title: Non-random arrangement of synonymous codons in archaea coding sequences.
abstract: Non-random arrangement of synonymous codons in coding sequences has been recently reported in eukaryotic and bacterial genomes, but the case in archaeal genomes is largely undetermined. Here, we systematically investigated 122 archaeal genomes for their synonymous codon co-occurrence patterns. We found that in most archaeal coding sequences, the order of synonymous codons is not arranged randomly, but rather some successive codon pairs appear significantly more often than expected. Importantly, such codon pairing bias (CPB) pattern in archaea does not seem to completely follow the co-tRNA codon pairing (CCP) rule previously reported for eukaryotes, but largely obeys an identical codon pairing (ICP) rule. Further, synonymous codon permutation test demonstrated that in many archaeal genomes, random mutation alone is unable to cause the observed high level of ICP bias, which strongly indicates that selection force has been involved to shape synonymous codon orders, potentially meeting a global requirement to optimize translation rate.
authors.affiliation: State Key Laboratory of Pharmaceutical Biotechnology, School of Life Sciences, Nanjing University, Nanjing, Jiangsu Province, 210093, China. zymei628@163.com
authors.forename: Yan-Mei
authors.initials: YM
authors.lastname: Zhang
authors.forename: Zhu-Qing
authors.initials: ZQ
authors.lastname: Shao
authors.forename: Le-Tian
authors.initials: LT
authors.lastname: Yang
authors.forename: Xiao-Qin
authors.initials: XQ
authors.lastname: Sun
authors.forename: Ya-Fei
authors.initials: YF
authors.lastname: Mao
authors.forename: Jian-Qun
authors.initials: JQ
authors.lastname: Chen
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
mesh_terms: D003062:Codon / Q000235:genetics*; D019143:Evolution, Molecular; D020745:Genome, Archaeal; D017020:Methanosarcina / Q000235:genetics*; D016366:Open Reading Frames; D010802:Phylogeny
chemical_list: D003062:Codon