protection Organization Intergovernmental organization
responsible for European cooperation in plant protection – www.eppo.org
EU Council Directive for legislationA1 (absent)
A2 (controlled)
Total
Fungi 36 26 62
Bacteria & phytoplasmas
12 24 36
Viruses & virus-like 23 21 44
Insects & mites 116 57 173
Nematodes 5 11 16
Parasitic plants 11 10 21
203 149 352
www.qbol.org
Problem definitionProblem definition Species on Q lists not linked to
specimens and associated metadata
Sometimes no sequence data or diagnostic protocols available
Morphology can be problematic (different larval stages, sterile fungal cultures, etc)
Taxonomy issues, e.g. different names for same species on different lists
EPPOregion
www.qbol.org
QBOL – QBOL – The projectThe project Call: FP7-KBBE-2008-2B; Theme KBBE-
2008-1-4-01: “Development of new diagnostic methods in support of Plant Health policy”
Small Collaborative Project in the Seventh Framework Programme of the EU
Project Proposal No.: 226482 “Development Of A New Diagnostic Tool
Using DNA Barcoding To Identify Quarantine Organisms In Support Of Plant Health” = QBOL
Run-time three years, starting 22/03/2009
www.qbol.org
QBOL –QBOL – 20 Global 20 Global
Partners Partners
www.qbol.org
QBOL – QBOL – The 11 workpackagesThe 11 workpackages WP1 – Coordination and
Management WP2-7 – Barcoding Fungi,
Arthropods, Bacteria, Nematodes, Viruses & Phytoplasmas
WP8 – DNA Banks WP9 – DNA barcode library /
Databases / Informatics WP10 – Validation / Evaluation WP11 – Dissemination
www.qbol.org
QBOL – QBOL – Four main objectivesFour main objectives Obtain or produce relevant vouchered
sequence data for individual pests or pest groups and position them in a correct taxonomic context – EU Council Directive and EPPO A1 and A2 lists
Develop generic diagnostic tools based on these barcode sequences
Enable the establishment of DNA banks and access to digital voucher specimens
Support better collaboration between EU and third-world country diagnostic laboratories
www.qbol.org
QBOL – QBOL – Overall progressOverall progress Midterm (21-22/09/2011) evaluation in
Bologna, Italy, with EU representatives – Very positive feedback!
Number of sequences obtained (09/2011): Fungi – 6,157 sequences (up to 8 loci) Arthropods – 1,221 (up to 2 loci) Bacteria – 1,749 (up to 20 loci) Nematodes – 720 (up to 6 loci) Viruses – 11 (whole genome) Phytoplasms – 285 (up to 3 loci)
Data being added to Q-bank database – www.q-bank.eu (see poster D16)
www.qbol.org
WP2 Fungi – WP2 Fungi – Q barcode resultsQ barcode resultsInterspecific
variationTEF CAL RPB
2ITS ACT TUB
Ceratocystis fimbriata f. sp.
platani
N/A 97%(551/569)
Ceratocystis virescens
N/A 92%(473/514)
Mycosphaerella gibsonii
99%(309/312)
N/D 93%(322/344)
100%(504/504)
99%(531/535)
97%(386/395)
Phaeoramularia angolensis
96%(127/132)
91%(152/166)
83%(173/206)
95%(503/524)
89%(478/536)
92%(104/113)
Monilinia fructicola
78%(376/482)
99%(495/499)
Note: Species names according to the EPPO lists
Mycosphaerella gibsoniihttp://photos.eppo.org/
www.qbol.org
WP2 Fungi – WP2 Fungi – Q barcode resultsQ barcode resultsInterspecific
variationTEF CAL RPB
2ITS ACT TUB
Mycosphaerella dearnessii
91%(127/139)
88%(283/319)
79%(155/195)
92%(432/468)
93%(310/332)
84%(177/210)
Mycosphaerella laricis-
leptolepidis
96%(124/128)
93%(255/273)
79%(142/179)
97%(484/497)
93%(338/361)
82%(179/217)
Davidiella (Mycosphaerella)
populorum
92%(132/142)
91%(167/182)
N/D 98%(459/467)
88%(377/425)
86%(370/428)
Septoria lycopersici var.
malagutii
99%(886/892)
97%(398/407)
99%(347/348)
99%(500/502)
98%(542/553)
99%(513/516)
Note: Species names according to the EPPO lists
Ceratocystis fagacearumhttp://photos.eppo.org/
www.qbol.org
QBOL – QBOL – ConclusionsConclusions
QBOL’s contribution to Q-bank database is essential for NPPO’s and other end-users
Links provided to specimens in physical collections (as far as possible) and nucleotide sequences extremely important
Identification with correct Q status irrespective of name used
Expand database with other Q-species not yet included (maybe international?)
www.qbol.org
Special thank you to:Special thank you to: EU 7th Framework programme funding All colleagues involved in QBOL The international contributors and
collaborators of QBOL
Thank you forThank you for
your attention!your attention!
Dothistroma septosporumStudies in Mycology 50:552
Visit www.qbol.org and www.q-bank.eu for more information.