title: Accelerated gene evolution and subfunctionalization in the pseudotetraploid frog Xenopus laevis.
abstract: BACKGROUND
  Ancient whole genome duplications have been implicated in the vertebrate and teleost radiations, and in the emergence of diverse angiosperm lineages, but the evolutionary response to such a perturbation is still poorly understood. The African clawed frog Xenopus laevis experienced a relatively recent tetraploidization ~40 million years ago. Analysis of the considerable amount of EST sequence available for this species together with the genome sequence of the related diploid Xenopus tropicalis provides a unique opportunity to study the genomic response to whole genome duplication.
  
  
  RESULTS
  We identified 2218 gene triplets in which a single gene in X. tropicalis corresponds to precisely two co-orthologous genes in X. laevis--the largest such collection published from any duplication event in animals. Analysis of these triplets reveals accelerated evolution or relaxation of constraint in the peptides of the X. laevis pairs compared with the orthologous sequences in X. tropicalis and other vertebrates. In contrast, single-copy X. laevis genes do not show this acceleration. Duplicated genes can differ substantially in expression levels and patterns. We find no significant difference in gene content in the duplicated set, versus the single-copy set based on molecular and biological function ontologies.
  
  
  CONCLUSIONS
  These results support a scenario in which duplicate genes are retained through a process of subfunctionalization and/or relaxation of constraint on both copies of an ancestral gene.
authors.affiliation: Department of Energy Joint Genome Institute, Walnut Creek, CA 94598, USA. uhellsten@lbl.gov
authors.forename: Uffe
authors.initials: U
authors.lastname: Hellsten
authors.forename: Mustafa K
authors.initials: MK
authors.lastname: Khokha
authors.forename: Timothy C
authors.initials: TC
authors.lastname: Grammer
authors.forename: Richard M
authors.initials: RM
authors.lastname: Harland
authors.forename: Paul
authors.initials: P
authors.lastname: Richardson
authors.forename: Daniel S
authors.initials: DS
authors.lastname: Rokhsar
mesh_terms: D000818:Animals; D002874:Chromosome Mapping; D004625:Embryo, Nonmammalian; D019143:Evolution, Molecular; D020224:Expressed Sequence Tags; D020440:Gene Duplication; D018507:Gene Expression Regulation, Developmental; D005796:Genes / Q000502:physiology*; D011123:Polyploidy; D017386:Sequence Homology, Amino Acid; D013997:Time Factors; D014981:Xenopus / Q000235:genetics; D014982:Xenopus laevis / Q000235:genetics*