title: Analysis of the relationship between genomic GC Content and patterns of base usage, codon usage and amino acid usage in prokaryotes: similar GC content adopts similar compositional frequencies regardless of the phylogenetic lineages.
abstract: The GC contents of 2670 prokaryotic genomes that belong to diverse phylogenetic lineages were analyzed in this paper. These genomes had GC contents that ranged from 13.5% to 74.9%. We analyzed the distance of base frequencies at the three codon positions, codon frequencies, and amino acid compositions across genomes with respect to the differences in the GC content of these prokaryotic species. We found that although the phylogenetic lineages were remote among some species, a similar genomic GC content forced them to adopt similar base usage patterns at the three codon positions, codon usage patterns, and amino acid usage patterns. Our work demonstrates that in prokaryotic genomes: a) base usage, codon usage, and amino acid usage change with GC content with a linear correlation; b) the distance of each usage has a linear correlation with the GC content difference; and c) GC content is more essential than phylogenetic lineage in determining base usage, codon usage, and amino acid usage. This work is exceptional in that we adopted intuitively graphic methods for all analyses, and we used these analyses to examine as many as 2670 prokaryotes. We hope that this work is helpful for understanding common features in the organization of microbial genomes.
authors.affiliation: Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Hui-Qi
authors.initials: HQ
authors.lastname: Zhou
authors.affiliation: Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Lu-Wen
authors.initials: LW
authors.lastname: Ning
authors.affiliation: Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Hui-Xiong
authors.initials: HX
authors.lastname: Zhang
authors.affiliation: Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China.
authors.forename: Feng-Biao
authors.initials: FB
authors.lastname: Guo
mesh_terms: D000596:Amino Acids / Q000235:genetics*; D001482:Base Composition; D003062:Codon / Q000235:genetics*; D020745:Genome, Archaeal / Q000235:genetics*; D016680:Genome, Bacterial / Q000235:genetics*; D023281:Genomics; D010802:Phylogeny
chemical_list: D000596:Amino Acids; D003062:Codon