dna barcoding of pacific invasive and pest species pacific science congress kuala lumpur
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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. - PowerPoint PPT PresentationTRANSCRIPT
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, invasivesShare information on projects and organizations in PacificDiscuss potential regional cooperation; andDiscuss 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 PaciNETPBIF: Pacific Node of GBIF
The DNA Barcoding InitiativeBarcoding is becoming a global standard for species identificationRapidly expanding by region, taxa, applicationsThe Barcoding Initiative is global with participants in 50+ countriesCBD, IPPC, Global Taxonomy Initiative, Census of Marine Life, others involvedGovernment agencies: USDA, FDA, NOAA
Species Identification MattersBasic research on evolution, ecologyInvasive 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
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
Typical Animal Cell
Mitochondrion
DNA
mtDNA
D-Loop
ND5
H-strand
ND4
ND4LND3
COIII
L-strand
ND6
ND2
ND1
COII
Small ribosomal RNA
ATPase subunit 8ATPase subunit 6
Cytochrome b
COICOI
The Mitochondrial Genome
Associating Life Stages, Processed Parts, Dimorphic Genders
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
exploredFungi:– CBOL Working Group met this week in Amsterdam– Agreed to recommend ITS; 72% effective
Protists:– CBOL Working Group July meeting, Berlin
How Barcoding WorksPHASE 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
● US$100-150K purchase ● 2-3 hours processing time● 150-500 samples per day ● US$3-5 per sample
Technology Development Partnership Goal
The DNA Sequencing
Lab of 2013?
NBII, 25 February 2009
BOLD System Workbench in Canada
USER
/GenBank
Key
Mirroring
Update Channel
Private Records
BARCODE Record Flow Chart
Barcode Sequence
Voucher Specimen
Species Name
Specimen Metadata
Literature(link to content or
citation)
BARCODE Records in INSDC
Indices - Catalogue of Life - GBIF/ECATNomenclators - Zoo Record - IPNI - NameBankPublication links - New species
GeoreferenceHabitat
Character setsImages
BehaviorOther genes
Trace filesOther
DatabasesPhylogenetic
Pop’n GeneticsEcological
Primers
Databases - Provisional sp.
Linkout from GenBank to BOLD
ISBER: 13 May 2009
Linkout from GenBank to Taxonomy
ISBER: 13 May 2009
Link from GenBank to Museums
Darwin Core TripletStructured Link to Vouchers
Institutional Acronym
Collection Code
Catalog ID: :
Structured Link to Vouchers
NHM LEP 123456: :
personal DHJanzen SRNP12345: :
NCBI’s Biorepository ListCompiled from Index Herbariorum, literature sources, GenBank submissions6,936 records1,177 records with non-unique acronyms517 homonymous acronyms374 shared by two records143 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
CBOL/GBIF/NCBI Registry of Biorepositories
www.biorepositories.org
31 Malaysian Biorepositories Recorded10 Confirmed, 21 Unconfirmed
Producing Barcode Data: 201?Barcode data anywhere, instantly
Data in seconds to minutesPennies per sampleLink to reference databaseA taxonomic GPSUsable 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 2007Nigeria, October 2008Beijing, May 2009India, 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 identificationBarcode reference libraries are being constructed for several endangered groupsCBOL and iBOL provide a global network of specialists capable of constructing barcode reference libraries on selected groupsPartnerships with national and regional groups and regulatory agencies are the critical missing components