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

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.