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OVERVIEW
Short course on DNA barcoding methodsNovember 29, 2011
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Overview of this training session
9:00 – 10:00. Module I: Introduction to Barcoding and its pipeline -Brief introduction to barcoding and the current goals, iBOL working groups and campaigns (Darío Lijtmaer) -The barcoding pipeline (Amy Driskell) -Barcode Data Standard compliance (David Schindel)
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Overview of this training session
10:00 – 12:30. Module II: Acquisition and Handling of specimens and tissue samples - Pros and cons of collecting specimens for barcoding vs. sampling existing collections (Sally Adamowicz) - Field Collection (Sally Adamowicz)
- Museum Harvesting (Jeremy deWaard)
- Front-end processing (Michelle Van der Bank)
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Overview of this training session
14:00 – 15:30. Module III: Brief description of laboratory methods and information management for small, medium and large-scale facilities -DNA Extraction (Darío Lijtmaer) -PCR Amplification (Darío Lijtmaer) -Information management and data quality (Amy Driskell)
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Overview of this training session
16:00 – 17:30. Module IV: Taxon-specific aspects of the barcoding pipeline -Short talks about taxon-specific key elements
-Plants (Dave Erickson)- Algae (Gary Saunders)- Fungi (Benjamin Stielow)- Marine invertebrates (Dirk Steinke)- Terrestrial invertebrates (Julie Stahlhut)- Vertebrates (Bob Ward)
- Round table for Q&A and discussions about taxon-specific aspects of the pipeline
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Brief introduction to barcoding and the current goals, iBOL working groups and campaigns
Darío LijtmaerMuseo Argentino de Ciencias Naturales “Bernardino Rivadavia”
Short course on DNA barcoding methodsNovember 29, 2011
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Problems with traditional, morphology-based identification
Genetic-based identification (DNA barcodes) can help
overcoming these problems
Species are variable
There are 10 -100 million species in our planet
There are cryptic species
Sometimes we can only access fragments
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The ideal genetic marker
Universal application Good recoverability Efficiency (smallest read necessary) Easy to align Easy to analyze The Mitochondrial Genome
D-Loop
H-strandCOIII
L-strand
ND6
ND2
COII
Small ribosomal RNA
COI
Cytb
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Organization of the project: CBOL
CBOL was established in 2004. Goals:
- help organizing the project.
- connect the members of the barcoding community.
- establish barcoding as a standard proceduree for species identification.
Distribution of CBOL institutions
NMNH, Washington
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Organization of the project: iBOL
iBOL was officially launched in 2009.
Main goal: to generate 5 million barcodes from 500,000 species by 2014.
Central nodes Regional nodes National nodes
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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Theme 2: Methodologies
WG2.1 Barcoding Biotas
WG2.2 Museum Life
WG2.3 Methodological Innovation
WG2.4 Paleobarcoding
iBOL organizationiBOL organization
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WG2.3 Methodological Innovation
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WG2.4 Paleobarcoding: Surveying the Past
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WG3.1 Core Functionality
WG3.2 Mirrors
iBOL organization
Theme 3: Informatics
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WG4.1 Environmental Barcoding
WG4.2 Handheld Barcoder
Theme 4: Technologies
iBOL organization
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WG4.1 Environmental Barcoding:Species identifications from ‘slurries’
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Agrawal et al 2007. A Pocket-Sized Convective PCR Thermocycler.
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WG5.1 Project management
WG5.2 Communications
iBOL organization
Theme 5: Administration
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Genomics and its Ethical,
Environmental, Economic, Legal
and Social aspects
iBOL organization
Theme 6: GE3LS
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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iBOL organization
Theme 1:DNA Barcode Library
WG1.1 VertebratesWG1.2 Land PlantsWG1.3 FungiWG1.4 Human Pathogens and ZoonosesWG1.5 Agricultural and Forestry PestsWG1.6 PollinatorsWG1.7 Freshwater Bio-SurveillanceWG1.8 Marine Bio-SurveillanceWG1.9 Terrestrial Bio-SurveillanceWG1.10 Polar Life
iBOL organization
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Specimen
Sample
Extract Amplify Sequence
Photographs
Collection data
Why are we here today?
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Thank you!
Questions?