David Schindel - DNA Barcoding and the consortium for the barcode of life (CBOL)


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Presentation explaining what and why is DNA barcoding? what are CBOL and iBOL? The activities of CBOL and the fourth International Barcode Conference

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David Schindel - DNA Barcoding and the consortium for the barcode of life (CBOL)

  1. 1. DNA Barcoding and the Consortium for theBarcode of Life (CBOL) 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. 2. What and why is DNA barcoding?What are CBOL and iBOL?CBOL’s activities concerning:– Biodiversity informatics– Taxonomic collections– Global participation– Access and Benefit SharingFourth International Barcode Conference
  3. 3. Species Identification MattersAcademic research in biologyFood security and safetyBorder inspection and export agreements:– Agricultural pests/beneficial species– Disease vectors/pathogens– Endangered/protected species– Invasive speciesEcosystem servicesEnvironmental quality assessment
  4. 4. A DNA barcode is a short gene sequence taken from standardized portions of the genome,used to identify species
  5. 5. Genomics Subgenomics Microbes - 16SCurrent Systematic Plants - RBCL Studies Animals - COI
  6. 6. Associating Life Stages, Processed Parts, Dimorphic Genders
  7. 7. An Internal ID System for All Animals The Mitochondrial Genome DNA D-Loop Small ribosomal RNA Cytochrome b ND1 ND6Typical Animal Cell ND5 COI ND2 mtDNA L-strand H-strand ND4 ND4L COII ND3 COIII ATPase subunit 8 Mitochondrion ATPase subunit 6
  8. 8. 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 for the Fourth International Barcode of Life Conference, November 2011
  9. 9. How Barcoding WorksFirst, build a barcode reference library:– Well-identified specimen– Tissue subsample– DNA extraction, PCR amplification– DNA sequencing– Data submission to GenBankSecond, use it to identify unknowns:– Any unidentified juvenile, adult, fragment, product– Tissue sample, DNA, sequencing– Comparison with sequences in reference library
  10. 10. The Barcoding Pipeline From specimen to sequence to species N N D C D 1 NO 2 DI 3I I Collecting DNA extraction CO1 gene DNA sequencing Trace file Database of BarcodeVoucher Specimen Records
  11. 11. Current Norm: High throughputLarge labs, hundreds of samples per day Large capacity PCR and sequencing reactions ABI 3100 capillary automated sequencer
  12. 12. ● US$100-165K purchase ● 2-3 hours processing time● 150-500 samples per day ● US$3-5 per sample
  13. 13. Technology Development Partnership Goal The DNA Sequencing Lab of 2013?
  14. 14. 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
  15. 15. 1 Million+ records, 100K+ species NBII, 25 February 2009
  16. 16. GenBank, EMBL, and DDBJGlobal, Open Access to Barcode Data http://www.insdc.org/ NBII, 25 February 2009
  17. 17. Specimen Webpages
  18. 18. Sequence Webpages
  19. 19. EOL Species Pages
  20. 20. BARCODE Records in INSDCSpecimen Voucher SpeciesMetadata Specimen Name Georeference Indices Habitat - Catalogue of Life Character sets Images Barcode - GBIF/ECAT Nomenclators Behavior Other genes Sequence - Zoo Record Trace files Primers - IPNI Other - NameBank Publication linksDatabases - New species Phylogenetic Literature DatabasesPop’n Genetics (link to content or - Provisional sp. Ecological citation)
  21. 21. Linkout from GenBank to BOLD
  22. 22. Linkout from GenBank to Taxonomy ISBER: 13 May 2009
  23. 23. Link from GenBank to Museums ISBER: 13 May 2009
  24. 24. Darwin Core TripletStructured Link to VouchersInstitutional : Collection : Catalog Acronym Code ID
  25. 25. Structured Link to Vouchers NHM : LEP : 123456personal : DHJanzen : SRNP12345
  26. 26. NCBI’s Biorepository ListCompiled from Index Herbariorum,literature sources, GenBank submissions6,936 records1,177 records with non-unique acronyms517 homonymous acronyms374 shared by two records143 shared by three records
  27. 27. Icelandic Institute of Natural History,AMNH Akureyri Division Akureyri IcelandAMNH American Museum of Natural History New York USA Monterrey, NuevoUNL Universidad Autónoma de Nuevo León León MexicoUNL University of Nebraska State Museum Lincoln, Nebraska USA Centro de Estratigrafia e Paleobiologia daUNL Universidade Nova de Lisboa Monte de Caparica PortugalZMK Zoological Musem, Kristiania Oslo NorwayZMK Zoologisches Museum der Universität Kiel Kiel GermanyZMK Zoological Museum, Copenhagen Copenhagen Denmark
  28. 28. CBOL/GBIF/NCBI Registry of Biorepositorieswww.biorepositories.org
  29. 29. How Complete is the Barcode Library?More than 1 million records in BOLDMore than 100,000 species representedProjects underway in all major groupsFocus on groups with commercial andsocietal importance:– Agricultural pests– Disease vectors– Endangered species
  30. 30. How Barcoding WorksFirst, build a barcode reference library:– Well-identified specimen– Tissue subsample– DNA extraction, PCR amplification– DNA sequencing– Data submission to GenBankSecond, use it to identify unknowns:– Any unidentified juvenile, adult, fragment, product– Tissue sample, DNA, sequencing– Comparison with sequences in reference library
