金花菜叶绿体基因组特征及密码子偏好性分析  

Sequence characteristic analyses of the Medicago polymorpha complete chloroplast genome and its codon usage bias

作　　者：尹明华[1,2,3,4] 胡佳欣 李瑶瑶 刘曼情 欧阳克蕙 YIN Minghua;HU Jiaxin;LI Yaoyao;LIU Manqing;OUYANG Kehui(College of Life Sciences,Shangrao Normal University,Shangrao 334001,Jiangxi,China;Shangrao Agricultural Technology Innovation Research Institute,Shangrao 334001,Jiangxi,China;Key Laboratory of protection and utilization of medicinal and edible plant resources in Shangrao City,Shangrao 334001,Jiangxi,China;Key Laboratory of germplasm conservation and utilization of potato and taro crops in Shangrao City,Shangrao 334001,Jiangxi,China;College of animal science and technology,Jiangxi Agricultural University,Nanchang 330045,Jiangxi,China)

机构地区：[1]上饶师范学院生命科学学院,江西上饶334001 [2]上饶农业技术创新研究院,江西上饶334001 [3]上饶市药食同源植物资源保护与利用重点实验室,江西上饶334001 [4]上饶市薯芋类作物种质保存与利用重点实验室,江西上饶334001 [5]江西农业大学动物科学技术学院,江西南昌330045

出　　处：《草业科学》2024年第4期884-898,共15页Pratacultural Science

基　　金：国家自然科学基金资助目(31860084、31960079、32060092);江西省科技厅重点研发计划一般项目(20202BBG73010);江西省教育厅科学技术研究项目(GJJ201704、GJJ211729);江西省现代农业产业技术体系建设专项(JXARS-13-赣东站);上饶市科技局平台载体建设项目(2020J001)。

摘　　要：本研究对金花菜(Medicago polymorpha,JHC,江苏)叶绿体基因组进行BGISEQ-500平台测序,对其基因进行Noveplastys组装和GeSeq注释,最后通过MISA、REPuter、Gview、VISTA tools、IRscope和DNADnaSP6.0等软件对其序列特征、基因种类、密码子偏好性以及系统发育进行分析。结果表明,JHC叶绿体基因组大小为124163 bp,无四分体结构,基因组总GC含量为34.09%,共注释出111个基因(76个CDS基因、30个tRNA基因、4个rRNA基因、1个假基因)、91个SSR位点和148个长重复序列;JHC叶绿体基因组的第三位密码子偏好以A和U作为末尾碱基,UUA、GCU、UAA、ACU、CCU、GAA、GUA、AUU、UGU、GGU、UUU、CUU为JHC叶绿体基因组的最优密码子;JHC与MZ772862(云南)亲缘关系较近,与MW971560(美国)、NC_042848(美国)关系较远,表明中国金花菜与美国金花菜的起源存在差异。We performed BGISEQ-500 platform sequencing of the chloroplast genome of Medicago polymorpha(JHC,Jiangsu)and assembled its genes using Noveplastys assembly and GeSeq annotation.we then analyzed its sequence characteristics,gene types,codon preferences,and phylogeny using MISA,REPuter,Gview,VISTA tools,IRscope,and DNADnaSP6.0.The JHC chloroplast genome size was 124163 bp.No tetrad structure was observed,and total genomic GC content was 34.09%.A total of 111 genes,including 76 CDS genes,30 tRNA genes,4 rRNA genes,and 1 pseudogene,were annotated from the chloroplast genome of JHC.A total of 91 SSR loci and a total of 148 long repeat sequences were also detected.The third position in JHC chloroplast genome codons preferentially used A and U,and UUA,GCU,UAA,ACU,CCU,GAA,GUA,AUU,UGU,GGU,UUU,CUU were the optimal codons of the chloroplast genome of JHC.JHC was closely related to MZ772862(Yunnan),and was more distantly related to MW971560(the United States)and NC_042848 the United States,indicating that the origins of American and Chinese Medicago polymorpha strains are different.

关 键 词：金花菜 叶绿体基因组 中性绘图分析 ENC-plot分析 PR2-plot分析 最优密码子 系统发育分析 

分 类 号：S542.9[农业科学—作物学]