![Page 1: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/1.jpg)
1
DNA BarcodingDNA BarcodingAmy Driskell
Laboratories of Analytical BiologyNational Museum of Natural HistorySmithsonian Institution, Wash. DC
![Page 2: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/2.jpg)
2
Outline
1. Barcoding in general2. Uses & Examples3. Barcoding Bocas Algae4. Data, Analysis, etc.
![Page 3: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/3.jpg)
3
What is a DNA barcode?
• A fingerprint for identification of everything• A short, easily and universally amplifiable, and
reasonably variable piece of DNA
![Page 4: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/4.jpg)
4
Requirements For “Barcode” label in GenBank, for “Reference” in BOLD
• Sequence is from a vouchered specimen - Re-identify• Voucher meta-information required: GPS coordinates,
photographs (in situ, in some cases), collector and identifier data - Re-collect
• DNA sequence is high quality (minimum length, minimum coverage, minimum “quality scores” - Compare
• Raw data (chromatograms) publicly available - Re-analyze
![Page 5: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/5.jpg)
5
Organizations
• Consortium for the Barcode of Life (CBOL) (www.barcoding.si.edu)
• Barcode of Life Database (BOLD) (www.barcodinglife.org)
• International Barcode of Life (iBOL)(www.ibolprojec.org)
• FishBOL, All Birds Barcoding Initiative, MarBOL, etc. etc.
![Page 6: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/6.jpg)
6
Barcode “Markers”
• Animals: Mitochondrial cytochrome oxidase subunit I (CO1/COX1) ~ 650 bp– BUT, not variable in cnidarians, 16S rDNA historically
more informative in many groups (e.g. frogs, some crustaceans). Second marker possible.
• Fungi: Nuclear internal transcribed spacer (ITS)– Non-coding gene and difficult to align. But long history
in fungal studies, large existing databases, CO1 contains introns.
![Page 7: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/7.jpg)
7
Barcode “Markers”
• Red & Brown Algae: CO1– Not nearly as “universally” amplifiable as in animals,
requires many different primers• Green Plants: Not decided
– SI botanists promote rBCL and the trnH-psbB spacer– Others prefer for rBCL and matK– All are chloroplast genes– Green algae? Still not clear
![Page 8: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/8.jpg)
8
DNA Barcoding is an imperfect science
• Evolutionary History:– Hybridization (plastid genomes)– Pseudogenes– Heteroplasmy or multiple copies (nuclear markers)– Lineage sorting, recent speciation– Slow rates of sequence divergence
• Practical Difficulties– Lack of universality– Co-amplification– Incomplete sampling– Lack of taxonomic experts
![Page 9: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/9.jpg)
9
Barcode of Life Database (BOLD)
![Page 10: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/10.jpg)
10
Today’s Statistics
• BOLD– Total: 570,000– Species: 62,000– “Reference”: 234,000– “Ref” species: 13,774
• GenBank– “Barcode” keyword: 37,000
![Page 11: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/11.jpg)
11
Algal Barcodes in BOLD
![Page 12: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/12.jpg)
12
SI’s Barcoding Philosophy
• Collaborate - taxonomic experts, students
• Train - students, interns, other researchers
• Assist - lab setup, protocol development, collecting
• Archive - a “lending library” of high quality, well-vouchered DNAs
Explore biodiversity in collaboration with taxonomists and phylogeneticists.
![Page 13: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/13.jpg)
13
Biologically Interesting Uses
Biodiversity Exploration– Discovery of sibling species– Quick assessment of local diversity– “DNA assisted alpha taxonomy”
• Ecological & Behavioral Studies– Habitat assessment– Stomach content analysis
![Page 14: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/14.jpg)
14
L.A.B. Examples
• LAB & Bocas taxonomic workshops• CeDAMAR Antarctic deep sea surveys• Caribbean Fish• Central American Frogs• Biocode Moorea
![Page 15: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/15.jpg)
15
Practical, Fundable Uses
• Method of identification, particularly useful to non-experts– Import/export and pest control– Fisheries management– Water and habitat quality assessment– Partial or fragmentary sample analysis– Associating different life stages
![Page 16: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/16.jpg)
16
L.A.B. Examples
• USAF/FAA “Bird Strike” Project• Larval Fish ID• US Food & Drug Agency• US Enviromental Protection Agency
![Page 17: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/17.jpg)
17
Barcoding Bocas Algae
• Collections 2007, 2008, 2009• ~1000 specimens• Red Algae: ~250 specimens sequenced• Lab protocol and primer development
![Page 18: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/18.jpg)
18
The Process of Barcoding
1. Extraction: methods, machines, timing
![Page 19: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/19.jpg)
19
The Process of Barcoding
2. Amplification - Polymerase Chain Reaction
-Primers
![Page 20: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/20.jpg)
20
The Process of Barcoding
3. Sequencing
![Page 21: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/21.jpg)
21
The Process of Barcoding
• Submission and organization of metadata• Quality control, data processing• Accuracy checking
![Page 22: 1 DNA Barcoding Amy Driskell Laboratories of Analytical Biology National Museum of Natural History Smithsonian Institution, Wash. DC](https://reader036.vdocuments.net/reader036/viewer/2022062409/56649e4f5503460f94b46ebe/html5/thumbnails/22.jpg)
22
Nov. 9-13, 2009Website: dnabarcodes2009.org