Phylogenomics, phylogeography and germplasms authentication of the Rheum palmatum complex based on complete chloroplast genomes
Phylogenomics, phylogeography and germplasms authentication of the Rheum palmatum complex based on complete chloroplast genomes
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基于完整叶绿体基因组的掌叶大黄复合体的系统基因组学、系统发育地理学和种质鉴定
DOI：
10.1007/s10265-023-01440-0
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发表时间：
2023-02
影响因子：
2.8
通讯作者：
Xumei Wang
中科院分区：
文献类型：
--
作者：
Yunyan Zhai;Tianyi Zhang;Yanbing Guo;Chenxi Gao;Lipan Zhou;Li Feng;Tao Zhou;Xumei Wang
作为一种中药，大黄被用来治疗几种疾病，如严重急性胰腺炎、败血症和慢性肾衰竭。然而，很少有研究关注于掌心大黄复合体的种质鉴定，也没有研究利用质体组数据来阐明掌心大黄复合体的进化史。因此，我们的目标是基于新测序的叶绿体基因组数据集，开发潜在的分子标记来鉴定大黄的优质种质，并探索掌叶复合体的分化和生物地理历史。对35份棕榈复合种质的叶绿体基因组进行了测序，其长度在160858 ~ 161204 bp之间。所有基因组的结构、基因含量和基因顺序高度保守。8个indel和61个SNPs位点可用于鉴定特定地区的大黄优质种质。系统发育分析表明，所有大黄种质均聚在同一支系，具有较高的自举支持值和贝叶斯后验概率。根据分子定年结果，该复合体的种内分化发生在第四纪，可能受气候波动的影响。生物地理重建表明，棕棕复合体的祖先可能起源于喜马拉雅-横断山脉或巴山-秦岭，然后向周边地区扩散。本研究开发了一些有用的分子标记，为大黄种质资源的鉴定提供依据，为进一步了解掌叶大黄复合体的物种形成、分化和生物地理提供依据。
As a traditional Chinese medicine, rhubarb is used to treat several diseases such as severe acute pancreatitis, sepsis and chronic renal failure. However, few studies focused on the authentication of germplasm for the Rheum palmatum complex, and no studies have been conducted to elucidate the evolutionary history of the R. palmatum complex using plastome datasets. Hence, we aim to develop the potential molecular markers to identify the elite germplasms of rhubarb and explore the divergence and biogeographic history of the R. palmatum complex based on the newly sequenced chloroplast genome datasets. Chloroplast genomes of thirty-five the R. palmatum complex germplasms were sequenced, and the length ranged from 160,858 to 161,204 bp. The structure, gene content and gene order were highly conserved across all genomes. Eight InDels and sixty-one SNPs loci could be used to authenticate the high-quality germplasms of rhubarb in specific areas. Phylogenetic analysis revealed that all rhubarb germplasms were clustered in the same clade with high bootstrap support values and Bayesian posterior probabilities. According to the molecular dating result, the intraspecific divergence of the complex occurred in the Quaternary, which might be affected by climatic fluctuation. The biogeography reconstruction indicated that the ancestor of the R. palmatum complex might originate from the Himalaya-Hengduan Mountains or/and Bashan-Qinling Mountains, and then spread to surrounding areas. Several useful molecular markers were developed to identify rhubarb germplasms, and our study will provide further understanding on speciation, divergence and biogeography of the R. palmatum complex.
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