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

Introduction to the Introduction to the Consortium for the Consortium for the

Barcode of Life Barcode of Life

(CBOL)(CBOL) Scott MillerScott Miller

Smithsonian Institution andSmithsonian Institution and

Consortium for the Barcode Consortium for the Barcode of Lifeof Life

Two views of genomicsTwo views of genomics

VerticalVertical: Complete genomes, deep but : Complete genomes, deep but narrow knowledgenarrow knowledge Few species and few individualsFew species and few individuals But evolving in humans, Drosophila, cropsBut evolving in humans, Drosophila, crops

HorizontalHorizontal: Short targeted sequences, : Short targeted sequences, shallow but broad knowledgeshallow but broad knowledge Many species and many individualsMany species and many individuals DNA barcoding as an exampleDNA barcoding as an example

Species Identification MattersSpecies Identification Matters Agricultural pests/beneficial speciesAgricultural pests/beneficial species Managing trade (e.g., IPPC)Managing trade (e.g., IPPC) Consumer protection, ensuring food qualityConsumer protection, ensuring food quality Invasive speciesInvasive species Environmental quality indicatorsEnvironmental quality indicators Quality of cell lines/culture collectionsQuality of cell lines/culture collections Globilization increasing invasive species Globilization increasing invasive species

spreadspread Changes of host and range with climate Changes of host and range with climate

changechange

Species Identification Species Identification Matters (2)Matters (2)

80% CGIAR impact in Africa ($17 billion) 80% CGIAR impact in Africa ($17 billion) from 4 biocontrol programsfrom 4 biocontrol programs

Cassava mealybug, mango mealybug, Cassava mealybug, mango mealybug, water hyacinth, cassava green mitewater hyacinth, cassava green mite

All involved significant taxonomic All involved significant taxonomic challenges in pest and/or biocontrol challenges in pest and/or biocontrol agentagent

Maredia & Raitzer Maredia & Raitzer 20062006

Historic challengesHistoric challenges

Problems with species concepts and their Problems with species concepts and their applicationapplication

Problems with species identificationsProblems with species identifications Character systems – morphology, genetics, Character systems – morphology, genetics,

etc.etc. Access to existing knowledgeAccess to existing knowledge Decline in expertiseDecline in expertise Decline in service availablityDecline in service availablity

Genomics and Internet offer new optionsGenomics and Internet offer new options

Poor representation of Poor representation of systematics infrastructure in systematics infrastructure in

AfricaAfrica

Human resources Human resources also thinly distributedalso thinly distributed

Stuckenberg (1964): most systematics Stuckenberg (1964): most systematics done outside of Africa, but only 7% of done outside of Africa, but only 7% of world entomologists working on Africaworld entomologists working on Africa

Gaston & May (1992): only 4% of Gaston & May (1992): only 4% of ecologists and 7% of systematists in ecologists and 7% of systematists in

AfricaAfrica

Surveys by CABI (1993), ICIPE (1996), Surveys by CABI (1993), ICIPE (1996), and SAFRINET (1998) show same trendsand SAFRINET (1998) show same trends

Associating Life Stages, Associating Life Stages, Processed Parts, and Dimorphic Processed Parts, and Dimorphic

GendersGenders

A DNA barcode is a A DNA barcode is a

short gene short gene sequence sequence

taken from taken from standardized standardized

portions portions of the genome,of the genome,

used to identify used to identify speciesspecies

An Internal ID System for All AnimalsAn 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

How Barcoding WorksHow Barcoding Works Building the reference library:Building the reference library:

Well-identified specimen (vouchers)Well-identified specimen (vouchers) Tissue subsampleTissue subsample DNA extraction, PCR amplificationDNA extraction, PCR amplification DNA sequencingDNA sequencing Data submission to GenBankData submission to GenBank

Using the reference library:Using the reference library: Unidentified specimenUnidentified specimen Tissue, DNA, sequencingTissue, DNA, sequencing Comparison with reference sequencesComparison with reference sequences

