基于同义密码子使用的原核生物基因组大、小染色体及质粒进化特征分析  

Evolutionary Analysis of Large and Small Chromosome and Plasmid in Prokaryotic Genomes Based on Synonymous Codon Usage

作　　者：毕胜男[1,2] 于家峰[1,3] 任景[1] 王吉华[1,4] 

机构地区：[1]山东省功能大分子生物物理重点实验室生物物理研究所德州学院,山东德州253023 [2]山东师范大学生命科学学院,济南250014 [3]生物电子学国家重点实验室东南大学,南京210096 [4]德州学院物理与电子信息学院,山东德州253023

出　　处：《生物物理学报》2015年第3期272-285,共14页Acta Biophysica Sinica

基　　金：国家自然科学基金项目(61302186);东南大学生物电子学国家重点实验室开放基金~~

摘　　要：基于同义密码子偏好分析,对54个原核基因组大、小染色体及质粒中蛋白质编码基因的序列特征进行了对比分析。结果表明,大、小染色体中蛋白质编码基因的GC含量分布相近,质粒中蛋白质编码基因的GC含量分布与所在物种全基因组的GC含量差别较大。进一步的分析表明,大、小染色体共同偏好的密码子最多,且具有相近的起始密码子和终止密码子使用特征。基于对应分析的同义密码子使用模式分析表明,大、小染色体具有相近的序列特征,且大、小染色体及质粒之间具有不尽相同的影响因素。这些结果可为今后原核生物基因组进化研究提供可靠的方法和理论依据。Synonymous codon usage analysis was performed on the protein coding genes in large chromosomes, small chromosomes and plasmids of 54 selected prokaryotic genomes. The results showed that the protein coding genes in large and small chromosomes shared similar GC content distributions, while the GC contents of the protein coding genes in plasmids were dispersed and different from the whole genomic GC contents of each species. In addition, there were more common preferred synonymous codons between large chromosomes and small chromosomes in comparison to plasmids, it was also found that the usages of initiation codons and termination codons in large chromosomes were coincident with that of small chromosomes. Further studies based on correspondence analysis indicated that there were similar sequence characteristics between large and small chromosomes, and the influencing factors for synonymous codon usage bias were different among large chromosomes, small chromosomes and plasmids to varying degrees. Therefore, this work can provide helpful information for future evolutionary analysis of prokaryotic genomes.

关 键 词：原核生物基因组 大染色体 小染色体 质粒 同义密码子偏好 

分 类 号：Q61[生物学—生物物理学]