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DNA Barcoding and the Consortium for the Barcode of Life

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Database: Designing/constructing the Barcode Section of GenBank ... Create a reference barcode database. Identify high-priority taxa and societal needs ... – PowerPoint PPT presentation

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Title: DNA Barcoding and the Consortium for the Barcode of Life


1
DNA Barcoding and the Consortium for the Barcode
of Life
  • David E. Schindel, Executive Secretary
  • National Museum of Natural History
  • Smithsonian Institution
  • SchindelD_at_si.edu http//www.barcoding.si.edu
  • 202/633-0812 fax 202/633-2938

2
Species Identification Matters
  • Endangered/protected species
  • Agricultural pests
  • Invasive species
  • Disease vectors/pathogens
  • Hazards (e.g., bird strikes on airplanes)
  • Environmental quality indicators
  • Unsustainable harvesting
  • Fidelity of cell lines/culture collections

3
Taxonomists
The Practice of Taxonomy
The Uses of Taxonomy
Socioeconomic Decisions
Taxonomic Decision-Making
Distributions of Character Variation
Concerns/ Regulations
Characters
Specimens
Specimens
4
The Problem…
  • Taxonomists are a limited resource
  • Taxonomic infrastructure is not widely available
  • Taxonomic decisions are difficult for
    non-specialists
  • Therefore, the practice of taxonomy does not
    scale up to meet the needs of society (or
    ecology, ecosystem studies, etc.)

5
A DNA barcode is a short gene sequence taken
from standardized portions of the genome, used
to identify species
6
Uses of DNA Barcodes
  • Triage tool for flagging potential new species
  • Undescribed and cryptic species
  • Research tool for assigning specimens to known
    species, including
  • Life history stages, damaged specimens, gut
    contents, droppings
  • Applied tool for identifying regulated species
  • Disease vectors, agricultural pests, invasives
  • Protected species, CITES listed, trade-sensitive

7
The Mitochondrial Genome

8
How much information is there in a DNA Barcode?
  • Human genome
  • Contains 3 billion base-pairs
  • Identified by 648 bp COI barcode sequence
  • Content-to-label ratio 5 X 106
  • Oxford English Dictionary, 2nd Ed.,1989
  • 20 volumes, 21,730 pages, 500,000 entries, 59
    million words, 350 million print characters
  • Identified by 10-character ISBN
  • Content-to-label ratio 4 X 107

9
Current Norm High throughput
Large capacity PCR and sequencing reactions
ABI 3100 capillary automated sequencer
10
Future Norm?
  • A taxonomic GPS
  • Link to reference database
  • Usable by non-specialists.

11
(No Transcript)
12
Consortium for the Barcode of Life (CBOL)
  • An international affiliation of
  • 80 Members Orgs, 35 countries, 6 continents
  • Natural history museums, biodiversity
    organizations
  • Users e.g., government agencies
  • Private sector biotech companies, database
    providers
  • First barcoding publications in 2002
  • Cold Spring Harbor planning workshops in 2003
  • Sloan Foundation grant, launch in May 2004
  • Secretariat opens at Smithsonian, September 2004
  • First international conference February 2005

13
CBOL Member Organizations (as of May 2005)
14
CBOLs Working Groups
  • Database Designing/constructing the Barcode
    Section of GenBank
  • DNA Protocols for formalin-fixed and old museum
    specimens Producing LIMS for dissemination
  • Data Analysis Beyond phenetic methods
    population genetics perspective
  • Plants Identify gene region(s) for barcoding

15
CBOLs Goals
  • Create a reference barcode database
  • Identify high-priority taxa and societal needs
  • Promote/facilitate barcoding projects and CBOL
    campaigns
  • Improve methods, address shared obstacles through
    WGs
  • Populate database from collections
  • More portability, less time/expense
  • Improve taxonomic research environment

16
Recent and Planned Activities
  • Data standards, Barcode records in GenBank
  • Launch of FishBOL, All Birds Initiatives
  • International Network for Barcoding Invasive and
    Pest Species (INBIPS)
  • APEC Workshop on Invasives, Beijing
  • Mosquitoes and disease vectors
  • Plans for CITES species, endangered Vertebrates,
    Bushmeat

17
Barcode Section of GenBank
Voucher Specimen
Species Name
Specimen Metadata
Indices - Catalog of Life - GBIF/ECAT Nomenclato
rs - Zoo Record - IPNI NameBank Publication
links - New species
Georeference Habitat Character sets Images Behavio
r Other genes
Barcode Sequence
Trace files
Other Databases
Literature (link to content or citation)
Phylogenetic Popn Genetics Ecological
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