Comparative genomics presentation


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PowerPoint for BI 520-01
Spring 2013

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Comparative genomics presentation

  1. 1. Comparative Genomicsand the Evolution ofGenes
  2. 2. Evolution of Genes and Genomes onthe Drosophila phylogeny Based on 12 way comparison
  3. 3. Phylogenetic Tree of Drosophila
  4. 4.
  6. 6. It is named by analogy with the rapidly-expanding, quasi-random firing patternof a shotgun.The technique was developed in the1970s by double Nobel prize laureateFrederick Sanger.
  7. 7. Craig Venter
  8. 8. W = dN/ds dN (non synonymous) dS (synonymous) Examined the ratio of non-synonymousW=d to synonymous divergence to explain distribution
  9. 9. • A major question in evolutionary biology is how important tinkering with promoter sequences is to evolutionary change, for example, the changes that have occurred in the human lineage after separating from chimps. Are evolution in promoter or regulatory regions more important than changes in coding sequences over such time frames? A key reason for the importance of promoters is the potential to incorporate endocrine and environmental signals into changes in gene expression[1]: A great variety of changes in the extracellular or intracellular environment[2]may have impact on gene expression, depending on the exact configuration of a given promoter [2]: the combination and arrangement of specific DNA sequences that constitute the promoter defines the exact groups of proteins that can be bound to the promoter, at a given time [3].
  10. 10. • Demonstrated the ability to place every one of these genomic comparisons on a phylogeny with a taxon separation that is ideal for asking a wealth of questions about evolutionary patterns and processes.• The use of multi-species orthology “provides” especially convincing evidence in support of particular gene models, not only for protein-coding genes, but also for miRNA and other ncRNA genes.
  11. 11. The methodology and principles are absolutelygeneral and they are applicable to any genome. The genomes of these species provide an excellent model for studying how conserved functions are maintained in the face ofsequence divergence. These genome sequences provide an unprecedented dataset to contrast genome structure, genome content, and evolutionary dynamics across the well-defined phylogeny of the sequenced species
  12. 12. • Species D. willistoni doesn’t appear to have genes to make proteins containing selenium – proteins that researches had thought were common to all animals.• analysis suggests that “some” gene families expand of contract at a rate of 0.0012 gains and losses per gene per million years or roughly one fixed gene gain/ loss across the genome every 60,000 yr.• Number of structural changes and rearrangements is much larger, for example, there are several different rearrangements of genes in the Hox cluster found in these Drosophila species
  13. 13. Brosius J, Erfle M, et al. (1985). "Spacing of the -10 and -35 regions in the TAC promoter -effect on its in vivo activity". Journal of Biological Chemistry 260 (6): 3539 –3541.Celniker SE, Drewell RA (2007). "Chromatin looping mediates boundary element promoterinteractions". Bioessays 29 (1): 7–10Vlahopoulos S, Zoumpourlis VC (2004). "JNK: a key modulator of intracellular signaling".Biochemistry (Mosc) 69 (8): 844–54. mom