水杉叶绿体基因组同义密码子使用偏好性  

Synonymous Codon Usage Bias in the Chloroplast Genome of Metasequoia glyptostroboides

作　　者：王茹 罗永坚 刘相泉 卢新雄[4] 尹广鹍[4] 邓志军 WANG Ru;LUO Yongjian;LIU Xiangquan;LU Xinxiong;YIN Guangkun;DENG Zhijun(Hubei Key Laboratory of Biologic Resources Protection and Utilization,Enshi 445000,China;Research Center for Germplasm Engineering of Characteristic Plant Resources in Enshi Prefecture,Enshi 445000,China;College of Forestry and Horticulture,Hubei Minzu University,Enshi 445000,China;Institute of Crop Sciences,Chinese Academy of Agricultural Sciences,Beijing 100081,China)

机构地区：[1]生物资源保护与利用湖北省重点实验室,湖北恩施445000 [2]恩施州特色植物资源种质工程技术研究中心,湖北恩施445000 [3]湖北民族大学林学园艺学院,湖北恩施445000 [4]中国农业科学院作物科学研究所,北京100081

出　　处：《湖北民族大学学报（自然科学版）》2022年第2期121-128,共8页Journal of Hubei Minzu University:Natural Science Edition

基　　金：国家自然科学基金项目(31860073);生物资源保护与利用湖北省重点实验室2020年度开放基金项目(PT012008).

摘　　要：水杉(Metasequoia glyptostroboides)是杉科水杉属唯一现存的孑遗种,也是我国一级保护的濒危特有树种,对其叶绿体基因组密码子使用偏好性及其主要影响因素进行分析,有利于水杉叶绿体基因组学研究、物种保护和种质创新.从在线数据库下载完整的水杉叶绿体基因组序列.共筛选出57条蛋白编码序列.总的GC平均含量和密码子第3位碱基的GC平均含量分别为37.44%和26.79%,密码子适应指数平均值为0.61,有效密码子数平均值为46.55,表明水杉叶绿体基因组密码子使用具有较弱偏好性.ENC-plot、PR2-plot分析及中性绘图分析表明,影响水杉叶绿体基因组密码子使用偏好性的最主要因素为自然选择.高频密码子有31个,高表达密码子24个,既是高频表达又是高密度表达的最优密码子有10个.Metasequoia glyptostroboides,an endangered endemic tree species under primary protection in China,is the only existing relict species in the genus Metasequoia of family Taxodiaceae.An analysis of the codon usage bias and its main influencing factors in Metasequoia glyptostroboides chloroplast genome will provide a reference to further research on its chloroplast genome,species conservation and germplasm innovation.The complete Metasequoia glyptostroboides chloroplast genome sequence was downloaded from the online database.A total of 57 protein-coding sequences were selected from the Metasequoia glyptostroboides chloroplast genome.The total mean GC content and mean GC content at the third base position was 37.44%and 26.79%,respectively.The mean CAI and ENC was 0.61 and 46.55 respectively.These results together described a weak bias for Metasequoia glyptostroboides chloroplast genomic codon usage.The ENC-plot analysis,the PR2-plot analysis,and the neutral mapping analysis showed that the uppermost factor affecting the codon usage bias in the Metasequoia glyptostroboides chloroplast genome is natural selection.There were 31 high-frequency codons,24 high-expression codons and 10 optimal codons.

关 键 词：水杉 叶绿体基因组 同义密码子使用偏好性 碱基组成 自然选择 最优密码子 

分 类 号：Q755[生物学—分子生物学]