红凤菜叶绿体全基因组特征及其序列比较分析

The Characteristics of the Complete Chloroplast Genome in Gynura bicolor DC.and Its Comparative Sequence Anaylsis

为了更好地了解红凤菜叶绿体基因组(cpDNA)特征及其进化关系,本研究对红凤菜cpDNA进行了测序、组装和注释,并与近缘种进行比较分析。结果表明,红凤菜cpDNA全长为150929 bp,总GC含量为37.18%,包含一个大单拷贝区(LSC,83112 bp)、一个小单拷贝区(SSC,18127 bp)以及两个反向重复区(IRa/IRb,24845 bp)。cpDNA共注释到131个功能基因,其中86个为蛋白编码基因,37个为tRNA基因,8个为rRNA基因;共鉴定出58个SSRs位点,其碱基组成以A-T类型为主。RSCU分析表明,红凤菜cpDNA明显偏好使用以A/T结尾的密码子。基因组比较分析显示,4种菊三七属植物cpDNA在结构和组成上非常保守,变异主要集中在LSC区和SSC区。系统发育分析表明,野茼蒿属与菊三七属亲缘关系最近;菊三七属种间,白子菜、狗头七与红凤菜亲缘关系最近。

In order to better understand the characteristics and evolutionary relationship of Gynura bicolor DC.chloroplast genome(cpDNA),the cpDNA of Gynura bicolor DC.were sequenced,assembled and annotated,which was compared with related species.The results showed that the total length of cpDNA was 150929 bp,the total GC content was 37.18%,including one large single copy region(LSC,83112 bp),one small single copy region(SSC,18127 bp)and two reverse repeat regions(IRa/IRb,24845 bp).A total of 131 functional genes were annotated by cpDNA,of which 86 were protein coding genes,37 were tRNA genes,and 8 were rRNA genes.A total of 58 SSRs sites were identified,and their base composition was mainly A-T type.RSCU analysis showed that cpDNA of Gynura bicolor DC.obviously preferred to use codons ending in A/T.Comparative genomic analysis showed that the cpDNA of the four species of Gynura Cass.plants was very conserved in structure and composition,and the variation was mainly concentrated in the LSC region and SSC region.Phylogenetic analysis showed that Crassocephalum Moench and Gynura Cass.were most closely related.Among the Gynura Cass.species,Gynura divaricata,Gynura pseudochina and Gynura bicolor DC.were most closely related.