Ewald (J.Z.) Groenewald - Opening Plenary
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Ewald (J.Z.) Groenewald - Opening Plenary

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

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 Ewald (J.Z.) Groenewald - Opening Plenary Presentation Transcript

  • Identifying Quarantine Organisms with DNA Barcodes – QBOL and its Contribution to Q-bank presented by Ewald (J.Z.) Groenewald www.qbol.org [email_address]
  • EPPO – European and Mediterranean Plant Protection Organization
    • Intergovernmental organization responsible for European cooperation in plant protection – www.eppo.org
    • EU Council Directive for legislation
    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
  • Problem 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
    EPPO region
  • QBOL – The 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
  • QBOL – 20 Global Partners
  • QBOL – The 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
  • QBOL – Four 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
  • QBOL – Overall 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)
  • 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)
  • 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)
  • QBOL – Conclusions
    • 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?)
  • Special thank you to:
    • EU 7 th Framework programme funding
    • All colleagues involved in QBOL
    • The international contributors and collaborators of QBOL
    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.