Bioinformatis and Evolutionary Genomics Genome Duplications

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Bioinformatis and Evolutionary GenomicsGenome
Duplications
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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

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Gene duplication trees
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Gene duplication blast

• These are all duplicates but we do not know the
  order in which they arose

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Segmental duplication
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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?)

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Vertebrate genome duplication
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Fish whole genome duplication in teleost fish
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Saccharomyces cerevisiae

• Absence of triplicate regions
• Limited portion of the genome mapped (50) other
  genomes needed

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Génolevures

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

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Génolevures part deux
Wong et al. 2002 PNAS
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Centromeres
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Unique amount of fungal genomes
600Mya
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Paramecium genome duplications
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Comparison of two scaffolds originating from a
common ancestor at the recent WGD
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Representation of the successive duplications of
the Paramecium genome.
BRH best reciprocal hits
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Percentage identity between paralogous proteins,
and comparisons with inter-species distances.
Orange human - mouse Brown human - fish Pink
Paramecium - Tetrahymena thermophila
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Plant genome duplications
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• 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.)