唇形科叶绿体系统发育基因组学研究 ——兼论假野芝麻属的系统学位置

	唇形科叶绿体系统发育基因组学研究 ——兼论假野芝麻属的系统学位置
	赵飞
导师	彭华向春雷
关键词	唇形科，野芝麻亚科，假野芝麻属，族间关系，系统发育基因组学 Lamiaceae, Lamioideae, Paralamium, tribe relationships, phylogenomic
摘要	I 唇形科叶绿体系统发育基因组学研究唇形科是被子植物第六大科，包含236属7200余种，全球分布，除极寒的高海拔地区以外，几乎占据了所有陆生生境。唇形科是一个重要的资源大科，具有重要的经济和生态价值。近年来对唇形科开展的系统发育研究非常之多，但其中仍有部分分支的系统发育关系未得到解决，由于缺乏可靠的系统发育框架，严重制约了该科的分类和生物地理的研究。随着系统发育基因组学的兴起，尤其是基于叶绿体基因组的系统发育基因组学成功解决了一些困难类群的系统发育。本研究在族级水平对唇形科进行全面的取样，选择唇形科12个亚科的79属170个物种以及22个外类群物种，共192个代表物种，利用二代测序技术进行基因组浅层测序，并基于最大似然法和贝叶斯推断对唇形科系统发育关系进行了重建。主要研究结果如下： 1）本研究提取79个叶绿体蛋白质编码基因构建串联矩阵，基于最大似然法和贝叶斯推断构建的唇形科系统发育拓扑结构高度一致，12个亚科均为单系且获得支持。 2）本研究澄清了荆芥亚科，豆腐柴亚科和筋骨草亚科及其近缘亚科的系统演化；明确了紫珠亚科与木薄荷亚科构成的分支是唇形科其它亚科的姐妹群；荆芥亚科是一个单系分支，具3细胞6沟型花粉和富含迷迭香酸为其共衍征；明确豆腐柴亚科是筋骨草亚科、梳齿木亚科、黄芩亚科、歧伞花亚科和野芝麻亚科分支的姐妹群。 3）本研究在族级水平上解决唇形科的演化关系，确认唇形科共包含22个族，并明确各族的范畴，其中恢复了筋骨草族、大青族、香科科族和鼬瓣花族；新建了火把花族、三对节族和药水苏族。 4）基于本研究系统发育的结果，对唇形科12个亚科和22个族的分类历史、物种多样性和地理分布进行了全面整理和综述。 II 假野芝麻属的系统位置假野芝麻属是一个单型属，该属自发表之时其系统位置一直存在争议。早期基于小坚果解剖学和花粉粒微形态的研究将其置于唇形科野芝麻亚科或筋骨草亚科，然而该属准确的系统位置一直没有得到解决，该属与其近缘属的系统关系也有待明确。本研究整合分子证据和小坚果形态证据，采用“两步走”的研究策略，对假野芝麻属的系统归属进行了研究。主要结果如下： 1）假野芝麻的叶绿体基因组比较保守，基因组成和顺序高度一致，没有发现重排和基因丢失现象，为典型的四分体结构，包含一个大单拷贝区，一个小单拷贝区以及一对反向重复区。叶绿体基因组大小为152,664 bp，共编码114个基因，包括80个蛋白质编码基因、30个tRNA、4个rRNA。 2）基于79个叶绿体蛋白质编码基因的系统发育研究结果表明，假野芝麻属隶属于野芝麻亚科刺蕊草族，且与簇序草属具有较近的亲缘关系。 3）基于5个叶绿体分子片段（matK，rbcL，trnL-trnF，rps16和trnH-psbA）和核基因ITS序列分别重建了刺蕊草族的系统发育关系。明确刺蕊草族是一个单系类群；在刺蕊草族内部，广防风属、刺蕊草属和冠唇花属的系统关系得到了解决；而其他九属，尤其是全唇花属、羽萼木属与簇序草属和假野芝麻属等单型属的系统发育关系有待进一步的研究。此外，基于本研究的结果重新界定了刺蕊草族的分类范畴，表明该族共包括12属，并为其建立了分属检索表。 4）小坚果形态研究表明假野芝麻属的小坚果为卵球形，表面具光泽，外果皮具不规则的网状纹饰与簇序草属较为相似，支持这两属具有较近的亲缘关系。; I Chloroplast phylogenomics of Lamiaceae Lamiaceae is the sixth largest family of angiosperms with a cosmopolitan distribution comprising more than 7,200 species in 238 genera. Species of the family occupy almost all terrestrial habitats except for extremely cold high-altitude areas. Lamiaceae is a major source of aromatic oil, wood, and medicinal herbs, making it an exceptionally important group in economically and ecologically. Molecular phylogenetic studies during the past two decades have clarified the circumscription of the family and 12 subfamilies were recognized. However, relationships among some subfamilies have not been resolved. The lack of a robust phylogenetic framework has thus far hindered the taxonomic and broad-scale biogeographic studies of this family. Chloroplast phylogenomic analysis has proven to be useful in clarifying amphibolous phylogenetic relationships among land plants in recent years. In this study, based on the comprehensive tribal-level sampling and genome skimming sequencing technology, 170 species of 79 genera from all 12 recognized subfamilies and all tribes in Lamiaceae were sampled as the ingroup and 22 species from Lamiales selected as the outgroup. In total, 192 representative species were included for phylogenetic analyses. Plastome sequences were obtained from the genome skimming data and the phylogenetic tree of Lamiaceae was reconstructed using the maximum likelihood (ML) and Bayesian inference (BI) methods. Our main results are as follows: 1）The 79 chloroplast protein-coding genes were extracted and concatenated, and the phylogenetic topology of Lamiaceae was consistent based on the ML and BI analyses, all 12 subfamilies were recovered as monophyletic. 2）The clade comprising Prostantheroideae and Callicarpoideae is confirmed as the basal clade in the Lamiaceae then sister to all other subfamilies. Nepetoideae is monophyletic, and hexacolpate and three-nucleate pollen containing rosmarinic acid are possible the synapomorphies for this subfamily. In addition, Premnoideae was resolved as the sister group to a large clade including Peronematoideae, Ajugoideae, Scutellarioideae, Cymarioideae and Lamioideae. 3）Based on the phylogenetic analyses, an updated tribal classification of the family Lamiaceae was proposed with 12 subfamilies and 22 tribes, among which Teucrieae, Clerodendreae, Ajugeae, and Galeopseae were recovered, and three tribe (i.e. Rotheceae, Colquhounieae and Betoniceae) were newly established. . 4）A detailed summary of taxonomic history, generic and species diversity, synapomorphies, and distribution for each subfamily and tribe has been summarized. II. Phylogenetic placement of Paralamium Paralamium is a monotypic genus within Lamiaceae, while the systematic position of the genus has been controversial since its establishment and it was variably placed within Lamioideae or Ajugoideae. To date, systematic placement of the genus and its relationship with related genera have been unclear
语种	中文
	2022-12
学位授予单位	中国科学院大学
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75228
专题	昆明植物所硕博研究生毕业学位论文
推荐引用方式 GB/T 7714	赵飞. 唇形科叶绿体系统发育基因组学研究 ——兼论假野芝麻属的系统学位置[D]. 中国科学院大学,2022.

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