title: Biased gene conversion and GC-content evolution in the coding sequences of reptiles and vertebrates.
abstract: Mammalian and avian genomes are characterized by a substantial spatial heterogeneity of GC-content, which is often interpreted as reflecting the effect of local GC-biased gene conversion (gBGC), a meiotic repair bias that favors G and C over A and T alleles in high-recombining genomic regions. Surprisingly, the first fully sequenced nonavian sauropsid (i.e., reptile), the green anole Anolis carolinensis, revealed a highly homogeneous genomic GC-content landscape, suggesting the possibility that gBGC might not be at work in this lineage. Here, we analyze GC-content evolution at third-codon positions (GC3) in 44 vertebrates species, including eight newly sequenced transcriptomes, with a specific focus on nonavian sauropsids. We report that reptiles, including the green anole, have a genome-wide distribution of GC3 similar to that of mammals and birds, and we infer a strong GC3-heterogeneity to be already present in the tetrapod ancestor. We further show that the dynamic of coding sequence GC-content is largely governed by karyotypic features in vertebrates, notably in the green anole, in agreement with the gBGC hypothesis. The discrepancy between third-codon positions and noncoding DNA regarding GC-content dynamics in the green anole could not be explained by the activity of transposable elements or selection on codon usage. This analysis highlights the unique value of third-codon positions as an insertion/deletion-free marker of nucleotide substitution biases that ultimately affect the evolution of proteins.
authors.affiliation: CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France emeric.figuet@gmail.com.
authors.forename: Emeric
authors.initials: E
authors.lastname: Figuet
authors.affiliation: CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France.
authors.forename: Marion
authors.initials: M
authors.lastname: Ballenghien
authors.affiliation: CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France Department of Ecology and Evolution, Biophore, University of Lausanne, Switzerland.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Romiguier
authors.affiliation: CNRS, Université Montpellier 2, UMR 5554, Institut des Sciences de l'Evolution de Montpellier, France.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Galtier
mesh_terms: D000818:Animals; D001482:Base Composition / Q000235:genetics*; D003062:Codon; D019143:Evolution, Molecular; D005091:Exons; D005785:Gene Conversion; D016678:Genome; D023281:Genomics; D008322:Mammals; D016366:Open Reading Frames / Q000235:genetics; D010802:Phylogeny; D011995:Recombination, Genetic; D012104:Reptiles / Q000235:genetics*
chemical_list: D003062:Codon
keywords: karyotype; phylogeny; third-codon positions