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Introduction to the Consortium for the Barcode of Life (CBOL)

Introduction to the Consortium for the Barcode of Life (CBOL). Scott Miller Smithsonian Institution and Consortium for the Barcode of Life. Two views of genomics. Vertical : Complete genomes, deep but narrow knowledge Few species and few individuals But evolving in humans, Drosophila, crops

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Introduction to the Consortium for the Barcode of Life (CBOL)

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  1. Introduction to the Consortium for the Barcode of Life (CBOL) Scott Miller Smithsonian Institution and Consortium for the Barcode of Life

  2. Two views of genomics • Vertical: Complete genomes, deep but narrow knowledge • Few species and few individuals • But evolving in humans, Drosophila, crops • Horizontal: Short targeted sequences, shallow but broad knowledge • Many species and many individuals • DNA barcoding as an example

  3. Species Identification Matters • Agricultural pests/beneficial species • Managing trade (e.g., IPPC) • Consumer protection, ensuring food quality • Invasive species • Environmental quality indicators • Quality of cell lines/culture collections • Globilization increasing invasive species spread • Changes of host and range with climate change

  4. Species Identification Matters (2) • 80% CGIAR impact in Africa ($17 billion) from 4 biocontrol programs • Cassava mealybug, mango mealybug, water hyacinth, cassava green mite • All involved significant taxonomic challenges in pest and/or biocontrol agent Maredia & Raitzer 2006

  5. Historic challenges • Problems with species concepts and their application • Problems with species identifications • Character systems – morphology, genetics, etc. • Access to existing knowledge • Decline in expertise • Decline in service availablity • Genomics and Internet offer new options

  6. Poor representation of systematics infrastructure in Africa

  7. Human resources also thinly distributed • Stuckenberg (1964): most systematics done outside of Africa, but only 7% of world entomologists working on Africa • Gaston & May (1992): only 4% of ecologists and 7% of systematists in Africa • Surveys by CABI (1993), ICIPE (1996), and SAFRINET (1998) show same trends

  8. Associating Life Stages, Processed Parts, and Dimorphic Genders

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

  10. 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

  11. How Barcoding Works • Building the reference library: • Well-identified specimen (vouchers) • Tissue subsample • DNA extraction, PCR amplification • DNA sequencing • Data submission to GenBank • Using the reference library: • Unidentified specimen • Tissue, DNA, sequencing • Comparison with reference sequences

  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. Example: Moths in Africa • Noctuid stem borers are species complexes • ICIPE and IRD studies • Their tachinid parasites are also (Dittrich et al 2006) • Leguminivora ptychora on legumes is as species complex (Miller unpubl. from IITA samples) • But some pests are widespread, e.g., Spoladearecurvalis and Maruca vitrata

  14. Quick and efficient • Hawk moths (Sphingidae) sampled on IITA Ibadan campus (agroscape and forest) • 49 species in six months, almost all the local fauna • DNA barcodes all well resolved in local context and almost well resolved in global context • Local sequence libraries can be assembled quickly and contribute to global library

  15. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Coordination with other fields of science • Adoption by regulatory agencies • Product development by private companies

  16. 2008: CBOL Member Organizations • 170+ Member organizations, 50+ countries • 54 Member organizations from 20+ developing countries

  17. Growth of CBOL Activities • Executive Committee from 4 continents • Implementation Board of 19 Members  Working Groups  Campaigns  GenBank, BOLD  Related Initiatives • Outreach meetings to Africa, South/Central America, Asia • Network of 15 “Leading Labs” in 9 countries • Strong partnerships with GenBank/EMBL/DDBJ, GBIF, EOL

  18. 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

  19. Preview of the Third International Barcode Conference (2009) • 1 million barcode records from 100,000 species • Rapid progress on plant and fungal barcoding • Identifying unknowns in 30 minutes for less than US$1 • Port inspectors starting to test unknowns with barcodes in several countries • Portable sequencing ? • Completion of the first local barcode biotic inventory

  20. Overview of DNA barcoding and its relations to other biodiversity initiatives Scott Miller Smithsonian Institution and Consortium for the Barcode of Life

  21. 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

  22. Producing Barcode Data: 2007 • Hundreds of samples per day • Dimes to dollars per sample Polymerase Chain Reaction Amplification units ABI 3100 capillary automated sequencer