How Barcoding is Done

From specimen to sequence to species

Voucher Specimen

DNA extraction CO1 gene DNA sequencing Trace file

Database of Barcode Records

Collecting

ND3

COIII

ND2

ND1

Example: Moths in AfricaExample: Moths in Africa

Noctuid stem borers are species Noctuid stem borers are species complexescomplexes ICIPE and IRD studiesICIPE and IRD studies Their tachinid parasites are also (Dittrich et Their tachinid parasites are also (Dittrich et

al 2006)al 2006) Leguminivora ptychoraLeguminivora ptychora on legumes is as on legumes is as

species complex (Miller unpubl. from species complex (Miller unpubl. from IITA samples)IITA samples)

But some pests are widespread, e.g., But some pests are widespread, e.g., SpoladeaSpoladea recurvalisrecurvalis and and Maruca vitrataMaruca vitrata

Quick and efficientQuick and efficient

Hawk moths (Sphingidae) sampled on IITA Hawk moths (Sphingidae) sampled on IITA Ibadan campus (agroscape and forest)Ibadan campus (agroscape and forest)

49 species in six months, almost all the local 49 species in six months, almost all the local faunafauna

DNA barcodes all well resolved in local DNA barcodes all well resolved in local context and almost well resolved in global context and almost well resolved in global contextcontext

Local sequence libraries can be assembled Local sequence libraries can be assembled quickly quickly andand contribute to global library contribute to global library

CBOL’s Mission:CBOL’s Mission:Promoting DNA BarcodingPromoting DNA Barcoding

as a Global Standard as a Global Standard1.1. Developing/raising community standardsDeveloping/raising community standards2.2. Barcode projects to populate databaseBarcode projects to populate database3.3. Global participation and coordinationGlobal participation and coordination4.4. Acceptance by taxonomic communityAcceptance by taxonomic community5.5. Coordination with other fields of scienceCoordination with other fields of science6.6. Adoption by regulatory agenciesAdoption by regulatory agencies7.7. Product development by private companiesProduct development by private companies

2008: CBOL Member Organizations

•170+ Member organizations, 50+ countries

•54 Member organizations from 20+ developing countries

Growth of CBOL Growth of CBOL ActivitiesActivities

• Executive Committee from 4 continentsExecutive Committee from 4 continents• Implementation Board of 19 MembersImplementation Board of 19 Members

Working GroupsWorking Groups CampaignsCampaigns GenBank, BOLDGenBank, BOLD Related Initiatives Related Initiatives

• Outreach meetings to Africa, Outreach meetings to Africa, South/Central America, AsiaSouth/Central America, Asia

• Network of 15 “Leading Labs” in 9 Network of 15 “Leading Labs” in 9 countriescountries

• Strong partnerships with Strong partnerships with GenBank/EMBL/DDBJ, GBIF, EOLGenBank/EMBL/DDBJ, GBIF, EOL

CBOL’s Global ProjectsCBOL’s Global Projects Fish Barcode of Life (FISH-BOL)Fish Barcode of Life (FISH-BOL)

30,000 marine/freshwater species by 201030,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI)All Birds Barcoding Initiative (ABBI)

10,000 species by 201010,000 species by 2010 Tephritid fruit fliesTephritid fruit flies

2,000 pest/beneficial species and relatives by 2,000 pest/beneficial species and relatives by 20082008

MosquitoesMosquitoes 3,300 species by 20083,300 species by 2008

Endangered speciesEndangered species Trees of the worldTrees of the world

Preview of the Third Preview of the Third International Barcode International Barcode

Conference (2009)Conference (2009)• 1 million barcode records from 100,000 1 million barcode records from 100,000

speciesspecies• Rapid progress on plant and fungal Rapid progress on plant and fungal

barcodingbarcoding• Identifying unknowns in 30 minutes for Identifying unknowns in 30 minutes for

less than US$1less than US$1• Port inspectors starting to test unknowns Port inspectors starting to test unknowns

with barcodes in several countrieswith barcodes in several countries• Portable sequencing ?Portable sequencing ?• Completion of the first local barcode biotic Completion of the first local barcode biotic

inventoryinventory

Overview of DNA Overview of DNA barcoding and its barcoding and its relations to other relations to other

biodiversity initiativesbiodiversity initiatives Scott MillerScott Miller

Smithsonian Institution andSmithsonian Institution and

Consortium for the Barcode Consortium for the Barcode of Lifeof Life

How Barcoding is Done

From specimen to sequence to species

Voucher Specimen

DNA extraction CO1 gene DNA sequencing Trace file

Database of Barcode Records

Collecting

ND3

COIII

ND2

ND1

Producing Barcode Data: Producing Barcode Data: 20072007

ABI 3100 capillary automated sequencer

• Hundreds of samples per day

• Dimes to dollars per sample

Polymerase Chain Reaction Amplification units

Producing Barcode Data: Producing Barcode Data: 20082008

Faster, more portable: Hundreds of samples Faster, more portable: Hundreds of samples per hourper hour

