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Evolutionary Genomics: Comparative Analysis and Evolution of Genomes

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  1. Chapter 21 Genomes and Their Evolution

  2. Bioinformatics • Use of computers, software, and math models to process and integrate data from sequencing projects

  3. Human Genome Project • Purpose: to sequence the entire human genome • Completed in 2003 • Genomes sequenced thus far*: 58,000 prokaryotes, 2700 eukaryotes, 5300 viruses * Data as of 1/27/16

  4. Human Genome Project

  5. Comparing Genomes of Bacteria, Archaea, & Eukaryotes

  6. Human DNA • 3 billion base pairs • ~20,000 genes • Only 1.5% codes for proteins (or RNA) • MostlyRepetitive DNA: sequences present in multiple copies

  7. Video Clip:What are SNPs?

  8. Transposable Elements • Make up 75% of repetitive DNA • Stretches of DNA that can be moved from one location to another in genome • Discovered by Barbara McClintock – corn breeding experiments • 2 Types: • Transposons • Retrotransposons

  9. Transposons • Moves within genome via DNA intermediate • “cut & paste” or “copy & paste” mechanisms • Requires enzyme transposase

  10. Retrotransposons • Move by means of RNA intermediate • Leaves copy at original site • Involves enzyme reverse transcriptase

  11. Genome Evolution • Insertion effects of transposons: • Can interrupt or alter gene function • Multiple copies of genes • Duplication  genes with related functions • Genes diverge by accumulating mutations • Some become nonfunctional pseudogenes • Eventually, new genes with new functions can occur

  12. Multigene Families • Collections of 2 or more identical or very similar genes • Eg. hemoglobin: -globin and -globin gene families

  13. Transpositions  chromosomal rearrangements

  14. Transposable elements contribute to evolution • Promote recombination, disrupt genes or control elements, & carry genes to new locations • May be harmful or lethal, but can also have small beneficial effects • Provides raw material for natural selection

  15. HHMI Short Film:The Birth & Death of Genes

  16. Illustrative Example: Antifreeze Gene in Fish • Antifreeze proteins (AFP): produced by vertebrates, plants, fungi, bacteria to aid survival in sub-zero environments • Function: bind to ice crystals and prevent growth • Antarctic fish: old protein gene transformed into a new gene with new structure/function • Gene mutates  duplicated  divergent evolution

  17. Evolutionary Development(Evo-devo) • Compares developmental processes to understand how changes can lead to evolution of organisms

  18. Homeotic genes: master regulatory genes • Control placement and spatial organization of body parts Homeobox: widely conserved 180-nucleotide sequence within homeotic (Hox) genes • Found in many groups (fungi, animals, plants) • Hints at relatedness between all life forms

  19. Conservation of homeotic genes

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