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Conserved Introns

Conservative Genome Evolution. Conserved Introns. An important component of eukaryotic genomes. 25% of the human genome 95% of the human transcriptome [Venter et al., (2001)] Numerous cis-regulatory elements reside within introns.

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Conserved Introns

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  1. Conservative Genome Evolution Conserved Introns

  2. An important component of eukaryotic genomes. • 25% of the human genome • 95% of the human transcriptome [Venter et al., (2001)] • Numerous cis-regulatory elements reside within introns. • Alternate transcripts greatly magnify transcriptome complexity. • Introns foster genetic recombination. Evolutionary Conservation of Introns

  3. PLANTAE FUNGI METAZOA APICOMPLEXA Evolutionary Conservation of Introns • Rogozin et al. (2003) compared the location of introns in 684 orthologous genes across a number of model eukaryotes. Arabidopsis Drosophila Caenorhabditis Anopheles Plasmodium Saccharomyces Homo • Surprisingly, Arabidopsis appeared most similar to human. • We added Nematostella to these taxa and performed a comparable analysis on a subset of the same orthologous genes (n=348 genes).

  4. Percentage of Shared Introns Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  5. Percentage of Shared Introns Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  6. Percentage of Shared Introns Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  7. Percentage of Shared Introns Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  8. (Introns shared by A & B) + (Introns shared by A & B) (Introns unique to A) + (Introns unique to B) Percentage of Shared Introns = Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  9. (Introns shared by A & B) + (Introns shared by A & B) (Introns unique to A) + (Introns unique to B) Percentage of Shared Introns = Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  10. (Introns shared by A & B) + (Introns shared by A & B) (Introns unique to A) + (Introns unique to B) Percentage of Shared Introns = Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  11. (Introns shared by A & B) + (Introns shared by A & B) (Introns unique to A) + (Introns unique to B) Percentage of Shared Introns = Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  12. (Introns shared by A & B) + (Introns shared by A & B) (Introns unique to A) + (Introns unique to B) Percentage of Shared Introns = Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  13. (Introns shared by A & B) + (Introns shared by A & B) (Introns unique to A) + (Introns unique to B) Percentage of Shared Introns = Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  14. Clustering of taxa based on shared introns • Parsimony analysis of intron presence/absence. • 1 = intron present at a given location (±2 nt). • 0 = intron absent. • Human and sea anemone are grouped to the exclusion of all other animals in the analysis. Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

  15. many intron losses relative stability abundant introns Mapping intron gain & loss on the organismal phylogeny • ACCTRAN character state optimization. • Suggests that the cnidarian-bilaterian ancestor was intron-rich. (880 introns) • And that there have been numerous intron losses in the line(s) leading to the model protostomes. • Finer taxonomic sampling is needed. Sullivan, Reitzel and Finnerty, Genome Informatics (2006)

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