星毛唐松草叶绿体基因组的测序及其密码子偏好性分析  

Characteristics of Thalictrum cirrhosum Chloroplast Genome and Its Analysis on Codon Usage Bias

作　　者：侯哲 娄晓鸣[1] 李昂 黄长兵[1] Hou Zhe;Lou Xiaoming;Li Ang;Huang Changbing(Suzhou Polytechnic Institute of Agriculture,Suzhou Jiangsu 215008,China)

机构地区：[1]苏州农业职业技术学院,江苏苏州215008

出　　处：《西南林业大学学报（自然科学）》2023年第5期47-56,共10页Journal of Southwest Forestry University：Natural Sciences

基　　金：江苏省特色花卉工程中心项目(苏发改高技发[2020]1460号)资助;江苏省省级作物种质资源库(球宿根花卉)项目(JS-ZW-K05)资助;四川省自然科学基金项目(2022NSFSC1141)资助。

摘　　要：通过全基因组重测序数据对星毛唐松草的叶绿体基因组进行组装,并对其密码子偏好性进行分析。结果表明:星毛唐松草的叶绿体基因组全长为155969 bp,具有非常典型的四分体结构;密码子偏好性分析表明,筛选的48条基因序列中,GC_(1)、GC_(2)、GC_(3)的平均含量分别为47.97,39.99,30.07,表现出显著的差异;有效密码子数(ENC)与GC_(1)和GC_(2)的相关性不显著,而与GC_(3)显著相关;中性绘图分析表明GC_(3)与GC_(12)的相关性显著,且密码子的偏好性受自然选择的影响;ENC-plot及ENC比值频数分布结果表明,大多数基因的ENC值低于预期值,仅有10个基因受到突变的影响,其他基因则主要受到自然选择的影响;同义密码子相对使用度(RSCU)分析表明,18个最优密码子均以A和U结尾。该研究为星毛唐松草叶绿体基因工程的开展奠定了基础,为其遗传多样性、遗传结构及群体遗传学的研究提供了参考信息。This study used whole-genome resequencing data to assemble the chloroplast genome(chloroplast,cp)of T.cirrhosum and to analyse its phylogenetic relationships within the genus Thalictrum.The results showed that the chloroplast genome of T.cirrhosum is 155969 bp in length,with a very typical quadripartite structure;the codon preference analysis showed that the average contents of GC_(1),GC_(2)and GC_(3)were 47.97,39.99 and 30.07,respectively,among the 48 gene sequences screened;the correlation of ENC values with GC_(1)and GC_(2)was not significant,while the correlation coefficient with GC_(3)was significantly correlated;the neutral mapping analysis shows significant correlation between GC_(3)and GC_(12) and that codon preference is influenced by natural selection;the ENC−plot and ENC ratio frequency distribution results show that most genes have ENC values lower than expected,with only 10 genes are affected by mutations,while the remaining genes are mainly affected by natural selection;the RSCU analysis showed that 18 optimal codons have A and U endings.This study lays the foundation for the genetic engineering of the chloroplasts of T.cirrhosum and provides reference information for the study of its genetic diversity,genetic structure and population genetics.

关 键 词：星毛唐松草 叶绿体基因组 密码子偏好性 最优密码子 

分 类 号：Q343.1[生物学—遗传学]