黄梅秤锤树叶绿体基因组特征及密码子偏好性分析  

Analysis of Chloroplast Genome Characteristics and Codon Preference of Sinojackia huangmeiensis

作　　者：余姣君 王红玉 陈丹格 方元平 Yu Jiaojun;Wang Hongyu;Chen Dange;Fang Yuanping(College of Biology and Agricultural Resources,Huanggang Normal University,Hubei Collaborative Innovation Center for the Characteristic Resources Exploitation of Dabie Mountains,Hubei Key Laboratory of Economic Forest Germplasm Improvement and Resources Comprehensive Utilization,Huanggang,438000)

机构地区：[1]黄冈师范学院生物与农业资源学院,大别山特色资源开发湖北省协同创新中心,经济林木种质改良与资源综合利用湖北省重点实验室,黄冈438000

出　　处：《分子植物育种》2025年第3期963-971,共9页Molecular Plant Breeding

基　　金：科技部科技基础资源调查专项(2019FY101809)资助。

摘　　要：为有效开发利用极小种群植物黄梅秤锤树(Sinojackia huangmeiensis J.W.Ge&X.H.Yao),本研究通过生物信息学分析了该物种的组装叶绿体基因组的重复序列和密码子偏好性。结果显示,黄梅秤锤树叶绿体基因组中检测到的重复结构多为正向重复、回文重复和反向重复,均分布在长单拷贝区(LSC)。MISA分析共发现有43个SSR位点,绝大多数属于单碱基重复的A/T类型,占比为97.5%。密码子偏好性分析显示,黄梅秤锤树叶绿体基因的所有密码子的平均GC含量为37.59%,不同位置的GC含量存在差异,表现为GC_(3)(28.92%)1,其中有96.7%的密码子以A或T结尾(以A结尾的为13个,以T结尾的为16个),说明黄梅秤锤树偏爱使用结尾为A和T的密码子。中性分析发现,GC_(12)和GC_(3)没有明显的相关性,表明密码子偏性主要受到自然选择的影响;ENC-plot分析发现有少部分基因落在曲线附近及其下方,表明突变也影响部分密码子偏好性的形成。以上结果说明黄梅秤锤树叶绿体基因组中偏性使用的密码子主要受到自然选择和突变的共同作用。本研究结果可为该物种的适应性、系统演化和叶绿体基因工程研究提供一定的参考依据。To effective utilize Sinojackia huangmeiensis J.W.Ge&X.H.Yao,a plant species with extremely small population,the chloroplast genome characteristics and the codon usage bias were bioinformatic analyzed.The re-sults showed that most of the repeats detected in the chloroplast genome were forward repeats,palindromic repeats and reverse repeats,all of which were distributed in the long single copy region(LSC).Totally,43 SSR loci were identified by MISA,most of which were single-base repeat(A/T type,accounting for 97.5%).Codon preference anal-ysis showed that the average GC content of all codons in chloroplast genes of S.huangmeiensis was 37.59%.The GC content of different codon positions was different,as results of GC_(3)(28.92%)<GC_(2)(39.12%)<GC_(1)(44.73%).The observation effective codon number(ENCobs)of all genes were greater than 35.19,indicating the bias of most codons were weak.Shows that there were 30 codons when relative synonymous codon usage(RSCU)value>1.Among them,the codons ended with A or T accounted for 96.7%(the ending of 13 codons were A and 16 codons were T),indicating that the codons preferred ending in A and T.Neutral analysis showed no significant correlation between GC_(12) and GC_(3),indicating that the codon bias was mainly affected by natural selection.The ENC-plot analysis found some genes fell below and around the curve,suggesting that mutations also affected some codon bias.Above all,natural selection and mutation both affected the codon usage bias of cp genome of S.huangmeiensis.The re-search results will provide basic data for further studying on this species'adaptability,phylogeny and chloroplast genetic engineering.

关 键 词：黄梅秤锤树 叶绿体基因组 密码子偏好性 极小种群 

分 类 号：Q943[生物学—植物学]