Abstract: In this study,the whole chloroplast genome of three cultivars of Medicago sect. Spirocarpos,which approved by the national grass variety examination and approval committee,were sequenced by Illumina NovaSeq 6000 platform,and comparatived analysis was performed by comparing with the chloroplast genome of Medicago polymorpha,M. lupulina and M. minima of M. sect. Spirocarpos. The results showed that the full length of cp-DNA in M. polymorpha ‘Chuxiong’,M. polymorpha ‘Huaiyin’ and M. lupulina ‘Longdong’ were 123 472 bp,124 229 bp,and 124 107 bp,respectively. Simultaneously,the total GC content of these three cultivars were 34.2%,34.1%,and 34.2%. In this study,a total of 110—111 genes were annotated. This was first report in M. lupulina ‘Longdong’ that a 226 bp sequence with IR region characteristics was found,which including rps12. Seventeen genes in M. polymorpha ‘Chuxiong’ and M. polymorpha ‘Huaiyin’ contain introns. However,in M. lupulina ‘Longdong’ only fourteen genes contain introns. SSR repeats sequences have been detected in accD and ycf1,which were two accelerated substitution rates gene. This might be related to SSR sequence insertion. Phylogenetic analysis showed that M. polymorpha ‘Chuxiong’ and M. polymorpha ‘Huaiyin’ had a close relationship with M. polymorpha. Meanwhile, M. lupulina ‘Longdong’ had a close relationship with M. lupulina. This study provides a theoretical basis for the classification of M. sect. Spirocarpos,and the study of IR region in chloroplast genome.

Key words: Medicago sect. Spirocarpos, Chloroplast genome evolution, Repeat sequence analysis, Phylogenetic analysis

摘要： 本文采用Illumina NovaSeq 6000平台对螺旋果苜蓿组3个国审品种进行叶绿体基因组测序、组装和注释，并与南苜蓿(Medicago polymorpha)、天蓝苜蓿(M. lupulina)和小苜蓿(M. minima)进行比较分析。结果表明：‘楚雄’南苜蓿(M. polymorpha ‘Chuxiong’)、‘淮阴’南苜蓿(M. polymorpha ‘Huaiyin’)和‘陇东’天蓝苜蓿(M. lupulina ‘Longdong’)叶绿体基因组长分别为123 472 bp，124 229 bp和124 107 bp，总GC含量分别为：34.2%，34.1%和34.2%，共编码110～111个基因。首次发现‘陇东’天蓝苜蓿具有一个226 bp的IR(Inverted repeat lacking clade)区特征序列(含rps12基因)。‘楚雄’南苜蓿和‘淮阴’南苜蓿各有17个内含子，但‘陇东’天蓝苜蓿只有14个内含子。在6个材料基因组中，在替换率加快的accD和ycf1中检测到简单重复序列，替换率加快可能与简单重复序列插入有关。系统进化树表明，‘楚雄’南苜蓿和‘淮阴’南苜蓿与南苜蓿亲缘关系较近，‘陇东’天蓝苜蓿与天蓝苜蓿亲缘关系最近。本研究为螺旋果苜蓿组分类和叶绿体基因组反向重复区研究提供理论依据。

关键词: 螺旋果苜蓿组, 叶绿体基因组进化, 重复序列分析, 系统发育