Chloroplast Genome Structure and Interspecies Relationship of Sanicula rubriflora
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摘要: 红花变豆菜(Sanicula rubriflora F.Schmidt)是有药用价值的植物，全株干燥后与其他药用同属植物易混淆，种间关系存在争议，通过高通量测序技术对红花变豆菜叶绿体基因组测序，利用生物信息学方法对测序数据进行拼接、注释，首次报道红花变豆菜叶绿体基因组结构及特点，利用叶绿体基因组数据，提供种间分类新证据，并且分析相关类群的进化关系。S.rubriflora叶绿体基因组序列的长度为155 721 bp，其中包括一个85 981bp的大单拷贝区(large single copy,LSC)和一个17 060 bp的小单拷贝区(small single-copy region,SSC)，它们被两个26 340 bp的反向重复区(inverted repeat sequence,IRs)隔开。红花变豆菜叶绿体基因组GC含量为38.20%，包含129个基因，其中84个蛋白质编码基因，37个tRNA基因和8个rRNA基因。红花变豆菜叶绿体基因组结构具有高度保守性，其中编码基因共有51 907个密码子，最多编码5 095个亮氨酸，最少编码689个色氨酸，简单重复序列分析共发现32个位点，大多数是单碱基重复的A/T类型。叶绿体基因组聚类结果支持天胡荽亚科(Hydrocotyloideae)是伞形科(Umbelliferae)内比较原始的类群；变豆菜亚科(Saniculoideae)和芹亚科(Apioideae)为姊妹类群，是伞形科较进化的类群；变豆菜属植物是一个相对自然的类群；红花变豆菜与黄花变豆菜(S.flavovirens)为近缘姊妹种，但是两者形态和地理分布差异较大。该研究结果为变豆菜属属下种间鉴定及其种间演化奠定基础。Abstract: As a kind of medicinal herb,Sanicula rubriflora F.Schmidt is easily confused with other medicinal plants of the same genus after drying and interspecific relationship is controversial.The structure and characteristics of the chloroplast genome of S.rubriflora were reported for the first time,the sequencing data was spliced and annotated using bioinformatics methods,and the chloroplast genome structure and phylogeny were further analyzed.The length of the chloroplast genome sequence of S.rubriflora was 155 721 bp,including a large single copy region（LSC）of 85 981 bp and a small single copy region（SSC）of 17 060 bp,and were separated by inverted repeat sequence（IRs）of 26 340 bp.The GC content of the chloroplast genome of S.rubriflora was 38.20% and contained 129 genes,84 protein-coding genes,37 tRNA genes and 8 rRNA genes respectively.The chloroplast genome structure of S.rubriflora was highly conservative.The coding genes contained a total of 51 907 codons,with 5 095 leucine and 689 tryptophan.Simple repeated sequence analysis revealed a total of 32 sites,and most of them were single base repeat A/T type.The clustering results of the chloroplast genome supported that the subfamily Hydrocotyloideae was a relatively primitive group in the Umbelliferae family.The subfamily Saniculoideae and Apioideae were sister groups,which were the more close relationship of the Umbelliferae.Sanicula was a relatively natural group.S.rubriflora and S.flavovirens were related sister species,but their morphology and geographical distribution were quite different.The results provid a basis for the interspecies identification of the genus Sanicula and lay the foundation for further study of its phylogenetic relationship and interspecies evolution.
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Keywords:
- Sanicula rubriflora /
- chloroplast genome /
- interspecies relationship
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