title: The compositional transition between the genomes of cold- and warm-blooded vertebrates: codon frequencies in orthologous genes.
abstract: The genomes of the ancestors of mammals and birds underwent a compositional change in which the gene-richest regions increased their GC levels. Here we investigated this compositional transition by analyzing the levels of G and C in third codon positions, as well as the codon frequencies of orthologous genes from human, chicken and Xenopus. The results may be summed up as follows: (i) GC-poor genes, that did not undergo the compositional transition, showed only minor differences in orthologous sets from Xenopus, human and chicken; this is remarkable in view of the very many nucleotide substitutions that occurred over the long evolutionary times separating these species; (ii) GC-rich genes, that underwent the compositional transition, showed large differences between Xenopus and warm-blooded vertebrates, but not between chicken and human. In other words, the independent changes that occurred in avian and mammalian genes, on the average, were the same.
authors.affiliation: Laboratorio di Evoluzione Molecolare, Stazione Zoologica Anton Dohrn, Villa Comunale, I-80121, Naples, Italy.
authors.forename: S
authors.initials: S
authors.lastname: Cruveiller
authors.forename: G
authors.initials: G
authors.lastname: D'Onofrio
authors.forename: G
authors.initials: G
authors.lastname: Bernardi
mesh_terms: D000596:Amino Acids / Q000235:genetics; D000818:Animals; D001482:Base Composition / Q000235:genetics*; D002645:Chickens; D003062:Codon / Q000235:genetics; D016208:Databases, Factual; D005787:Gene Frequency; D005796:Genes / Q000235:genetics; D016678:Genome; D006801:Humans; D010802:Phylogeny; D014714:Vertebrates / Q000235:genetics*; D014981:Xenopus
chemical_list: D000596:Amino Acids; D003062:Codon