栽培丹参居群rbcL基因遗传多样性及系统学分析
首发时间:2021-03-26
摘要:为了解丹参栽培居群叶绿体SmrbcL基因的遗传多样性及其系统发育关系,本研究以征集到的国内40份栽培丹参居群为材料,采用PCR 首次扩增其SmrbcL基因,利用生物信息学手段分析比较了其基因及其推定氨基酸序列的差异。结果表明:克隆得到的丹参SmrbcL基因部分序列经与参考序列对位排齐后长度为1275bp;共有43个SNP变异位点,其中转换位点33个、颠换位点10个,变异率为3.4%;基于丹参SmrbcL基因的SNP指纹可区别6个栽培丹参类群;SmrbcL基因的推定氨基酸序列差异分析首次发现了10个氨基酸变异位点,其中有5个实质性变异很可能与其与SmrbcS的聚合的结构和生物学活性密切关联,基于丹参SmrbcL基因的推定氨基酸序列指纹可区别5个栽培丹参类群。基于贝叶斯法构建的SmrbcL基因对位序列的系统发育树表明:40个丹参居群聚在两个系支上,其中30个丹参居群聚在一个系支上,其余10个丹参居群聚在另一个系支上;基于SmrbcL基因扩增产物序列的系统发育树表明:40个丹参居群同样聚类在两个系支上,其中35个居群聚在一系支上,另5个居群聚在另一系支上;基于其推定氨基酸序列构建的系统发育树表明:居群V-JSSY-V-2单独聚在一个系支上,其余39个居群聚成一支,后者又分聚两个亚支上,一个亚支包括35个居群,另一个亚支包括4个居群。本研究基于SmrbcL基因揭示了不同地区丹参种质资源的遗传多样性和系谱关系,为丹参材料的遗传鉴定和光合能力差异的分子机制研究奠定了基础。
关键词: 药用植物学 丹参 栽培居群 rbc L基因 遗传多样性 系统发育关系
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The genetic diversity and phylogenetic analyses of rbcL gene of the cultivated Salvia miltiorrhiza populations
Abstract:In order to understand the genetic diversity and phylogenetic relations of the chloroplast rbcL gene in cultivated populations of Danshen (Salvia miltiorrhiza), 40 populations were collected in China and used as materials to amplify the SmrbcL gene by PCR, and to analyze the variations in the gene and the putative amino acid sequences by bio-informatics methods for the first time. Results showed that the cloned 40 partial SmrbcL sequences is 1275bp in length when aligned with the reference; there were 43 SNP variation sites in total, 33 transformations and 10 transversions, with a variation rate of 3.4%; the SNP fingerprints of SmrbcL identified can discriminate the 40 populations into 6 categories. The analysis of the putative amino acid sequences of the SmrbcL gene for the first time identified 10 amino acid variation sites, 5 of which are substantial and probably intimately related to the structure and biological activity when polymerize with SmrbcS. Five categories of populations can be discriminated based on the putative amino acid sequence fingerprints of Smrbc L. The constructed Bayes-based phylogenetic tree of the SmrbcL gene aligned sequences showed that the 40 populations are clustered in two clades, one of 30, and the other 10 populations; phylogenetic tree based on the PCR amplified SmrbcL product sequences also showed two clades, one of 35, and the other 5 populations. The phylogenetic tree based on the putative amino acid sequences showed that V-JSSY-V-2 alone formed a clade, and the remaining 39 populations, another clade, and the later could be subdivided into two subclades, one of 35, the other, 4 populations.The the genetic diversity and phylogenetic relations revealed by SmrbcL gene of the different cultivated S. miltiorrhiza populations in this research laid an excellent basis for the genetic identification of the cultivation germplasm and for further mechanismal studies on the differences of photosynthetic capacity of the cultivated S. miltiorrhiza populations.
Keywords: Medicinal botany Danshen (Salvia miltiorrhiza Bunge) Cultivated population rbcL Genetic diversity Phylogenetic relation
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