Integrated DNA microchips Table-top microfluidic systems

Producing Barcode Data: Producing Barcode Data: 2010?2010?

Barcode data anywhere, instantlyBarcode data anywhere, instantly

Data in seconds Data in seconds to minutesto minutes

Pennies per Pennies per samplesample

Link to reference Link to reference databasedatabase

A taxonomic GPSA taxonomic GPS Usable by non-Usable by non-

specialistsspecialists

Barcode Sequence

Voucher Specimen

Species Name

Specimen Metadata

Literature(link to content or

citation)

BARCODE Records in GenBank

Indices - Catalogue of Life - GBIF/ECAT

Nomenclators - Zoo Record - IPNI - NameBank

Publication links - New species

GeoreferenceHabitat

Character setsImages

BehaviorOther genes

Trace filesOther

DatabasesPhylogenetic

Pop’n GeneticsEcological

Primers

Databases - Provisional sp.

GenBank, EMBL, and DDBJGenBank, EMBL, and DDBJGlobal, Open Access to Global, Open Access to

Barcode DataBarcode Data

http://www.insdc.org/

Linking GenBank to Linking GenBank to VouchersVouchers

Specimen WebpageSpecimen Webpage

Sequence WebpageSequence Webpage


as a Global Standard as a Global Standard

1.1. Developing/raising community standardsDeveloping/raising community standards2.2. Barcode projects to populate databaseBarcode projects to populate database3.3. Global participation and coordinationGlobal participation and coordination4.4. Acceptance by taxonomic communityAcceptance by taxonomic community5.5. Coordination with other fields of scienceCoordination with other fields of science6.6. Adoption by regulatory agenciesAdoption by regulatory agencies7.7. Product development by private companiesProduct development by private companies



CBOL’s Global ProjectsCBOL’s Global Projects Fish Barcode of Life (FISH-BOL)Fish Barcode of Life (FISH-BOL)

30,000 marine/freshwater species by 201030,000 marine/freshwater species by 2010 All Birds Barcoding Initiative (ABBI)All Birds Barcoding Initiative (ABBI)

10,000 species by 201010,000 species by 2010 Tephritid fruit fliesTephritid fruit flies

2,000 pest/beneficial species and relatives by 2,000 pest/beneficial species and relatives by 20082008

MosquitoesMosquitoes 3,300 species by 20083,300 species by 2008

Endangered speciesEndangered species Trees of the worldTrees of the world



Leading Labs NetworkLeading Labs Network

BioCode

STRI SI-LAB

CCDB

BOLD GenBank

Linking to International Linking to International Initiatives through the Initiatives through the

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

Global Biodiversity Information Facility (GBIF)Global Biodiversity Information Facility (GBIF) Taxonomic databases (Species 2000, ITIS)Taxonomic databases (Species 2000, ITIS) Voucher specimen databasesVoucher specimen databases BioNet InternationalBioNet International CBD Global Taxonomy InitiativeCBD Global Taxonomy Initiative Projects such as SABONET & BOZONETProjects such as SABONET & BOZONET Biodiversity Heritage Library/Encyclopedia of Biodiversity Heritage Library/Encyclopedia of

LifeLife Genbank/EMBL/DDBJ partnershipGenbank/EMBL/DDBJ partnership

Access and Benefit SharingAccess and Benefit SharingNovember 2008 international workshop on non-November 2008 international workshop on non-

commercial biodiversity research; workshop commercial biodiversity research; workshop goals:goals:

Develop code of conduct for researchersDevelop code of conduct for researchers Develop off-the-shelf options for:Develop off-the-shelf options for:

Standard PICs, MATs, MTAs (Plant Treaty as Standard PICs, MATs, MTAs (Plant Treaty as model?)model?)

