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DNA Barcoding of Pacific Invasive and Pest Species Pacific Science Congress Kuala Lumpur

DNA Barcoding of Pacific Invasive and Pest Species Pacific Science Congress Kuala Lumpur. David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu ; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938. Today’s Goals.

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DNA Barcoding of Pacific Invasive and Pest Species Pacific Science Congress Kuala Lumpur

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  1. DNA Barcoding of Pacific Invasive and Pest SpeciesPacific Science Congress Kuala Lumpur David E. Schindel, Executive Secretary National Museum of Natural History Smithsonian Institution SchindelD@si.edu; http://www.barcoding.si.edu 202/633-0812; fax 202/633-2938

  2. Today’s Goals • Share information on barcoding, invasives • Share information on projects and organizations in Pacific • Discuss potential regional cooperation; and • Discuss possible formation of a PSA Working Group on DNA barcoding of invasive/pest species: • Participants (individuals, labs, institutes, agencies) • Activities (training, workshops, collecting, producing data) • Deliverables (data, publications, websites)

  3. Existing Activities • National quarantine agencies (NPPOs) • Regional agencies and initiatives (RPPOs, Quads, QBOL) • Global Initiatives (IPPC, CABI, GISP) • BioNET INTERNATIONAL LOOP PaciNET • PBIF: Pacific Node of GBIF

  4. The DNA Barcoding Initiative • Barcoding is becoming a global standard for species identification • Rapidly expanding by region, taxa, applications • The Barcoding Initiative is global with participants in 50+ countries • CBD, IPPC, Global Taxonomy Initiative, Census of Marine Life, others involved • Government agencies: USDA, FDA, NOAA

  5. Species Identification Matters • Basic research on evolution, ecology • Invasive species (e.g., in ballast water) • Agricultural pests/beneficial species • Endangered/protected species • Disease vectors/pathogens • Environmental quality indicators • Managing for sustainable harvesting • Consumer protection, ensuring food quality • Fidelity of seedbanks, culture collections

  6. A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species

  7. Small ribosomal RNA The Mitochondrial Genome D-Loop mtDNA DNA Cytochrome b ND1 ND6 ND5 COI ND2 COI L-strand H-strand Typical Animal Cell ND4 ND4L COII ND3 COIII ATPase subunit 8 ATPase subunit 6 Mitochondrion An Internal ID System for All Animals

  8. Associating Life Stages, Processed Parts, Dimorphic Genders

  9. Non-COI regions for other taxa • Land plants: • Chloroplast matK and rbcL approved Nov 09 • 70-75% resolvingability, higher in angiosperms • Non-coding plastid and nuclear regions being explored • Fungi: • CBOL Working Group met this week in Amsterdam • Agreed to recommend ITS; 72% effective • Protists: • CBOL Working Group July meeting, Berlin

  10. How Barcoding Works • PHASE 1: Build a barcode reference library: • Well-identified specimen • Tissue subsample • DNA extraction, PCR amplification • DNA sequencing • Data submission to GenBank • PHASE 2: Identify unknowns: • Any unidentified juvenile, adult, fragment, product • Tissue sample, DNA, sequencing • Comparison with sequences in reference library

  11. Current Norm: High throughput Large labs, hundreds of samples per day Large capacity PCR and sequencing reactions ABI 3100 capillary automated sequencer

  12. ● US$100-150K purchase ● 2-3 hours processing time ● 150-500 samples per day ● US$3-5 per sample

  13. Technology Development Partnership Goal The DNA Sequencing Lab of 2013?

  14. BOLD System Workbench in Canada NBII, 25 February 2009

  15. BARCODE Record Flow Chart Key Mirroring Update Channel Private Records USER /GenBank

  16. BARCODE Records in INSDC Specimen Metadata Voucher Specimen Species Name GeoreferenceHabitatCharacter setsImagesBehaviorOther genes Indices - Catalogue of Life - GBIF/ECAT Nomenclators - Zoo Record - IPNI - NameBank Publication links - New species Barcode Sequence Trace files Primers Other Databases Literature(link to content or citation) PhylogeneticPop’n GeneticsEcological Databases - Provisional sp.

  17. Linkout from GenBank to BOLD

  18. Linkout from GenBank to Taxonomy ISBER: 13 May 2009

  19. Link from GenBank to Museums ISBER: 13 May 2009

  20. Darwin Core TripletStructured Link to Vouchers Institutional Acronym Collection Code Catalog ID : :

  21. Structured Link to Vouchers : : NHM LEP 123456 : : personal DHJanzen SRNP12345

  22. NCBI’s Biorepository List • Compiled from Index Herbariorum, literature sources, GenBank submissions • 6,936 records • 1,177 records with non-unique acronyms • 517 homonymous acronyms • 374 shared by two records • 143 shared by three records

  23. CBOL/GBIF/NCBI Registry of Biorepositories www.biorepositories.org

  24. 31 Malaysian Biorepositories Recorded 10 Confirmed, 21 Unconfirmed

  25. Producing Barcode Data: 201?Barcode data anywhere, instantly • Data in seconds to minutes • Pennies per sample • Link to reference database • A taxonomic GPS • Usable by non-specialists

  26. Barcode of Life Community 1,264,000 specimens already barcoded from 104,500 species Networks, Projects, Organizations • Promote barcoding as a global standard • Build participation • Working Groups • BARCODE standard • International Conferences • Increase production of public BARCODE records

  27. The International Barcode of Life Project (iBOL) 5 Million specimens, 500,000 species in 5 years $150 million with core funding from Genome Canada iBOL website, University of Guelph, Ontario: www.ibol.org

  28. iBOL Theme 1: DNA Barcode Library WG 1.1 Vertebrates WG 1.2 Land Plants WG 1.3 Fungi WG 1.4 Human Pathogens and Zoonoses WG 1.5 Agricultural and Forestry Pest and Parasitoids WG 1.6 Pollinators WG 1.7 Freshwater Bio-Surveillance WG 1.8 Marine Bio-Surveillance WG 1.9 Terrestrial Bio-Surveillance WG 1.10 Polar Life

  29. Consortium for the Barcode of Life (CBOL)CBOL Member Organizations: 2010 • 200+ Member organizations, 50 countries • 35+ Member organizations from 20+ developing countries

  30. Outreach Activities • Cape Town, South Africa, April 2006, SANBI • Scale insects in African agriculture • Nairobi, Kenya, October 2006 • Commercial fisheries in Rift Valley lakes • Brazil, March 2007 • Hardwood tree species • Endangered mammals, reptiles, amphibians • Taiwan, September 2007 • Nigeria, October 2008 • Beijing, May 2009 • India, November 2010

  31. Adoption by Regulators • International Plant Protection Commission • CBOL and APHIS to host Diagnostic Protocol Panel meeting, July 2010 • Federal Aviation Administration – $500K for birds • Environmental Protection Agency • $250K pilot test, water quality bioassessment • Food and Drug Administration • Reference barcodes for commercial fish • NOAA/NMFS • $100K for Gulf of Maine pilot project • CITES, National Agencies, Conservation NGOs

  32. Conclusions • Barcoding is a cost-effective system for rapid identification • Barcode reference libraries are being constructed for several endangered groups • CBOL and iBOL provide a global network of specialists capable of constructing barcode reference libraries on selected groups • Partnerships with national and regional groups and regulatory agencies are the critical missing components

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