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

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