DNA Barcoding of Pacific Invasive and Pest Species Pacific Science Congress Kuala Lumpur David E....
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Transcript of DNA Barcoding of Pacific Invasive and Pest Species Pacific Science Congress Kuala Lumpur David E....
DNA Barcoding of Pacific Invasive and Pest Species
Pacific Science Congress Kuala Lumpur
David E. Schindel, Executive SecretaryNational Museum of Natural History
Smithsonian [email protected]; http://www.barcoding.si.edu
202/633-0812; fax 202/633-2938
Today’s GoalsShare 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 ActivitiesNational 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 MattersBasic research on evolution, ecology
Invasive species (e.g., in ballast water)Agricultural pests/beneficial speciesEndangered/protected species Disease vectors/pathogensEnvironmental quality indicatorsManaging for sustainable harvestingConsumer protection, ensuring food qualityFidelity of seedbanks, culture collections
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
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
Non-COI regions for other taxaLand 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 throughputLarge labs, hundreds of samples per day
ABI 3100 capillary
automated sequencer
Large capacity PCR and
sequencing reactions
Barcode Sequence
Voucher Specimen
Species Name
Specimen Metadata
Literature(link to content or
citation)
BARCODE Records in INSDC
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.
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
AMNHIcelandic 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
UNLCentro 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
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 non-specialists
• Promote barcoding as a global standard
• Build participation• Working Groups• BARCODE standard• International
Conferences• Increase production
of public BARCODE records
Networks, Projects, Organizations
Barcode of Life Community1,264,000 specimens already barcoded from 104,500 species
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 VertebratesWG 1.2 Land PlantsWG 1.3 FungiWG 1.4 Human Pathogens and ZoonosesWG 1.5 Agricultural and Forestry Pest and ParasitoidsWG 1.6 PollinatorsWG 1.7 Freshwater Bio-SurveillanceWG 1.8 Marine Bio-SurveillanceWG 1.9 Terrestrial Bio-SurveillanceWG 1.10 Polar Life
• 200+ Member organizations, 50 countries
• 35+ Member organizations from 20+ developing countries
Consortium for the Barcode of Life (CBOL)CBOL
Member Organizations: 2010
Outreach ActivitiesCape 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 RegulatorsInternational Plant Protection Commission– CBOL and APHIS to host Diagnostic Protocol Panel
meeting, July 2010Federal Aviation Administration – $500K for birdsEnvironmental 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
ConclusionsBarcoding 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