title: Doublet preference and gene evolution.
abstract: Doublet preference analysis was carried out on coding and noncoding regions of Escherichia coli, Saccharomyces cerevisiae, and human mitochondrial and nuclear DNA. The preference pattern in 1-2 and 2-3 doublets in E. coli and S. cerevisiae correlated with that in noncoding regions. The 3-1 doublet preference in E. coli genes with low optimal codon frequency and in S. cerevisiae genes also showed a correlation with each of their noncoding doublet preference. A mechanism to explain these double preference correlations in doublet preference is presented: mutational biases, the origin of the noncoding region doublet preference, evolved so as to maintain the 1-2 and 2-3 doublet preference, which is determined by codon usage. These biases then acted on the 3-1 doublet, which was almost free of coding constraints, resulting in a similar preference in this doublet.
authors.affiliation: Department of Physics, Faculty of Science, University of Tokyo, Japan.
authors.forename: R
authors.initials: R
authors.lastname: Hanai
authors.forename: A
authors.initials: A
authors.lastname: Wada
mesh_terms: D001482:Base Composition; D005075:Biological Evolution; D003062:Codon / Q000235:genetics*; D004269:DNA, Bacterial / Q000235:genetics; D004271:DNA, Fungal / Q000235:genetics; D004272:DNA, Mitochondrial / Q000235:genetics; D004926:Escherichia coli / Q000235:genetics; D006801:Humans; D012333:RNA, Messenger / Q000235:genetics*; D012441:Saccharomyces cerevisiae / Q000235:genetics; D013045:Species Specificity
chemical_list: D003062:Codon; D004269:DNA, Bacterial; D004271:DNA, Fungal; D004272:DNA, Mitochondrial; D012333:RNA, Messenger