小黑麦叶绿体基因组密码子偏好性分析与基因功能相关性分析  

Correlation Between Codon Usage Patterns and Gene Functions in the Chloroplast Genome of Triticale

作　　者：田甜 张银霞 杜文华[1] TIAN Tian;ZHANG Yin-xia;DU Wen-hua(College of Grassland Science,Gansu Agricultural University/Key Laboratory of Grassland Ecosystem,Gansu Agricultural University,Ministry of Education/Pratacultural Engineering Laboratory of Gansu Province/Sino-U.S.Centers for Grazingland Ecosystem Sustainability,Lanzhou,Gansu Province 730070,China)

机构地区：[1]甘肃农业大学草业学院/草业生态系统教育部重点实验室/甘肃省草业工程实验室/中-美草地畜牧业可持续发展研究中心,甘肃兰州730070

出　　处：《草地学报》2025年第3期707-718,共12页Acta Agrestia Sinica

基　　金：农业生物育种重大专项(2023ZD0402605-02);国家自然科学基金(32260339);甘肃省高等学校产业支撑计划(2022CYZC-49);甘肃省重大专项(21ZD4NA012);西藏重大专项(XZ202101ZD003N)资助。

摘　　要：为揭示小黑麦(Triticale)的密码子使用偏好性及其影响因素,用CodonW 1.4.2和在线软件CUSP(Codon Usage and Synonymous Condon Usage Profile)对小黑麦叶绿体基因组中52个编码序列(Coding sequence,CDS)特征进行分析。结果表明:小黑麦叶绿体基因组密码子第三位主要偏向以A/U为主;有效密码子数(Effective number of codon,ENC)值在37.64~61.00之间,平均值为47.31,大于45的有42个;密码子适应指数(Codon adaptation index,CAI)在0.12~0.33之间,平均值为0.17,说明小黑麦叶绿体基因组密码子偏好性较弱;16个均以A/U结尾的密码子被筛选为最优密码子。中性绘图、ENC-GC_(3s)和偏倚性绘图分析(Parity Rule 2,PR2-plot)结果表明多数功能基因的密码子使用偏好性受自然选择压力影响为主。小黑麦叶绿体基因组中与光合作用密切相关的基因可能受到了突变和选择的强烈作用,使这些基因的密码子使用频率具有共同特征,表现为密码子使用模式与基因功能有较大的相关性。To investigate the codon usage bias and its influencing factors in triticale(Triticale),CodonW 1.4.2 and the online tool CUSP(Codon Usage and Synonymous Condon Usage Profile)were used to analyze the characteristics of 52 coding sequences(CDS)in the chloroplast genome of triticale.The results showed that the third codon position in the triticale chloroplast genome predominantly favored A/U bases.The effective number of codons(ENC)ranged from 37.64 to 61.00,with an average of 47.31,and 42 sequences had ENC values greater than 45.The codon adaptation index(CAI)ranged 0.12-0.33,with an average of 0.17,indicating a weak codon usage bias in the triticale chloroplast genome.Sixteen codons ending in A/U were identified as opti⁃mal codons.Neutral plotting,ENC-GC_(3s)analysis,and PR2-plot analysis(Parity Rule 2)revealed that the codon usage bias of most functional genes was mainly influenced by natural selection.Genes in the triticale chlo⁃roplast genome closely related to photosynthesis were likely subjected to strong mutation and selection pressures,resulting in shared codon usage patterns among these genes.This suggests a significant correlation between codon usage patterns and gene functions.

关 键 词：小黑麦 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：S544.9[农业科学—作物学]