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. DNA Barcoding and the Consortium for the Barcode 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. What and why is DNA barcoding? What are CBOL and iBOL? CBOL’s activities concerning: – Biodiversity informatics – Taxonomic collections – Global participation – Access and Benefit Sharing Fourth International Barcode Conference
- 3. Species Identification Matters Academic research in biology Food security and safety Border inspection and export agreements: – Agricultural pests/beneficial species – Disease vectors/pathogens – Endangered/protected species – Invasive species Ecosystem services Environmental quality assessment
- 4. A DNA barcode is a short gene sequence taken from standardized portions of the genome, used to identify species
- 5. Genomics Subgenomics Microbes - 16S Current Systematic Plants - RBCL Studies Animals - COI
- 6. Associating Life Stages, Processed Parts, Dimorphic Genders
- 7. An Internal ID System for All Animals The Mitochondrial Genome DNA D-Loop Small ribosomal RNA Cytochrome b ND1 ND6 Typical Animal Cell ND5 COI ND2 mtDNA L-strand H-strand ND4 ND4L COII ND3 COIII ATPase subunit 8 Mitochondrion ATPase subunit 6
- 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
- 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. 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 Barcode Voucher Specimen Records
- 12. Current Norm: High throughput Large labs, hundreds of samples per day Large capacity PCR and sequencing reactions ABI 3100 capillary automated sequencer
- 13. ● US$100-165K purchase ● 2-3 hours processing time ● 150-500 samples per day ● US$3-5 per sample
- 14. Technology Development Partnership Goal The DNA Sequencing Lab of 2013?
- 15. 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
- 16. 1 Million+ records, 100K+ species NBII, 25 February 2009
- 17. GenBank, EMBL, and DDBJ Global, Open Access to Barcode Data http://www.insdc.org/ NBII, 25 February 2009
- 21. BARCODE Records in INSDC Specimen Voucher Species Metadata 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 links Databases - New species Phylogenetic Literature Databases Pop’n Genetics (link to content or - Provisional sp. Ecological citation)
- 24. Linkout from GenBank to BOLD
- 26. Linkout from GenBank to Taxonomy ISBER: 13 May 2009
- 28. Link from GenBank to Museums ISBER: 13 May 2009
- 29. Darwin Core Triplet Structured Link to Vouchers Institutional : Collection : Catalog Acronym Code ID
- 30. Structured Link to Vouchers NHM : LEP : 123456 personal : DHJanzen : SRNP12345
- 31. 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
- 32. Icelandic Institute of Natural History, AMNH Akureyri Division Akureyri Iceland AMNH American Museum of Natural History New York USA Monterrey, Nuevo UNL Universidad Autónoma de Nuevo León León Mexico UNL University of Nebraska State Museum Lincoln, Nebraska USA Centro de Estratigrafia e Paleobiologia da UNL Universidade Nova de Lisboa Monte de Caparica Portugal ZMK Zoological Musem, Kristiania Oslo Norway ZMK Zoologisches Museum der Universität Kiel Kiel Germany ZMK Zoological Museum, Copenhagen Copenhagen Denmark
- 33. CBOL/GBIF/NCBI Registry of Biorepositories www.biorepositories.org
- 38. How Complete is the Barcode Library? More than 1 million records in BOLD More than 100,000 species represented Projects underway in all major groups Focus on groups with commercial and societal importance: – Agricultural pests – Disease vectors – Endangered species
- 39. 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
- 40. 40
- 42. 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
- 43. 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
- 44. 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
- 45. Investments in Barcoding ~US $5 million per year CAN $80 million over 2005-2015 Commitments of ~CAN $75 million from iBOL partners over 2010-2015 Mexico $3M, Brazil $4M, India $10M iBOL Project – 5 million specimens, 500K species – 26 partner countries – Canada, US, EU, China are “central nodes”
- 47. 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
- 48. 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
- 49. CBOL Member Organizations: 2011 • 200+ Member organizations, 50 countries • 35+ Member organizations from 20+ developing countries
- 50. Building the Community Internal communication through Community Network (http://connect.barcodeoflife.net) Outreach communication through o www.barcodeoflife.org o CBOL Webinars Coordination with other barcoding projects through CBOL’s Implementation Board Steering Committee planning meetings Assistance in preparing and submitting proposals
- 55. 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
- 56. 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
- 57. 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
- 58. CBOL iBOL Promote adoption of Make barcoding an barcoding 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 protocols Representation to CBD, CITES, Implement agreements and FAO and other international projects within Convention bodies guidelines
- 61. ABS Workshop, Museum Koenig 17-19 November 2008 ABS 7, UNESCO, Paris: 6 April 2009
- 62. 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%
- 63. Nature magazine 7 October 2010
- 64. CBD International Regime for Access and Benefit Sharing In 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
- 65. International Barcode Conferences Natural History Museum, London: 2005 Academia Sinica, Taipei: 2007 UNAM, Mexico City: 2009 University of Adelaide, Australia: 2011 All-Africa Conference: 2012 30-60 Travel Bursaries awarded for participants from developing countries