Ewald (J.Z.) Groenewald - Opening Plenary

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Identifying Quarantine Organisms with DNA Barcodes – QBOL and its Contribution to Q-bank

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  • 13/12/11
  • Ewald (J.Z.) Groenewald - Opening Plenary

    1. 1. Identifying Quarantine Organisms with DNA Barcodes – QBOL and its Contribution to Q-bank presented by Ewald (J.Z.) Groenewald www.qbol.org [email_address]
    2. 2. EPPO – European and Mediterranean Plant Protection Organization <ul><li>Intergovernmental organization responsible for European cooperation in plant protection – www.eppo.org </li></ul><ul><li>EU Council Directive for legislation </li></ul>A1 (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
    3. 3. Problem definition <ul><li>Species on Q lists not linked to specimens and associated metadata </li></ul><ul><li>Sometimes no sequence data or diagnostic protocols available </li></ul><ul><li>Morphology can be problematic (different larval stages, sterile fungal cultures, etc) </li></ul><ul><li>Taxonomy issues , e.g. different names for same species on different lists </li></ul>EPPO region
    4. 4. QBOL – The project <ul><li>Call: FP7-KBBE-2008-2B; Theme KBBE-2008-1-4-01: “Development of new diagnostic methods in support of Plant Health policy” </li></ul><ul><li>Small Collaborative Project in the Seventh Framework Programme of the EU </li></ul><ul><li>Project Proposal No.: 226482 </li></ul><ul><li>“ Development Of A New Diagnostic Tool Using DNA Barcoding To Identify Quarantine Organisms In Support Of Plant Health” = QBOL </li></ul><ul><li>Run-time three years, starting 22/03/2009 </li></ul>
    5. 5. QBOL – 20 Global Partners
    6. 6. QBOL – The 11 workpackages <ul><li>WP1 – Coordination and Management </li></ul><ul><li>WP2-7 – Barcoding Fungi, Arthropods, Bacteria, Nematodes, Viruses & Phytoplasmas </li></ul><ul><li>WP8 – DNA Banks </li></ul><ul><li>WP9 – DNA barcode library / Databases / Informatics </li></ul><ul><li>WP10 – Validation / Evaluation </li></ul><ul><li>WP11 – Dissemination </li></ul>
    7. 7. QBOL – Four main objectives <ul><li>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 </li></ul><ul><li>Develop generic diagnostic tools based on these barcode sequences </li></ul><ul><li>Enable the establishment of DNA banks and access to digital voucher specimens </li></ul><ul><li>Support better collaboration between EU and third-world country diagnostic laboratories </li></ul>
    8. 8. QBOL – Overall progress <ul><li>Midterm (21-22/09/2011) evaluation in Bologna, Italy, with EU representatives – Very positive feedback! </li></ul><ul><li>Number of sequences obtained (09/2011): </li></ul><ul><ul><li>Fungi – 6,157 sequences (up to 8 loci) </li></ul></ul><ul><ul><li>Arthropods – 1,221 (up to 2 loci) </li></ul></ul><ul><ul><li>Bacteria – 1,749 (up to 20 loci) </li></ul></ul><ul><ul><li>Nematodes – 720 (up to 6 loci) </li></ul></ul><ul><ul><li>Viruses – 11 (whole genome) </li></ul></ul><ul><ul><li>Phytoplasms – 285 (up to 3 loci) </li></ul></ul><ul><li>Data being added to Q-bank database – www.q-bank.eu (see poster D16) </li></ul>
    9. 9. WP2 Fungi – Q barcode results Note: Species names according to the EPPO lists Mycosphaerella gibsonii http://photos.eppo.org/ Interspecific variation TEF CAL RPB2 ITS 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)
    10. 10. WP2 Fungi – Q barcode results Note: Species names according to the EPPO lists Ceratocystis fagacearum http://photos.eppo.org/ Interspecific variation TEF CAL RPB2 ITS 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)
    11. 11. QBOL – Conclusions <ul><li>QBOL ’ s contribution to Q-bank database is essential for NPPO ’ s and other end-users </li></ul><ul><li>Links provided to specimens in physical collections (as far as possible) and nucleotide sequences extremely important </li></ul><ul><li>Identification with correct Q status irrespective of name used </li></ul><ul><li>Expand database with other Q-species not yet included (maybe international?) </li></ul>
    12. 12. Special thank you to: <ul><li>EU 7 th Framework programme funding </li></ul><ul><li>All colleagues involved in QBOL </li></ul><ul><li>The international contributors and collaborators of QBOL </li></ul>Thank you for your attention! Dothistroma septosporum Studies in Mycology 50:552 [email_address] Visit www.qbol.org and www.q-bank.eu for more information.

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