Download Taxonomic Value Chain (in rough sequence)

Species Identification,
Regulatory Agencies and
DNA Barcoding
David E. Schindel, Executive Secretary
National Museum of Natural History
Smithsonian Institution
[email protected]; http://www.barcoding.si.edu
202/633-0812; fax 202/633-2938
Genomics
Subgenomics
Current Systematic
Studies
Microbes - 16S
Plants - RBCL
Animals - COI
Species Identification Matters
Basic research on evolution, ecology
Endangered/protected species
Agricultural pests/beneficial species
Disease vectors/pathogens
Invasive species (e.g., in ballast water)
Environmental quality indicators
Managing for sustainable harvesting
Consumer protection, ensuring food quality
Fidelity of seedbanks, culture collections
5
The Practice of
Taxonomy
Distributions of
Character
Variation
Characters
Specimens
Taxonomists
Taxonomic DecisionMaking
The Uses of
Taxonomy
Socioeconomic
Decisions
Concerns/
Regulations
Specimens
Taxonomic Processes
Formal
Taxa
Taxon
Concepts
Characters
Specimens
Growth of Biodiversity Databases
Voucher
Specimen
Biodiversity
Heritage
Library
Journal
Publication
Museum
databases of
associated data
Species
Name
Authority files
of taxonomic
names
A DNA barcode is a
short gene sequence
taken from
standardized portions
of the genome,
used to identify species
An Internal ID System for All Animals
The Mitochondrial Genome
DNA
D-Loop
Small ribosomal RNA
Cytochrome b
ND1
ND6
Typical Animal Cell
COI
ND5
mtDNA
ND2
L-strand
H-strand
ND4
ND4L
ND3
Mitochondrion
COII
COIII
ATPase subunit 8
ATPase subunit 6
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 in 2010
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
Associating Life Stages, Processed Parts,
Dimorphic Genders
How Barcoding is Done
From specimen to sequence to species
C
NO
DI
3I
I
Collecting
Voucher Specimen
DNA extraction
CO1 gene
N
N
D
1D
2
DNA sequencing
Trace file
Database of Barcode
Records
GenBank, EMBL, and DDBJ
Global, Open Access to Barcode Data
http://www.insdc.org/
NBII, 25 February 2009
Current Norm: High throughput
Large labs, hundreds of samples per day
Large capacity PCR and
sequencing reactions
ABI 3100 capillary
automated sequencer
Emerging Norm: Table-top Labs
Faster, more portable: Hundreds of samples per hour
Integrated DNA microchips
Table-top microfluidic systems
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 nonspecialists
Barcode of Life Community
Networks, Projects, Organizations
• Promote barcoding
as a global standard
• Build participation
• Working Groups
• BARCODE standard
• International
Conferences
• Increase production
of public BARCODE
records
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: 2009
• 200+ Member organizations, 50 countries
• 35+ Member organizations from 20+ developing countries
BARCODE Records in INSDC
Specimen
Metadata
Georeference
Habitat
Character sets
Images
Behavior
Other genes
Other
Databases
Phylogenetic
Pop’n Genetics
Ecological
Voucher
Specimen
Barcode
Sequence
Trace files
Primers
Literature
(link to content or
citation)
Species
Name
Indices
- Catalogue of Life
- GBIF/ECAT
Nomenclators
- Zoo Record
- IPNI
- NameBank
Publication links
- New species
Databases
- Provisional sp.
Outreach Activities
Cape 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
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
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
Why barcodes are short
Low cost and simplicity
– Single capillary reads adequate
– Avoid post-sequencing IT needed for pyroseq
Adequate for taxonomy
– Miminizes uniformative sequence length
– Limiting supply rate of identified specimens
– Technology more accessible to small labs
Regulatory/inspection applications easier
Barcoding and Metagenomics
Lots of interest for ecology, less for regulation
Pyrosequencing of environmental mixtures
– Construct species list from mixture
– Predator-prey relations from gut contents, feces
– Food-web reconstruction
Relies on high accuracy (some species differ
by only a few percent)
Not cost-effective for single specimens
What barcode providers have
and are producing
770,000 records from ~100,000 species
– Agricultural pests
– Water quality indicators
– Disease vectors
– Endangered species
– Commercial species of food, feed, commodities
5 million records from 500K species by 2015
International Barcode of Life Project (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
What barcode providers want
High PCR and sequencing success rates
Bigger window into older, compromised
samples
Better software integration to eliminate
bottlenecks
Smaller labs/developing countries:
– Lower equipment and maintenance costs
– Simplification for techs with less training
– Install anywhere without lab renovations
– Willing to accept slower throughput
What barcode users want
Answers to specific questions:
– Is this thing on this list of species or not?
– Is this thing a member of this genus/family?
– Which of the species on this list is this thing?
– What species is this thing?
Production-scale capabilities:
– Hundreds to thousands of installations
– Lower but constant throughput
– Rapid turnaround
– The right price-point and limited life cycle costs
What barcode users would do
with the reference libraries
Inspection stations at every port and international
airport for:
– Agricultural pest control
– Illegal trade in endangered species
– Violations of trade quotas
Regular Federal and State water quality surveys
Federal, State and local food inspection
Public health monitoring and diagnoses
GenBank, EMBL, and DDBJ
Global, Open Access to Barcode Data
http://www.insdc.org/
NBII, 25 February 2009
Linkout from GenBank to BOLD
NBII, 25 February 2009
Linkout from GenBank to Taxonomy
NBII, 25 February 2009
Link from GenBank to Museums
NBII, 25 February 2009