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Bioinformatis and Evolutionary Genomics Genome Duplications

Bioinformatis and Evolutionary Genomics Genome Duplications . Genome duplications / polyploidy. Polyploid plants are very common and can arise spontaneously in nature by several mechanisms, including meiotic or mitotic failures, and fusion of unreduced (2n) or gametes . Gene duplication: trees.

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Bioinformatis and Evolutionary Genomics Genome Duplications

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  1. Bioinformatis and Evolutionary GenomicsGenome Duplications

  2. Genome duplications / polyploidy • Polyploid plants are very common and can arise spontaneously in nature by several mechanisms, including meiotic or mitotic failures, and fusion of unreduced (2n) or gametes

  3. Gene duplication: trees

  4. Gene duplication: blast • These are all duplicates but we do not know the order in which they arose

  5. Segmental duplication

  6. Whole Genome duplication • Synonym: Polyploidy • Proposed by Ohno (1970) to be a possible major force in genome evolution • Result of errors in meiosis (not in bacteria?)

  7. Vertebrate genome duplication

  8. Fish: whole genome duplication in teleost fish

  9. Saccharomyces cerevisiae • Absence of triplicate regions • Limited portion of the genome mapped (50%); other genomes needed

  10. Génolevures • Gene family size in S. cerevisiae is generally conserved in other species • Observation of small duplicated segments from strict & pairwise comparisons

  11. Génolevures part deux Wong et al. 2002 PNAS

  12. Centromeres

  13. 235Mya 125Mya 727Mya Unique amount of fungal genomes 600Mya

  14. Paramecium genome duplications

  15. Comparison of two scaffolds originating from a common ancestor at the recent WGD

  16. Representation of the successive duplications of the Paramecium genome. BRH: best reciprocal hits

  17. Percentage identity between paralogous proteins, and comparisons with inter-species distances. Orange: human - mouse Brown: human - fish Pink: Paramecium - Tetrahymena thermophila

  18. Plant genome duplications

  19. Detection of genome duplications • Trees • Ks/Similarity “bumps” • Synteny, indirect synteny (comparative genomics), BRH/BBH vs normal blast • Effect of WGD • Most duplicates are lost • Nevertheless thought to be important (origin of flowering plants, origin of vertebrates etc.)

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