Transcript Taxonomic Value Chain (in rough sequence)

DNA Barcoding of Pacific
Invasive and Pest Species
Pacific Science Congress Kuala
Lumpur
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
Today’s Goals
Share information on barcoding, invasives
Share information on projects and organizations
in Pacific
Discuss potential regional cooperation; and
Discuss possible formation of a PSA Working
Group on DNA barcoding of invasive/pest
species:
– Participants (individuals, labs, institutes, agencies)
– Activities (training, workshops, collecting, producing
data)
– Deliverables (data, publications, websites)
Existing Activities
National quarantine agencies (NPPOs)
Regional agencies and initiatives
(RPPOs, Quads, QBOL)
Global Initiatives (IPPC, CABI, GISP)
BioNET INTERNATIONAL LOOP
PaciNET
PBIF: Pacific Node of GBIF
The DNA Barcoding Initiative
Barcoding is becoming a global standard
for species identification
Rapidly expanding by region, taxa,
applications
The Barcoding Initiative is global with
participants in 50+ countries
CBD, IPPC, Global Taxonomy Initiative,
Census of Marine Life, others involved
Government agencies: USDA, FDA,
NOAA
Species Identification Matters
Basic research on evolution, ecology
Invasive species (e.g., in ballast
water)
Agricultural pests/beneficial species
Endangered/protected species
Disease vectors/pathogens
Environmental quality indicators
Managing for sustainable harvesting
Consumer protection, ensuring food quality
Fidelity of seedbanks, culture collections
6
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
Associating Life Stages, Processed Parts,
Dimorphic Genders
Non-COI regions for other taxa
Land plants:
– Chloroplast matK and rbcL approved Nov 09
– 70-75% resolving ability, higher in angiosperms
– Non-coding plastid and nuclear regions being
explored
Fungi:
– CBOL Working Group met this week in Amsterdam
– Agreed to recommend ITS; 72% effective
Protists:
– CBOL Working Group July meeting, Berlin
How Barcoding Works
PHASE 1: Build a barcode reference library:
– Well-identified specimen
– Tissue subsample
– DNA extraction, PCR amplification
– DNA sequencing
– Data submission to GenBank
PHASE 2: Identify unknowns:
– Any unidentified juvenile, adult, fragment, product
– Tissue sample, DNA, sequencing
– Comparison with sequences in reference library
Current Norm: High throughput
Large labs, hundreds of samples per day
Large capacity PCR and
sequencing reactions
ABI 3100 capillary
automated sequencer
● US$100-150K purchase
● 150-500 samples per day
● 2-3 hours processing time
● US$3-5 per sample
Technology Development Partnership Goal
The DNA
Sequencing
Lab of
2013?
BOLD System Workbench in Canada
NBII, 25 February 2009
BARCODE Record Flow Chart
Key
Mirroring
Update Channel
Private Records
USER
/GenBank
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.
Linkout from GenBank to BOLD
Linkout from GenBank to Taxonomy
ISBER: 13 May 2009
Link from GenBank to Museums
ISBER: 13 May 2009
Darwin Core Triplet
Structured Link to Vouchers
Institutional
Acronym
:
Collection
Code
:
Catalog
ID
Structured Link to
Vouchers
:
NHM
personal
:
LEP
:
123456
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
31 Malaysian Biorepositories Recorded
10 Confirmed, 21 Unconfirmed
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
1,264,000 specimens already barcoded from 104,500 species
Networks, Projects, Organizations
• Promote barcoding
as a global standard
• Build participation
• Working Groups
• BARCODE standard
• International
Conferences
• Increase production
of public BARCODE
records
The International Barcode of Life Project (iBOL)
5 Million specimens, 500,000 species in 5 years
$150 million with core funding from Genome Canada
iBOL website, University of Guelph, Ontario: www.ibol.org
iBOL Theme 1:
DNA Barcode Library
WG 1.1
WG 1.2
WG 1.3
WG 1.4
WG 1.5
WG 1.6
WG 1.7
WG 1.8
WG 1.9
WG 1.10
Vertebrates
Land Plants
Fungi
Human Pathogens and Zoonoses
Agricultural and Forestry Pest and Parasitoids
Pollinators
Freshwater Bio-Surveillance
Marine Bio-Surveillance
Terrestrial Bio-Surveillance
Polar Life
Consortium for the
Barcode of Life (CBOL)CBOL
Member Organizations: 2010
• 200+ Member organizations, 50 countries
• 35+ Member organizations from 20+ developing countries
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, November 2010
Adoption by Regulators
International Plant Protection Commission
– CBOL and APHIS to host Diagnostic Protocol Panel
meeting, July 2010
Federal Aviation Administration – $500K for birds
Environmental Protection Agency
– $250K pilot test, water quality bioassessment
Food and Drug Administration
– Reference barcodes for commercial fish
NOAA/NMFS
– $100K for Gulf of Maine pilot project
CITES, National Agencies, Conservation NGOs
Conclusions
Barcoding is a cost-effective system for
rapid identification
Barcode reference libraries are being
constructed for several endangered groups
CBOL and iBOL provide a global network of
specialists capable of constructing barcode
reference libraries on selected groups
Partnerships with national and regional
groups and regulatory agencies are the
critical missing components