  23. Producing Barcode Data: 2008Faster, more portable: Hundreds of samples per hour Integrated DNA microchips Table-top microfluidic systems

  24. Producing Barcode Data: 2010?Barcode data anywhere, instantly • Data in seconds to minutes • Pennies per sample • Link to reference database • A taxonomic GPS • Usable by non-specialists

  25. BARCODE Records in GenBank 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.

  26. GenBank, EMBL, and DDBJGlobal, Open Access to Barcode Data http://www.insdc.org/

  27. Linking GenBank to Vouchers

  28. Specimen Webpage

  29. Sequence Webpage

  30. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Coordination with other fields of science • Adoption by regulatory agencies • Product development by private companies

  31. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Coordination with other fields of science • Adoption by regulatory agencies • Product development by private companies

  32. 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

  33. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Coordination with other fields of science • Adoption by regulatory agencies • Product development by private companies

  34. Leading Labs Network STRI SI-LAB BOLD GenBank CCDB BioCode

  35. Linking to International Initiatives through the Consortium for the Barcode of Life (CBOL) • Global Biodiversity Information Facility (GBIF) • Taxonomic databases (Species 2000, ITIS) • Voucher specimen databases • BioNet International • CBD Global Taxonomy Initiative • Projects such as SABONET & BOZONET • Biodiversity Heritage Library/Encyclopedia of Life • Genbank/EMBL/DDBJ partnership

  36. Access and Benefit Sharing November 2008 international workshop on non-commercial biodiversity research; workshop goals: • Develop code of conduct for researchers • Develop off-the-shelf options for: • Standard PICs, MATs, MTAs (Plant Treaty as model?) • Release of barcode and specimen data • Publication of results • Ownership and safeguarding of voucher specimens • Access to tissue for barcoding • Restrictions on subsequent use of DNA

  37. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Coordination with other fields of science • Adoption by regulatory agencies • Product development by private companies

  38. Old and new techniques • CBOL builds on existing taxonomic knowledge • Sequence library built on vouchered specimens • Voucher specimens make science testable and repeatable; vital to quality control • Voucher specimens link historic, current and future research

  39. Building Collaborations Beyond Taxonomy • Workshops with  Assembling the Tree of Life projects  Population biologists (“Banbury 3”) • EMBO Conference on Molecular Biodiversity • Co-sponsor of e-Biosphere 09 Conference on Biodiversity Informatics, June 2009, London

  40. Links to Taxonomic Literature • London meeting on electronic access to taxonomic literature, 2005 • Catalyzed Biodiversity Heritage Library www.biodiversitylibrary.org • Proactive steps with PubMed to add taxonomic journals to online abstracts • Aggressive negotiation with publishers of barcoding papers • Involvement in Encyclopedia of Life

  41. CBOL’s Mission:Promoting DNA Barcoding as a Global Standard • Developing/raising community standards • Barcode projects to populate database • Global participation and coordination • Acceptance by taxonomic community • Coordination with other fields of science • Adoption by regulatory agencies • Product development by private companies

  42. Adoption by Regulators International: • FISH-BOL and fish regulatory agencies • CBOL workshop in Taipei, September 2007 • FAO and International Plant Protection Convention • Proposal for Diagnostic Protocols for fruit flies • CITES, National Agencies, Conservation NGOs • International Steering Committee, identifying pilot projects National examples from USA: • Federal Aviation Administration – Birds • Environmental Protection Agency – Aquatic insects • Nat’l Oceanic and Atmospheric Administration - Fish • Department of Agriculture – Fruit flies

  43. BOLI versus CBOL versus iBOL?? Projects, Networks, Organizations • Promote barcoding as a global standard • Build participation • Working Groups • BARCODE standard • International Conferences • Increase production of public BARCODE records

  44. BOLI, CBOL, iBOL and BOLD • BOLI is the umbrella term • Includes projects, networks, organizations • CBOL is a catalytic organization • Launched in 2004 • Now in its third grant period (2008-2010) • iBOL is a $25M Genome Canada proposal • Part of $150M project plan, with a 3:1 match • Proposal submitted September 2008 • BOLD is a system of databases at Guelph • Open access workbench

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