Transcript Amsterdam 2004 - Theoretical Biology & Bioinformatics

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
Gene duplication: blast
• These are all duplicates but we do not know the
order in which they arose
Segmental duplication
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?)
Vertebrate genome duplication
Fish: whole genome duplication in teleost fish
Saccharomyces cerevisiae
• Absence of
triplicate regions
• Limited portion
of the genome
mapped (50%);
other genomes
needed
Génolevures
• Gene family size in S. cerevisiae is generally
conserved in other species
• Observation of small duplicated segments from
strict & pairwise comparisons
Génolevures part deux
Wong et al. 2002 PNAS
Centromeres
Unique amount of fungal genomes
235Mya
600Mya
727Mya
125Mya
Paramecium genome duplications
Comparison of two scaffolds originating
from a common ancestor at the recent
WGD
Representation of the successive
duplications of the Paramecium genome.
BRH: best reciprocal hits
Percentage identity between paralogous
proteins, and comparisons with interspecies distances.
Orange: human - mouse
Brown: human - fish
Pink: Paramecium - Tetrahymena thermophila
Plant genome duplications
• 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.)