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
投稿时间:2018-09-19  修订日期:2019-03-18
DOI:
中文关键词:  RAD测序  杜鹃花  单核苷酸多态性  资源利用
英文关键词:RAD-seq  Rhododendron  SNPs  resources utilization
基金项目:深圳市科技计划项目(JCYJ20150831201123287)、深圳作物分子设计聚合育种工程实验室提升项目(深发改[2015]946号)、广东省农作物核心资源开发应用企业重点实验室(2011A091000047)
作者单位E-mail
马永鹏 中国科学院昆明植物研究所 mayongpeng@mail.kib.ac.cn 
李云飞 深圳华大生命科学研究院  
李世明 深圳华大生命科学研究院  
金鑫 深圳华大生命科学研究院  
程书 深圳华大生命科学研究院  
王松波 深圳市华大农业应用研究院  
侯军亮 深圳市华大农业应用研究院  
刘家劲 深圳市华大农业应用研究院  
段肖霞 深圳市华大农业应用研究院  
马宏 中国林业科学研究院资源昆虫研究所  
张耕耘 深圳市华大农业应用研究院  
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中文摘要:
      [目的]杜鹃花作为世界著名观赏植物,具有重要的科学、生态和经济价值。然而由于杜鹃花属植物快速的辐射演化与种间频繁的自然杂交,对其科学的分类与物种鉴定带来挑战,这在一定程度上制约了我国杜鹃花资源的挖掘与利用。本研究通过对中国杜鹃花属6个亚属85个种的RAD-seq高通量测序和基于这些数据的群体遗传学分析,探讨RAD-seq技术在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基因组,获得高质量SNP位点;并进一步通过 ADMIXTURE、PCA、GCTA 及 FastTree等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份材料比对到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620,423个SNP 位点。基于PCA、Structure聚类及系统发育树的分析结果表明: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)支持目前形态学的分类处理,并突出了鳞片在杜鹃属植物分类中的重要作用。 [结论]RAD-seq技术在复杂类群分类与物种界定方面具有可行性。同时,本研究结果对我国杜鹃花属植物种质资源利用具有启示作用。
英文摘要:
      [Objective] As the world famous horticultural plant, Rhododendron has great values for both research, ecology and economy. Accurate classification and species delimitation with regards to Rhododendron species are still challenging due to rapid radiation and frequent natural hybridization between sympatric species, which greatly impedes resources exploration and utilization of Rhododendrons. In the present study, we aim to examine the application of RAD-seq in classifications of the genus. [Method] We firstly sequenced 85 species of Rhododendron using dd-RAD and evaluate basic characteristics of these data. Then the whole genome sequence of Rhododendron delavayi were used as the reference genome and SNP were effectively mapped and obtained. In the end we use these SNPs to construct the phylogenomic relationships among each group employed by ADMIXTURE、PCA、GCTA and FastTree software. [Result] On average 87.52% of reads were mapped to the Rhododendron delavayi genome and average coverage to the genome is 5.21%. After cleaning and filtering these data, a total of 620,423 SNPs were obtained. Preliminary analysis of these observed SNP by ADMIXTURE、PCA and FastTree revealed that species grouping is corresponding to subgenus division from Floral of China, though different subsections with subgenus were not clearly differentiated. Moreover scale underside leaf is emphasized as the key character to distinguishing subgenus with genus Rhododendron. [Conclusion] We proved the potential application of RAD-seq in classifications of the large genus Rhododendron and our results will provide insights into resources exploration and utilization of Rhododendrons in the future in China.
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