  31. 31. 40
  32. 32. 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
  33. 33. Investments in Barcoding~US $5 million per year– Smithsonian Laboratories for Analytical Biology– Smithsonian barcoding projects– Sloan Foundation support for CBOL– Project support by USDA, EPA, FDA, FAA…– Barcoding in NSF-funded biodiversity grants
  34. 34. Adoption by RegulatorsFood and Drug Administration– Reference barcodes for commercial fishNOAA/NMFS– $100K for Gulf of Maine pilot project– FISH-BOL workshop with agencies, Taipei, Sept 2007Federal Aviation Administration – $500K for birdsEnvironmental Protection Agency– $250K pilot test, water quality bioassessmentFAO International Plant Protection Commission– Proposal for Diagnostic Protocols for fruit fliesCITES, National Agencies, Conservation NGOs– International Steering Committee, identifying pilot projects
  35. 35. Investments in Barcoding~US $5 million per yearCAN $80 million over 2005-2015Commitments of ~CAN $75 million fromiBOL partners over 2010-2015Mexico $3M, Brazil $4M, India $10MiBOL Project– 5 million specimens, 500K species– 26 partner countries– Canada, US, EU, China are “central nodes”
  36. 36. iBOL Partner Nodes
  37. 37. 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
  38. 38. Consortium for the Barcode of Life (CBOL)Established May 2004 with Sloan Foundation grantSecretariat opens at Smithsonian, September 2004Now in its third two-year funding periodWorkshops, Working Groups, networking,representation/marketingNow an international affiliation of 200+ members in50+ countries:– Natural history museums, biodiversity organizations– Users: e.g., government agencies– Private sector biotech companies, database providers
  39. 39. CBOL Member Organizations: 2011 • 200+ Member organizations, 50 countries • 35+ Member organizations from 20+ developing countries
  40. 40. Building the CommunityInternal communication through CommunityNetwork (http://connect.barcodeoflife.net)Outreach communication througho www.barcodeoflife.orgo CBOL WebinarsCoordination with other barcoding projectsthrough CBOL’s Implementation BoardSteering Committee planning meetingsAssistance in preparing and submittingproposals
  41. 41. Connect.barcodeoflife.org
  42. 42. www.barcodeoflife.org
  43. 43. Outreach ActivitiesCape Town, South Africa, April 2006, SANBI– Scale insects in African agricultureNairobi, Kenya, October 2006– Commercial fisheries in Rift Valley lakesBrazil, March 2007– Hardwood tree species– Endangered mammals, reptiles, amphibiansTaiwan, September 2007Nigeria, October 2008Beijing, May 2009India, March 2010
  44. 44. Developing Country Involvement CBOL’s outreach meetings – Raise awareness, identify priorities, plan and promote barcoding projects – Support from Swiss SDC CBOL training courses and fellowships – Courses in South Africa, South America – iBOL and Smithsonian leadership Canadian IDRC support to South Africa, Peru, Costa Rica and Kenya French MFA and IRD: Sud Experts Plantes
  45. 45. CBOL’s Global ProjectsFish Barcode of Life (FISH-BOL)– 30,000 marine/freshwater species by 2010All Birds Barcoding Initiative (ABBI)– 10,000 species by 2010Tephritid fruit flies– 2,000 pest/beneficial species and relatives by 2008Mosquitoes– 3,300 species by 2008Endangered speciesTrees of the world
  46. 46. CBOL iBOL Promote adoption of Make barcoding anbarcoding as global standard operational reality Working Groups set Working Groups generate standards, promote barcode data and new development of new barcoding protocols technology and analysis Promote international Conduct international participation barcoding activities Networking, training and Training related to iBOL WGs dissemination of protocolsRepresentation to CBD, CITES, Implement agreements and FAO and other international projects within Convention bodies guidelines
  47. 47. ABS Workshop, Museum Koenig 17-19 November 2008 ABS 7, UNESCO, Paris: 6 April 2009
  48. 48. 51 Participants from 24 Countries Sector Research Agency Other 29 10 12 56.9% 19.6% 23.5% Geographic Representation Latin OECD Africa Asia Pacific America 28 8 4 9 2 54.9% 15.7% 7.8% 17.6% 3.9%
  49. 49. Nature magazine7 October 2010
  50. 50. CBD International Regime for Access and Benefit SharingIn the development and implementation of their national legislation on access and benefit-sharing, [and on the basis of the sovereign right of Parties who regulate access to genetic resources and its derivatives,] Parties shall: (a) Create conditions to promote and encourage research which contributes to the conservation and sustainable use of biological diversity, particularly in developing countries, including through simplified measures on access for non-commercial research purposes, taking into account the need to address a change of intent for such research
  51. 51. International Barcode ConferencesNatural History Museum, London: 2005Academia Sinica, Taipei: 2007UNAM, Mexico City: 2009University of Adelaide, Australia: 2011All-Africa Conference: 201230-60 Travel Bursaries awarded forparticipants from developing countries
  52. 52. www.dnabarcodes2011.org