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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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DNA Barcoding and the
Consortium for the
Barcode of Life (CBOL)
David E. Schindel, Executive SecretaryNational Museum of Natural History
Smithsonian Institution
[email protected]; http://www.barcoding.si.edu202/633-0812; fax 202/633-2938
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
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
A DNA barcode is a
short gene sequence
taken from
standardized portions
of the genome,
used to identify species
Genomics
Subgenomics
Current Systematic
Studies
Microbes - 16SPlants - RBCLAnimals - COI
Associating Life Stages, Processed Parts,
Dimorphic Genders
An Internal ID System for All Animals
Typical Animal Cell
Mitochondrion
DNA
mtDNA
D-Loop
ND5
H-strand
ND4
ND4L
ND3COIII
L-strand
ND6
ND2
ND1
COII
Small ribosomal RNA
ATPase subunit 8
ATPase subunit 6
Cytochrome b
COICOI
The Mitochondrial Genome
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
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
The Barcoding Pipeline
From specimen to sequence to species
Voucher Specimen
DNA extraction CO1 gene DNA sequencing Trace file
Database of Barcode
Records
Collecting
N
D
3
C
O
I
I
I
N
D
2
N
D
1
Current Norm: High throughputLarge labs, hundreds of samples per day
ABI 3100 capillary
automated sequencer
Large capacity PCR and
sequencing reactions
● US$100-165K purchase ● 2-3 hours processing time
● 150-500 samples per day ● US$3-5 per sample
Technology Development Partnership Goal
The DNA
Sequencing
Lab of
2013?
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
NBII, 25 February 2009
1 Million+ records, 100K+ species
NBII, 25 February 2009
GenBank, EMBL, and DDBJGlobal, Open Access to Barcode Data
http://www.insdc.org/
Specimen Webpages
Sequence Webpages
EOL Species Pages
Barcode
Sequence
Voucher
Specimen
Species
Name
Specimen
Metadata
Literature(link to content or
citation)
BARCODE Records in INSDC
Indices
- Catalogue of Life
- GBIF/ECAT
Nomenclators
- Zoo Record
- IPNI
- NameBank
Publication links
- New species
Georeference
Habitat
Character sets
Images
Behavior
Other genesTrace files
Other
DatabasesPhylogenetic
Pop’n Genetics
Ecological
Primers
Databases
- Provisional sp.
Linkout from GenBank to BOLD
ISBER: 13 May 2009
Linkout from GenBank to Taxonomy
ISBER: 13 May 2009
Link from GenBank to Museums
Darwin Core Triplet
Structured Link to Vouchers
Institutional
Acronym
Collection
Code
Catalog
ID: :
Structured Link to
Vouchers
NHM LEP 123456: :
personal DHJanzen SRNP12345: :
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
AMNH
Icelandic Institute of Natural History,
Akureyri Division Akureyri Iceland
AMNH American Museum of Natural History New York USA
UNL Universidad Autónoma de Nuevo León
Monterrey, Nuevo
León Mexico
UNL University of Nebraska State Museum Lincoln, Nebraska USA
UNL
Centro de Estratigrafia e Paleobiologia da
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
CBOL/GBIF/NCBI
Registry of Biorepositories
www.biorepositories.org
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
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
• Promote barcoding
as a global standard
• Build participation
• Working Groups
• BARCODE standard
• International
Conferences
• Increase production
of public BARCODE
records
Networks, Projects, Organizations
Barcode of Life Community
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
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
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”
iBOL Partner Nodes
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
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
CBOL Member Organizations: 2011
• 200+ Member organizations, 50 countries
• 35+ Member organizations from 20+ developing countries
Building the Community
Internal communication through Community
Network (http://connect.barcodeoflife.net)
Outreach communication through
owww.barcodeoflife.org
oCBOL Webinars
Coordination with other barcoding projects
through CBOL’s Implementation Board
Steering Committee planning meetings
Assistance in preparing and submitting
proposals
Connect.barcodeoflife.org
www.barcodeoflife.org
Outreach ActivitiesCape 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
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
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
CBOL iBOLPromote adoption of
barcoding as global standardMake barcoding an operational reality
Working Groups set standards, promote development of new
technology and analysis
Working Groups generate barcode data and new
barcoding protocols
Promote international participation
Conduct international barcoding activities
Networking, training and dissemination of protocols
Training related to iBOL WGs
Representation to CBD, CITES, FAO and other international
bodies
Implement agreements and projects within Convention
guidelines
ABS 7, UNESCO, Paris: 6 April 2009
ABS Workshop, Museum Koenig17-19 November 2008
51 Participants from 24 Countries
Sector
Research Agency Other
29 10 12
56.9% 19.6% 23.5%
Geographic Representation
OECD AfricaLatin
AmericaAsia Pacific
28 8 4 9 2
54.9% 15.7% 7.8% 17.6% 3.9%
Nature magazine
7 October 2010
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
International Barcode
ConferencesNatural 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
www.dnabarcodes2011.org