title: Differential retention and divergent resolution of duplicate genes following whole-genome duplication.
abstract: The Paramecium aurelia complex is a group of 15 species that share at least three past whole-genome duplications (WGDs). The macronuclear genome sequences of P. biaurelia and P. sexaurelia are presented and compared to the published sequence of P. tetraurelia. Levels of duplicate-gene retention from the recent WGD differ by > 10% across species, with P. sexaurelia losing significantly more genes than P. biaurelia or P. tetraurelia. In addition, historically high rates of gene conversion have homogenized WGD paralogs, probably extending the paralogs' lifetimes. The probability of duplicate retention is positively correlated with GC content and expression level; ribosomal proteins, transcription factors, and intracellular signaling proteins are overrepresented among maintained duplicates. Finally, multiple sources of evidence indicate that P. sexaurelia diverged from the two other lineages immediately following, or perhaps concurrent with, the recent WGD, with approximately half of gene losses between P. tetraurelia and P. sexaurelia representing divergent gene resolutions (i.e., silencing of alternative paralogs), as expected for random duplicate loss between these species. Additionally, though P. biaurelia and P. tetraurelia diverged from each other much later, there are still more than 100 cases of divergent resolution between these two species. Taken together, these results indicate that divergent resolution of duplicate genes between lineages acts to reinforce reproductive isolation between species in the Paramecium aurelia complex.
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47408, USA;
authors.forename: Casey L
authors.initials: CL
authors.lastname: McGrath
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47408, USA;
authors.forename: Jean-Francois
authors.initials: JF
authors.lastname: Gout
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47408, USA;
authors.forename: Parul
authors.initials: P
authors.lastname: Johri
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47408, USA; National Center for Genome Analysis Support at Indiana University, Bloomington, Indiana 47408, USA.
authors.forename: Thomas G
authors.initials: TG
authors.lastname: Doak
authors.affiliation: Department of Biology, Indiana University, Bloomington, Indiana 47408, USA; milynch@indiana.edu.
authors.forename: Michael
authors.initials: M
authors.lastname: Lynch
mesh_terms: D019143:Evolution, Molecular; D005785:Gene Conversion; D020440:Gene Duplication; D018503:Genome, Protozoan; D048489:Paramecium aurelia / Q000145:classification* / Q000235:genetics*; D010802:Phylogeny; D016415:Sequence Alignment
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