Ancient%20Polyploidy

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Ancient Polyploidy

• Alice Ecker
• February 27th, 2007

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Ancient Polyploidy

• Definition (ancient vs. neopolyploidy)
• Importance of ancient polyploidy
• Known ancient genome doublings
• Saccharomyces
• Arabidopsis

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Ancient vs. Neopolyploidy

• Neopolyploidy is characterized by...
• Multivalent chromosome pairing
• Multisomic inheritance
• Unbalanced gamete production
• Ramsey Schemske, 2002.

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Ancient vs. Neopolyploidy

• Ancient polyploidy can be difficult to detect
  because...
• Disomic segregation is reestablished
• Chromosomal synteny becomes scrambled by
  rearrangements
• Changes in or loss of duplicate genes
• Otto Whitton, 2000

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What is interesting about ancient polyploidy?

• ...polyploidy has contributed little to
  progressive evolution.
• Stebbins, 1971
• ...polyploidy, far from playing a secondary role
  in evolution, has provided the additional,
  uncommitted gene loci necessary for major steps
  in the evolution of animals.
• Schultz, 1980
• Selection of quotes by Otto Whitton, 2000.

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What is interesting about ancient polyploidy?

• Clearly, scientists feel differently about the
  role that polyploidy plays in shaping the
  eukaryotic tree of life!
• By recognizing and studying paleopolyploidy, we
  can come closer to understanding the impact
  polyploidy has on the tempo and mode of evolution

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Specific ancient polyploidizations

• Detection made relatively easy by availability of
  sequenced genomes
• Dating (or at least relative dating) made
  possible by availability of sequences from many
  taxa
• Mode of polyploid formation often unclear (allo-
  or autopolyploidy)
• Genome doublings have been detected in the human
  genome, but how many or when they occurred
  remains contentious

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Saccharomyces cerevisiae

• Wolfe and Shields (1997) and Seoighe and Wolfe
  (1999) presented evidence that Saccharomyces
  cerevisiae is a degenerate tetraploid

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Ancient tetraploidy in S. cerevisiae

• One duplication is proposed, but the method of
  polyploid formation is unclear
• This hypothesis is supported by two lines of
  evidence
• Large, duplicated chromosomal regions (Wolfe
  Shields, 1997)
• Gene order and comparisons to closely related
  species (Seoighe Wolfe, 1997)

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Evidence for ancient tetraploidy in S. cerevisiae

• Duplicated chromosomal regions were detected by
  BLASTPing all yeast protein sequences against one
  another
• Results were plotted duplicate regions are
  visible as diagonal series
• Wolfe Shields, 1997

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Evidence for ancient tetraploidy in S. cerevisiae

• A total of 55 duplicated regions, containing 376
  pairs of homologous genes were identified
• These regions are argued to have arisen by
  polyploidy because...
• In a significantly non-random number of
  duplicated regions, both duplicates are oriented
  the same way relative to the centromere
• 55 independent duplications would statistically
  be expected to result in 7 triplicate regions
  however, none were observed

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• Gene order as evidence for ancient tetraploidy in
  S. cerevisiae
• Kluyveromyces is demonstrated to have diverged
  from the Saccharomyces lineage before the
  duplication event
• Seoighe Wolfe, 1997

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• The date of tetraploid formation was estimated
  from the molecular clock date for the
  Kluyveromyces / Saccharomyces divergence
  (1.5x108 years)

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Aftermath of the S. cerivisiae genome duplication

• Roughly 12.9 of S. cerivisiae's genes are
  polyploidy derived duplicates
• Wolfe Shields, 1997

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• Gene duplicates do not appear to have diverged
  greatly in function
• Genes retained in duplicate are non-randomly
  partitioned between functional categories
• This suggests that duplicates were retained to
  increase the efficiency of the processes they
  already controlled
• Wolfe Shields, 1997

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Aftermath of the S. cerivisiae genome duplication

• High expression genes were preferentially
  retained in duplicate
• Seoighe Wolfe, 1997

