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基于RAD高通量测序探讨中国85种杜鹃花属植物的分类

Phylogenomic Analysis of 85 Rhododendron Species in China Based on RAD Sequencing

    摘要
  • 摘要:
    目的 探讨RAD-seq技术在中国杜鹃花复杂类群分类与物种界定方面的优势。
    方法 本研究对杜鹃花属85个种进行了RAD-seq测序，评估了数据的基本特征；同时，以马缨杜鹃基因组作为参考，获得高质量SNP位点，并进一步通过ADMIXTURE、PCA、GCTA及FastTree软件对其进行基因分型、聚类与系统树构建。
    结果 本研究中85份材料比对至马缨杜鹃的平均比对率87.52%，在参考基因组上的平均覆盖度为5.21%，最终获得了620 371个SNP位点。基于PCA、Structure聚类及系统发育树的分析结果，本研究支持目前在亚属水平（杜鹃亚属、常绿杜鹃亚属、马银花亚属、羊踯躅亚属、映山红亚属和长蕊杜鹃亚属）的形态学分类处理，并突出了鳞片在杜鹃属植物分类中的重要作用。
    结论 RAD-seq数据产生的大量SNP位点可区分杜鹃花亚属和组内的大部分物种，说明其在复杂类群分类与物种界定方面具有可行性。

     

    Abstract:
    Objective This study aims at examining the application of RAD-seq in classifications of the genus Rhododendron.
    Method  85 species of Rhododendron were sequenced using dd-RAD and the basic characteristics data obtained were evaluated. Then, the whole genome sequence of Rh. delavayi were used as the reference genome and the SNP loci were effectively mapped and obtained. These SNP loci were used to construct the phylogenomic relationship among groups employed by ADMIXTURE, PCA, GCTA and FastTree software.
    Result  On average, 87.52% of reads were mapped to the Rh. delavayi genome and the average coverage to the genome was 5.21%. After cleaning and filtering these data, a total of 620 371 SNPs were obtained. Preliminary analysis of these observed SNP loci by ADMIXTURE, PCA and FastTree revealed that the species grouping was corresponding to subgenus division from Floral of China, though different subsections with subgenus were not clearly differentiated. Moreover, the scale underside leaf was emphasized as the key character to distinguishing subgenus with genus Rhododendron.
    Conclusion  The study proves the potential application of RAD-seq in classifications of the large genus Rhododendron and the results will provide insights into resources exploration and utilization of Rhododendrons in China.

     

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