叶绿体全基因组序列在香薷属（唇 形科）系统发育中的应用

	叶绿体全基因组序列在香薷属（唇形科）系统发育中的应用
	孙增朋
导师	向春雷王焕冲
关键词	香薷属 Elsholtzia 叶绿体基因组 Plastomes 系统发育重建 Phylogenetic reconstruction 生物地理学 Biogeography 高变区 Highly variable region
摘要	香薷属（Elsholtzia Willd.）隶属于唇形科（Lamiaceae）荆芥亚科（Nepetoideae）香薷族（Elsholtzieae），是该族最大的属，共有40种，主要分布在亚洲。我国西南山区是香薷属的分布中心，目前共分布有该属植物29种。香薷属植物具有重要的经济价值，可供药用、观赏和食用，然而该属形态变异较大，已有的分子系统学研究未能较好解决属内系统发育关系，导致全面开展其生物地理学、性状演化研究等受到阻碍。本论文在全球范围选取了香薷属36种47个个体和外类群6属9个个体，利用叶绿体基因组序列重建了香薷属内的系统发育关系，在构建稳定的系统发育树的基础上，进一步筛选出可用于建立属下分类系统的有效性状，并结合化石证据开展了该属的生物地理学分析。此外，本论文还全面分析了香薷属的叶绿体基因组特征并筛选了叶绿体高变区，以用于后期开展物种分子鉴定DNA条形码的筛选。本论文得到了以下主要研究结果：（1）香薷属和外类群的叶绿体基因组都是典型的四分体结构，即由两个反向重复序列将整个环状的叶绿体基因组分为大单拷贝区和小单拷贝区。叶绿体基因组的长度变化为148,276 bp至152,031 bp之间，GC含量为37.8%至38.2%之间。香薷属共有编码基因113个，其中蛋白编码基因80个（密花香薷IR区的ycf15丢失），tRNA基因29个，rRNA基因4个。叶绿体基因组各区域的交界有两种类型，第一种：LSC/IRb交界位于rps19-rpl2间（异叶香薷、东紫苏、密花香薷和小头花香薷）；第二种：LSC/IRb交界处，IRb部分扩张进入rps19基因，在IRa区产生rps19的假基因片段，除上述四种香薷外，其余香薷属植物属于此类型。（2）利用最大似然法与贝叶斯推断法对叶绿体全基因组序列的九个矩阵（叶绿体全基因组序列、LSC、SSC、IR、LSC＋IR、LSC＋SSC、IR＋SSC、80CDS、基因间隔区）进行了系统发育分析，结果显示各系统发育树的拓扑结构基本一致，且比基于叶绿体和核基因片段构建的系统发育树的支持率高，能更好解决该属的系统演化关系。所有的分析结果均表明香薷属为单系，属下可分为支持率极高的三大分支（Clade I–III）。传统属下分类系统中各组和系均不是单系，基于可靠的系统育树及物种演化关系，筛选出小坚果≥1.8 mm、苞片钻形或披针形、生活习性和叶型等作为建立属下分类系统的重要形态学性状。（3）生物地理学研究结果表明，香薷属可能起源于始新世末期约37.25 Mya的横断山区，并于始新世-渐新世约35.52 Mya发生分化。属内3大分支的分化时间都是在中新世。香薷属演化过程中，至少发生过两次扩散，一次是自横断山区向中国-日本扩散，另一次是横断山区向南亚和东南亚扩散。香薷属物种演化可能与青藏高原的隆升密不可分，青藏高原的隆升引起气温降低和亚洲内陆干旱加剧，可能使香薷属植物衍生出适应干旱的性状。（4）本论文从叶绿体全基因组中初步筛选了23个高变区，并与通用DNA条形码分别构建了香薷属的系统发育树，最终确定4个高变区（trnC-GCA-rpoB、trnV-UAC-ndhC、ndhF和ycf1的SSC部分）可作为潜在的DNA条形码以用于香薷属或香薷族的物种分子鉴定，并优先推荐ycf1作为开展香薷属物种鉴定研究的首选片段。; As the largest genus of Elsholtzieae (Lamiaceae; Nepetoideae), Elsholtzia Willd. comprises 40 species, and mainly distributed in Asia. China accommodates 29 species of Elsholtzia and southwest China is considered as the distribution center of the genus. Though species of Elsholtzia are economically important that they can be used as medicine, ornament, and flavour, the genus is morphological variable. Previous molecular phylogenetic studies failed to resolve the phylogenetic relationships with in Elsholtzia, which further hindered the biogeographic and character evolutionary analyses of the genus. In the present study, a total of 47 individuals of 36 species of Elsholtzia and 9 species of 6 genus of outgroups were selected, and the phylogenetic relationship was reconstructed based on plastome sequence. We further screened out effective traits, and the biogeographic history of this genus was also elucidated based on fossil evidence. Furthermore, the plastome characteristics were analyzed to sift out the chloroplast highly variable region, which could be used for DNA barcoding or phylogenetic research of Elsholtzieae. Major results of present study are as follows: (1) Plastomes of Elsholtzia and outgroup species are arranged in a typical quadripartite structure, that the whole plastome is divided into a large single copy (LSC) region and a small single copy (SSC) region by two reverse repeat sequences (IR). The length of plastomes of Elsholtzia ranges from 148,276 bp to 152,031 bp, and GC content ranges from 37.8% to 38.2%. A total of 113 genes are encoded, including 80 protein coding genes (CDS) (ycf15 is deleted in E. densa), 29 tRNA and 4 rRNA. Two types of the LSC/IRb junction can be recognized. 1): the junction between LSC/IRb is located between the genes rps19 and rpl2 (Type I: E. heterophylla, E. bodinieri, E. densa and E. eriostachya); 2): the IRb region expands into rps19 gene and generates a pseudogene (part of rps19) within IRa (Type II: all species of Elsholtzia except for the above four species). (2) Based on Maximum likelihood and Bayesian inference analyses, the phylogenetic relationship of Elsholtzia were reconstructed based on nine matrices (plastomes, LSC, SSC, IR, LSC + IR, LSC + SSC, IR + SSC, 80 CDS, and inter-gene regions) respectively. Topologies generated by different datasets are largely congruent, with the phylogenetic trees based on the dataset 80CDS being the most-well resolved. All the analyses results show that Elsholtzia is monophyletic, and can be divided into three strongly supported clades (Clade I–III). Traditional cicumscribed, sections and series within Elsholtzia were not monophyletic. Based on the reliable phylogenetic relationship, we selected six features (e.g. nutlet size, bract shape, habits and leaf type) as important morphological traits to establish the infrageneric system. (3）Biogeographic analyses showed that Elsholtzia originated in Hengduan Mountainous region at ca. 37.25 Mya during late Eocene, a
语种	中文
	2022-05
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/151853/75094
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	孙增朋. 叶绿体全基因组序列在香薷属（唇形科）系统发育中的应用[D]. 中国科学院大学,2022.

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