Release of barcode and specimen dataRelease of barcode and specimen data Publication of resultsPublication of results Ownership and safeguarding of voucher specimensOwnership and safeguarding of voucher specimens Access to tissue for barcodingAccess to tissue for barcoding Restrictions on subsequent use of DNARestrictions on subsequent use of DNA



Old and new techniquesOld and new techniques

CBOL builds on existing taxonomic CBOL builds on existing taxonomic knowledgeknowledge

Sequence library built on vouchered Sequence library built on vouchered specimensspecimens

Voucher specimens make science Voucher specimens make science testable and repeatable; vital to testable and repeatable; vital to quality controlquality control

Voucher specimens link historic, Voucher specimens link historic, current and future researchcurrent and future research

Building Collaborations Building Collaborations Beyond TaxonomyBeyond Taxonomy

• Workshops withWorkshops with Assembling the Tree of Life projectsAssembling the Tree of Life projects

Population biologists (“Banbury 3”)Population biologists (“Banbury 3”)• EMBO Conference on Molecular EMBO Conference on Molecular

BiodiversityBiodiversity• Co-sponsor of e-Biosphere 09 Co-sponsor of e-Biosphere 09

Conference on Biodiversity Informatics, Conference on Biodiversity Informatics, June 2009, LondonJune 2009, London

Links to Taxonomic Links to Taxonomic LiteratureLiterature

• London meeting on electronic access London meeting on electronic access to taxonomic literature, 2005to taxonomic literature, 2005

• Catalyzed Biodiversity Heritage Catalyzed Biodiversity Heritage LibraryLibrarywww.biodiversitylibrary.orgwww.biodiversitylibrary.org

• Proactive steps with PubMed to add Proactive steps with PubMed to add taxonomic journals to online abstractstaxonomic journals to online abstracts

• Aggressive negotiation with Aggressive negotiation with publishers of barcoding paperspublishers of barcoding papers

• Involvement in Encyclopedia of LifeInvolvement in Encyclopedia of Life



Adoption by RegulatorsAdoption by RegulatorsInternational:International:• FISH-BOL and fish regulatory agenciesFISH-BOL and fish regulatory agencies

CBOL workshop in Taipei, September 2007CBOL workshop in Taipei, September 2007• FAO and International Plant Protection ConventionFAO and International Plant Protection Convention

Proposal for Diagnostic Protocols for fruit flies Proposal for Diagnostic Protocols for fruit flies • CITES, National Agencies, Conservation NGOsCITES, National Agencies, Conservation NGOs

International Steering Committee, identifying International Steering Committee, identifying pilot projectspilot projects

National examples from USA:National examples from USA:• Federal Aviation Administration – BirdsFederal Aviation Administration – Birds• Environmental Protection Agency – Aquatic insectsEnvironmental Protection Agency – Aquatic insects• Nat’l Oceanic and Atmospheric Administration - FishNat’l Oceanic and Atmospheric Administration - Fish• Department of Agriculture – Fruit fliesDepartment of Agriculture – Fruit flies

• Promote barcoding as a global standard

• Build participation

• Working Groups

• BARCODE standard

• International Conferences

• Increase production of public BARCODE records

Projects, Networks, Organizations

BOLI versus CBOL versus BOLI versus CBOL versus iBOL??iBOL??

BOLI, CBOL, iBOL and BOLI, CBOL, iBOL and BOLDBOLD

BOLI is the umbrella termBOLI is the umbrella term Includes projects, networks, organizationsIncludes projects, networks, organizations

CBOL is a catalytic organizationCBOL is a catalytic organization Launched in 2004Launched in 2004 Now in its third grant period (2008-2010)Now in its third grant period (2008-2010)

iBOL is a $25M Genome Canada proposaliBOL is a $25M Genome Canada proposal Part of $150M project plan, with a 3:1 matchPart of $150M project plan, with a 3:1 match Proposal submitted September 2008Proposal submitted September 2008

BOLD is a system of databases at GuelphBOLD is a system of databases at Guelph Open access workbenchOpen access workbench

Documents

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