DNA Barcodes: Linking GenBank records to Museum Specimens

1
DNA BarcodesLinking GenBank records to Museum
Specimens

• David E. Schindel, Executive Secretary, CBOL
• Robert Hanner, University of Guelph

2
Washington Airport Gate 3

• Dulles, National, or Baltimore-Washington?
• 2 concourses at BWI concourse A or B?
• 3 concourses at National
• 4 Dulles concourses

3
The Controlled Vocabulary of Airport Codes
4
Biodiversity InformaticsWhat Connects the Parts?
5
DNA BarcodesA Key Variable for Biodiversity
Informatics
Museum databases of associated data
Databases of species occurrences and distribution
(OBIS)
Authority files of taxonomic names
6
A DNA barcode is a short gene sequence taken
from standardized portions of the genome, used
to identify species
7
The Mitochondrial Genome

8
Projects, Networks, Organizations

• Promote barcoding as a global standard
• Build participation
• Working Groups
• BARCODE standard
• International Conferences
• Increase production of public BARCODE
  records

9
Uses of DNA Barcodes

• Research tool for improving species-level
  taxonomy
• Associating all life history stages, genders
• Testing species boundaries, finding new variants
• Applied tool for identifying regulated species
• Disease vectors, agricultural pests, invasives
• Environmental indicators, protected species
• Using minimal samples, damaged specimens, gut
  contents, droppings
• Triage tool for flagging potential new species
• Undescribed and cryptic species
• Taxonomic groups with few morphological features

10
Adoption by Regulators

• US Federal Aviation Administration All Birds
• US Environmental Protection Agency
• 250K pilot test, water quality bioassessment
• US Food and Drug Administration
• Reference barcodes for commercial fish
• FISH-BOL and fish regulatory agencies
• CBOL workshop in Taipei, September 2007
• FAO International Plant Protection Commission
• Proposal for Diagnostic Protocols for fruit flies
  
• CITES, National Agencies, Conservation NGOs
• International Steering Committee, identifying
  pilot projects

11
(No Transcript)
12
International Nucleotide Sequence Database
Collaboration
http//www.insdc.org/
13
Direct Submission to GenBank
14
BOLD Data System

• Developed/hosted by Univ. Guelph
• Workbench for assembling data
• 300,000 records from 30,000 species
• Management and Analysis System
• Identification system for matching unknowns to
  reference records
• Uploading to GenBank

15
Barcode of Life Data Systems (BOLD)
16
BARCODE Data Standards

• Consensus results of Front Royal meeting
• GBIF ? ITIS ? GRIN
• NBII ? Species2000 ? IPNI
• ICZN ? ZooRecord ? OBIS
• Structured link to voucher specimen
• Species name selected from authority
• Trace files, primers, and quality scores
• Minimum sequence length

17
BARCODE Records in INSDC
Voucher Specimen
Species Name
Specimen Metadata
GeoreferenceHabitatCharacter setsImagesBehavio
rOther genes
Indices - Catalogue of Life -
GBIF/ECAT Nomenclators - Zoo Record - IPNI -
NameBank Publication links - New species
Barcode Sequence
Trace files
Primers
Other Databases
Literature(link to content or citation)
PhylogeneticPopn GeneticsEcological
Databases - Provisional sp.
18
(No Transcript)
19
Link from GenBank to Museums
20
(No Transcript)
21
Linkout from GenBank to BOLD
22
Linkout from GenBank to Taxonomy
23
BARCODE Records in INSDC
Voucher Specimen
Species Name
Specimen Metadata
GeoreferenceHabitatCharacter setsImagesBehavio
rOther genes
Indices - Catalogue of Life -
GBIF/ECAT Nomenclators - Zoo Record - IPNI -
NameBank Publication links - New species
Barcode Sequence
Trace files
Primers
Other Databases
Literature(link to content or citation)
PhylogeneticPopn GeneticsEcological
Databases - Provisional sp.
24
Structured Link to Vouchers
Institutional Acronym
Collection Code
Catalog ID


25
Structured Link to Vouchers


NHM
LEP
123456


personal
DHJanzen
SRNP12345
26
NCBIs Biorepository List

• Compiled from literature sources, GenBank
  submissions
• 6,936 institutions
• 1,177 institutions with non-unique acronyms
• 660 homonymous acronyms
• 514 shared by two institutions
• 146 shared by three institutions

27
CBOL/GBIF/NCBI Registry of Biorepositories
www.biorepositories.org
28
www.biorepositories.org
29
(No Transcript)
30
(No Transcript)
31
(No Transcript)
32
Long-term data curationof BARCODE records
Data records assembled in BOLD
Community feedback
Compliant with BARCODE standards?
Update records (audit trail of species names
retained)
Data records released on INSDC
IDs consistent with other records?
GenBank adds BARCODE flag
CBOL control of BARCODE flag
Data records published in BOLD