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Evolutionary Genomics: Comparative Analysis and Evolution of Genomes

Explore the use of bioinformatics and sequencing projects to analyze and compare genomes. Learn about the Human Genome Project, transposable elements, genome evolution, and the role of homeotic genes in evolutionary development.

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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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