Zhou Hui-Qi, Ning Lu-Wen, Zhang Hui-Xiong, Guo Feng-Biao
Center of Bioinformatics and Key Laboratory for NeuroInformation of the Ministry of Education, University of Electronic Science and Technology of China, Chengdu, China.
PLoS One. 2014 Sep 25;9(9):e107319. doi: 10.1371/journal.pone.0107319. eCollection 2014.
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.
本文分析了2670个属于不同系统发育谱系的原核生物基因组的GC含量。这些基因组的GC含量范围为13.5%至74.9%。我们针对这些原核生物物种GC含量的差异，分析了三个密码子位置的碱基频率距离、密码子频率以及各基因组间的氨基酸组成。我们发现，尽管某些物种的系统发育谱系关系较远，但相似的基因组GC含量促使它们在三个密码子位置、密码子使用模式以及氨基酸使用模式上采用相似的碱基使用模式。我们的研究表明，在原核生物基因组中：a）碱基使用、密码子使用和氨基酸使用随GC含量变化呈线性相关；b）每种使用的距离与GC含量差异呈线性相关；c）在决定碱基使用、密码子使用和氨基酸使用方面，GC含量比系统发育谱系更为重要。这项工作的特别之处在于，我们在所有分析中都采用了直观的图形方法，并且利用这些分析研究了多达2670种原核生物。我们希望这项工作有助于理解微生物基因组组织中的共同特征。
