葫芦茶叶绿体基因组密码子偏好性分析  

Analysis of Codon Usage Bias in the Chloroplast Genome of Tadehagi triquetrum

作　　者：王芳 周盛茂 赵雪利 Wang Fang;Zhou Shengmao;Zhao Xueli(College of Forestry,Southwest Forestry University,Kunming Yunnan 650233,China)

机构地区：[1]西南林业大学林学院,云南昆明650233

出　　处：《西南林业大学学报(自然科学)》2025年第1期34-43,共10页Journal of Southwest Forestry University:Natural Sciences

基　　金：国家自然科学基金项目(31800170)资助;云南省教育厅科学研究基金项目(2022Y585)资助。

摘　　要：为探究葫芦茶叶绿体基因组密码子的使用模式及其成因,利用Illumina NovaSeq 6000平台进行建库测序,组装、注释获得了葫芦茶叶绿体的全基因组,并利用Codon W、CUSP、OriginPro等工具对筛选到的52条蛋白编码序列进行密码子偏好性分析。结果表明:葫芦茶叶绿体基因组密码子GC平均含量为GC_(1)(45.64%)>GC_(2)(38.17%)>GC_(3)(25.56%),编码氨基酸的同义密码子中T_(3S)和A_(3S)的含量明显高于C_(3S)和G_(3S);ENC值为38.43~55.04,平均值为45.64;CAI值为0.1~0.18,平均值为0.16;说明其密码子偏好性弱。相关性、中性绘图、ENC-plot以及PR2-plot分析表明,突变和选择共同影响葫芦茶叶绿体基因组密码子的使用偏好性。通过RSCU值和ENC值筛选出CUU、AUU、AUA、GUU、GAU、UCA、GGA共7个密码子,为葫芦茶叶绿体基因组的最优密码子,均偏向以A/U结尾。To investigate the patterns and causes of the codon usage in the chloroplast genome of Tadehagi triquetrum,the complete chloroplast genome of T.triquetrum was sequenced using the Illumina NovaSeq 6000 platform,assembled and annotated,with the analysis of codon usage of the 52 screened CDS was performed by Codon W,CUSP and OriginPro.The results showed that the average GC content of T.triquetrum chloroplast gen-ome codons was GC_(1)(45.64%)>GC_(2)(38.17%)>GC_(3)(25.56%),and the content of T_(3S) and A_(3S) in the synonym-ous codons encoding amino acids was significantly higher than that of C_(3S) and G_(3S).The ENC values ranged from 38.43 to 55.04 with an average of 45.64,and the CAI values ranged from 0.1 to 0.18 with an average of 0.16,in-dicating that their codon bias was weak.Analysis of correlation,neutral plotting,ENC‒plot,and PR2‒plot,indic-ating that mutation and selection jointly affect codon usage bias in the chloroplast genome of T.triquetrum.The optimal 7 codons(CUU,AUU,AUA,GUU,GAU,UCA,GGA)were selected of T.triquetrum by RSCU and ENC values,which were biased to end in A/U.

关 键 词：葫芦茶 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：R282.71[医药卫生—中药学]