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F.A.C. and the S. cerivisiae genome duplication

• Saccharomyces is able to vigorously ferment
  sugars under anaerobic conditions, setting it
  apart physiologically from other yeasts
• Several sets of duplicate genes encode sugar
  transporters or pairs of genes that are regulated
  differently in aerobic vs. anaerobic conditions

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F.A.C. and the S. cerivisiae genome duplication

• The proposed genome doubling event may have been
  crucial to Saccharomyces' ability to ferment
  rapidly in anaerobic conditions
• It may also be significant that the doubling
  occurred around the time that angiosperms became
  abundant

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Arabidopsis

• Bowers, Chapman, Rong, and Peterson searched the
  Arabidopsis genome for duplicated regions
• Three ancient duplications were identified

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Arabidopsis genome analysis

• A database of 26,028 protein sequences was
  searched for matches
• 34 nonoverlapping chromosomal segment pairs were
  identified, encompassing 89 of the genes
  searched (23,117 genes)
• The doubling event that formed these duplicate
  regions was dubbed a

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(No Transcript)
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Arabidopsis genome analysis

• Using the duplicated regions, researchers next
  reconstructed the gene order of the diploid that
  gave rise to the a polyploid
• Nested within 26 a regions were another 29
  duplications
• These duplications fell into two groups based on
  degree of similarity between gene copies, termed
  ß and gamma, which represent another two ancient
  polyploidizations

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The ß and ? duplications

• The ß population consists of 22 non-overlapping
  duplicate regions and 13,449 genes (51.6 of the
  transcriptome)
• The ? population conists of 7 duplicate regions,
  some of which overlap with ß duplicates, and
  5,287 genes (20.3 of the transcriptome)

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Dating the Arabidopsis genome duplications

• To date the a, ß, and ? duplications, Arabidopsis
  gene pairs were compared to genes from both
  distantly and closely related plants
• If the two Arabidopsis gene copies had more in
  common with each other than with the heterologous
  genes, then the polyploidy that generated those
  copies post-dated divergence from the source of
  the heterologous sequence
• Both rooted trees and PAM comparisons were used

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Estimated duplication dates

• a Sometime between the divergences from
  Brassica (14.5-20.4 mya) and Malvaceae (83-86
  mya)
• ß After divergence from monocots (170-235mya)
  but before divergence from other dicots in the
  study
• ? Possibly after divergence from gymnosperms
  (300mya), definitely before divergence from
  angiosperms included in the study

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Implications of the Arabidopsis duplications

• Most or all angiosperms are paleopolyploid
• Synteny between Arabidopsis and other plants
  which diverged before the a polyploidization may
  have been underestimated
• Inference of ancestral gene orders in model
  organisms has the potential to greatly aid
  mapping of large genomes in other organisms that
  may not be fully sequenced soon

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• Synteny in diploid
• relatives of ancient
• polyploids
• Seoighe, 2003

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Literature Cited

• Bowers, John E., Brad A. Chapman, Junkang Rong,
  Andrew H. Peterson. 2003. Unraveling angiosperm
  evolution by phylogenetic analysis of chromsomal
  duplication events. Nature, 422433-438.
• Otto, Sarah P. and Jeannette Whitton. 2000.
  Polyploid Incidence and Evolution. Annu. Rev.
  Genet, 34401-37.
• Ramsey, Justin and Douglas W. Schemske. 2002.
  Neopolyploidy in Flowering Plants. Annu. Rev.
  Ecol. Syst., 33 589-639.
• Seoighe, Cathal. 2003. Turning the clock back
  on ancient genome duplication. Current Opinion
  in Genetics and Development, 13636-643.
• Seoighe, Cathal and Kenneth H Wolfe. 1999.
  Yeast genome evolution in the post-genome era.
  Current Opinion in Microbiololgy, 2548-554.
• Wolfe, Kenneth H. and Denis C. Shields. 1997.
  Molecular evidence for an ancient duplication of
  the entire yeast genome. Nature, 387708-713.