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Genomes and their evolution

Genomes and their evolution. How do we study genomes? What can we learn from them?. Why study genomes?. We can look at similarities and differences We can learn more about gene interaction and control of gene expression We can learn more about the history of life on Earth

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Genomes and their evolution

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  1. Genomes and their evolution How do we study genomes? What can we learn from them?

  2. Why study genomes? • We can look at similarities and differences • We can learn more about gene interaction and control of gene expression • We can learn more about the history of life on Earth • Genomics: “the study of whole sets of genes and their interactions within a species, as well as genome comparisons between species” • Bioinformatics:”The use of computers, software, and mathematical models to process and integrate biological information from large data sets” • Dependent on technological advances!

  3. How do you sequence a genome? Human Genome Project • Built on previous technologies • Linkage map: the order of markers through the chromosomes • Physical maps: how far apart are the markers? • Sequencing: break up DNA into pieces and sequence them

  4. Shotgun approach: Venter and Celera • “Competed” with hierarchical approach • Competition probably hastened completion of sequencing • Metagenomics: sequences from organisms within a specified environment

  5. Bioinformatics: you have all that data, what do you do with it? • Databases and centers • National Center for Biotechnology Information • NCBI houses Genbank • BLAST allows sequences to be compared • Predicted amino acids sequences; comparison to others • Comparions can be useful for gene identification • Other centers around the world

  6. What does bioinformatics look like?

  7. ENCODE ushered in the approach of studying DNA- protein interactions

  8. What do we learn by comparing genomes? Introns primarily a feature of eukaryotes, as is noncoding DNA What does this mean?

  9. Significance of noncoding DNA? • Most is repetitive DNA • Transposable elements • Almost half the human genome • Unique noncoding; pseudogenes

  10. Transposons • DNA intermediates • May be excised and moved, or copied and moved

  11. Retrotransposons • May be origin of reverse transcriptase • Alu elements • LINE-1 retrotransposons • LINE: long interspersed nuclear element • SINE: short… • ERV: endogenous retroviruses • LTRs: long terminal repeats • May include promoters and enhancers

  12. STRs: short tandem repeats • 2 to 5 nuleotides • Actual number of repeats can vary in individuals • Tends to be at centromeres and telomeres • May have stabilizing effect

  13. (Multi)Gene families • Collection of two or more related genes • Identical: to make many copies of an essential protein (like rRNA) • Non-identical: different versions of a protein • Developmental significance?

  14. How does genome evolve? • Mutation • Duplication • Alteration of structure • Some regions are conserved among species • Might contribute to speciation • Some sites are more susceptible to mutation than others

  15. How does duplication occur?

  16. A model for evolution of gene families

  17. Exon shuffling: production of novel proteins • Typically, exon shuffling produces different versions of proteins • Can lead to formation of new genes • Transposable elements may be responsible for arrangement of genes on chromosomes

  18. What can be learned by comparing genome sequences? • When did species diverge? • What are their common genes? • Variation within a species • Closely related species: which regions are stable, which have changed rapidly? • Study genes associated with species differences

  19. Conservation of developmental genes • “homeodomain” (regulatory sequence) • Hox genes contain this region • Generally associated with development • Changes can affect body plan • Regulatory sequences very different in plants

  20. Conservation of developmental genes • “homeodomain” (regulatory sequence) • Hox genes contain this region • Generally associated with development • Changes can affect body plan • Regulatory sequences very different in plants

  21. Summary • Genomics and proteomics are rapidly developing fields • Bioinformatics allows for the analysis of genomes and proteins in a system-wide approach • Genomes vary widely among organisms • Eukaryotic genomes are complex and have much noncoding DNA • Comparing genomes gives insights into evolution and development

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