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Species Identification, Regulatory Agencies and DNA Barcoding

Species Identification, Regulatory Agencies and DNA Barcoding. 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. Genomics. Subgenomics. Current Systematic Studies.

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Species Identification, Regulatory Agencies and DNA Barcoding

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  1. Species Identification, Regulatory Agencies and DNA Barcoding 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. Genomics Subgenomics Current Systematic Studies Microbes - 16S Plants - RBCL Animals - COI

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

  4. Taxonomists The Practice of Taxonomy The Uses of Taxonomy Socioeconomic Decisions Taxonomic Decision-Making Distributions of Character Variation Concerns/ Regulations Characters Specimens Specimens

  5. Taxonomic Processes Formal Taxa Taxon Concepts Characters Specimens

  6. Growth of Biodiversity Databases Museum databases of associated data Biodiversity Heritage Library Authority files of taxonomic names

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

  8. 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

  9. Non-COI regions for other taxa • Land plants: • Chloroplast matK and rbcL approved Nov 09 • Non-coding plastid and nuclear regions being explored • Fungi and protists: • CBOL Working Groups convened • Recommendations expected in 2010

  10. How Barcoding Works • First, build a barcode reference library: • Well-identified specimen • Tissue subsample • DNA extraction, PCR amplification • DNA sequencing • Data submission to GenBank • Second, use it to identify unknowns: • Any unidentified juvenile, adult, fragment, product • Tissue sample, DNA, sequencing • Comparison with sequences in reference library

  11. Associating Life Stages, Processed Parts, Dimorphic Genders

  12. ND1 ND2 ND3 COIII How Barcoding is Done From specimen to sequence to species Collecting DNA extraction CO1 gene DNA sequencing Trace file Database of Barcode Records Voucher Specimen

  13. GenBank, EMBL, and DDBJGlobal, Open Access to Barcode Data NBII, 25 February 2009 http://www.insdc.org/

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

  15. Emerging Norm: Table-top LabsFaster, more portable: Hundreds of samples per hour Integrated DNA microchips Table-top microfluidic systems

  16. 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

  17. Barcode of Life Community Networks, Projects, Organizations • Promote barcoding as a global standard • Build participation • Working Groups • BARCODE standard • International Conferences • Increase production of public BARCODE records

  18. Consortium for the Barcode of Life (CBOL) • Established May 2004 with Sloan Foundation grant • Secretariat opens at Smithsonian, September 2004 • Now in its third two-year funding period • Workshops, Working Groups, networking, representation/marketing • Now an international affiliation of 200+ members in 50+ countries: • Natural history museums, biodiversity organizations • Users: e.g., government agencies • Private sector biotech companies, database providers

  19. CBOL Member Organizations: 2009 • 200+ Member organizations, 50 countries • 35+ Member organizations from 20+ developing countries

  20. 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.

  21. 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, March 2010

  22. CBOL’s Global Projects • Fish Barcode of Life (FISH-BOL) • 30,000 marine/freshwater species by 2010 • All Birds Barcoding Initiative (ABBI) • 10,000 species by 2010 • Tephritid fruit flies • 2,000 pest/beneficial species and relatives by 2008 • Mosquitoes • 3,300 species by 2008 • Endangered species • Trees of the world

  23. Adoption by Regulators • Food and Drug Administration • Reference barcodes for commercial fish • NOAA/NMFS • $100K for Gulf of Maine pilot project • FISH-BOL workshop with agencies, Taipei, Sept 2007 • Federal Aviation Administration – $500K for birds • Environmental Protection Agency • $250K pilot test, water quality bioassessment • FAO International Plant Protection Commission • Proposal for Diagnostic Protocols for fruit flies • CITES, National Agencies, Conservation NGOs • International Steering Committee, identifying pilot projects

  24. Why barcodes are short • Low cost and simplicity • Single capillary reads adequate • Avoid post-sequencing IT needed for pyroseq • Adequate for taxonomy • Miminizesuniformative sequence length • Limiting supply rate of identified specimens • Technology more accessible to small labs • Regulatory/inspection applications easier

  25. Barcoding and Metagenomics • Lots of interest for ecology, less for regulation • Pyrosequencing of environmental mixtures • Construct species list from mixture • Predator-prey relations from gut contents, feces • Food-web reconstruction • Relies on high accuracy (some species differ by only a few percent) • Not cost-effective for single specimens

  26. What barcode providers have and are producing • 770,000 records from ~100,000 species • Agricultural pests • Water quality indicators • Disease vectors • Endangered species • Commercial species of food, feed, commodities • 5 million records from 500K species by 2015

  27. International Barcode of Life Project (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 Their 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

  28. What barcode providers want • High PCR and sequencing success rates • Bigger window into older, compromised samples • Better software integration to eliminate bottlenecks • Smaller labs/developing countries: • Lower equipment and maintenance costs • Simplification for techs with less training • Install anywhere without lab renovations • Willing to accept slower throughput

  29. What barcode users want • Answers to specific questions: • Is this thing on this list of species or not? • Is this thing a member of this genus/family? • Which of the species on this list is this thing? • What species is this thing? • Production-scale capabilities: • Hundreds to thousands of installations • Lower but constant throughput • Rapid turnaround • The right price-point and limited life cycle costs

  30. What barcode users would do with the reference libraries • Inspection stations at every port and international airport for: • Agricultural pest control • Illegal trade in endangered species • Violations of trade quotas • Regular Federal and State water quality surveys • Federal, State and local food inspection • Public health monitoring and diagnoses

  31. GenBank, EMBL, and DDBJGlobal, Open Access to Barcode Data NBII, 25 February 2009 http://www.insdc.org/

  32. Linkout from GenBank to BOLD NBII, 25 February 2009

  33. Linkout from GenBank to Taxonomy NBII, 25 February 2009

  34. Link from GenBank to Museums NBII, 25 February 2009

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