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DNA Barcoding

DNA Barcoding. From DNA to ID. Inspiring Excellence. What is DNA Barcoding?. ACGAGTCGGTAGCTGCCCTCTGACTGCATCGAATTGCTCCCCTACTACGTGCTATATGCGCTTACGATCGTACGAAGATTTATAGAATGCTGCTAGCTGCTCCCTTATTCGATAACTAGCTCGATTATAGCTACGATG. ?. =. Inspiring Excellence. What DNA Barcoding Works On. CHLOROPLAST.

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DNA Barcoding

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  1. DNA Barcoding From DNA to ID Inspiring Excellence

  2. What is DNA Barcoding? ACGAGTCGGTAGCTGCCCTCTGACTGCATCGAATTGCTCCCCTACTACGTGCTATATGCGCTTACGATCGTACGAAGATTTATAGAATGCTGCTAGCTGCTCCCTTATTCGATAACTAGCTCGATTATAGCTACGATG ? = Inspiring Excellence

  3. What DNA Barcoding Works On CHLOROPLAST MITOCHONDRION matK rbcL CO1

  4. Why DNA Barcoding Works Win: Sequence shows ~70% conservation, good for PCR, good as barcode Fail: Sequence is completely conserved, good for PCR, but uninformative as barcode Fail: Sequence shows no conservation, impossible for PCR, but good as barcode

  5. Why DNA Barcoding Works CHLOROPLAST MITOCHONDRION matK rbcL CO1

  6. How DNA Barcoding Works 1. Sample Organism 2. Extract DNA 3. Amplify “Barcode” DNA ACGAGTCGGTAGCTGCCCTCTGACTGCATCGAATTGCTCCCCTACTACGTGCTATATGCGCTTACGATCGTACGAAGATTTATAGAATGCTGCTAGCTGCTCCCTTATTCGATAACTAGCTCGATTATAGCTACGATG 4. Sequence DNA 5. Compare sequence against database

  7. Why is DNA Barcoding Important? ACGAGTCGGTAGCTGCCCTCTGACTGCATCGAATTGCTCCCCTACTACGTGCTATATGCGCTTACGATCGTACGAAGATTTATAGAATGCTGCTAGCTGCTCCCTTATTCGATAACTAGCTCGATTATAGCTACGATG Inspiring Excellence

  8. Issue #1: No one knows how many species there are.

  9. How Many Species Can You Name? How many Animals did you name? How many mammals? How many plants? How many insects? “Dog” Canis lupus familiaris “Shark” Ginglymostoma cirratum “Beetle” Popillia japonica “Cat” Felis catus “Oak Tree” Quercus alba

  10. Currently between 1.5 and 2 million species aredescribed/known • This number may represent as little as half of the true number of species • Perhaps more than 1/3 of all species are threatened (IUCN Red list version 2010.1)

  11. Issue #2: There is a lack of agreement of what “species” means.

  12. Defining “species” is complex and • depends on many factors: • Interbreeding capabilities • Morphological variation • Ecological context • Genetic similarities Canis lupus Canis lupus (familiaris) Anas platyrhynchos

  13. ?

  14. Issue #3: Traditional taxonomic identification methods may be inadequate and too slow to capture vanishing biodiversity

  15. Classical taxonomy is difficult for non-experts to understand Leaves alternate proximally, opposite and ultimately decussate distally, 6–16 × 4–13 cm; petiole ca. as long as blade, winged, base clasping, basal lobes stipulate, growing as extensions of wings, less than 1 mm wide; blade 5–7-veined, ovate, glabrous, base typically sagittate, margins entire, apex acute to acuminate. Staminate inflorescences axillary, 1–2 per axil, paniculate, fasciculate; panicles bearing flowers singly,bracteolate, in a zigzag pattern along rachis, internodes less than 2 mm; rachis to 25 cm, secondary axes 1–3(–6), fasciculate, less than 3 cm, each subtended by deltate-ovatebracteole shorter than 1 mm. Pistillateinflorescences solitary, 4–8(–20)-flowered, 6–35 cm, internodes ca. 1 cm. Adding to the complexity: immature, damaged or incomplete specimen may make identification impossible.

  16. Issue #4: DNA Barcoding provides opportunities to investigate things

  17. DNA Barcoding Engages and Transforms Curiosity Into Practical Inquiry

  18. Kate Stoeckle August 23, 2008

  19. What research questions could you ask? Research questions can be about any living thing or about non-living things (foods or other products) that have DNA. Examples: • Are there invasive (non-native) plants in my local park? • What are the most popular types of flowers in my city? • Do the teas I buy at my supermarket really contain the • ingredients on the package? • How many different living organisms can I find in an office building? • Whose droppings are these? Inspiring Excellence

  20. Materials & Equipment for DNA Barcoding • DNA extraction Kit • PCR machine and reagents • DNA sequencing (Genewiz, other) • Bioinformatic tools (analysis of DNA sequence) Inspiring Excellence

  21. DNA Barcoding Analysis • Sequence • Prepare • Compare • Identify • Share Inspiring Excellence

  22. Contributing to big science BOLD GenBank Inspiring Excellence

  23. How DNA Barcoding Works 1. Sample Organism 2. Extract DNA 3. Amplify “Barcode” DNA ACGAGTCGGTAGCTGCCCTCTGACTGCATCGAATTGCTCCCCTACTACGTGCTATATGCGCTTACGATCGTACGAAGATTTATAGAATGCTGCTAGCTGCTCCCTTATTCGATAACTAGCTCGATTATAGCTACGATG 4. Sequence DNA 5. Compare sequence against database

  24. Assignments • Find NCBI’s MapViewer; identify difference between human and chimpanzee genome; check situation in all 4 other primate genomes provided • Make sea shell phylogenetic tree, work through hhmi.org/biointeractive/activities/shells/online/index.html • Review users.ugent.be/~avierstr/principles/phylogeny.html* • Review http://www.hiv.lanl.gov/content/sequence/TUTORIALS/TREE_TUTORIAL/Tree-tutorial.html* • Review Constructing an Evolutionary Tree (Binder) • Review Stockle paper on DNA, Taxonomy & Barcode of Life (pre-Readings) * Links worked on 2012 05 31; if they fail, find the 2 sites through Google

  25. Questions? Inspiring Excellence

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