锦葵科椴树属（Tilia L.）的叶绿体系统发育基因组学研究

发布时间：2018-03-13 12:01

本文选题：椴树属　切入点：锦葵科　出处：《云南大学》2016年博士论文　论文类型：学位论文

【摘要】：椴树属(Tilia L.)隶属于锦葵科(Malvaceae),包括了23个种和14个亚种。椴树属植物主要间断分布于欧洲至西西伯利亚-东亚和北美洲的温带和亚热带地区。椴树属中大部分物种是北温带森林的优势树种,具有重要的生态功能和经济价值。虽然椴树属的花序或果序上具大型的叶状苞片使其很容易与其他类群区别,但因为缺乏有效的形态分类性状,且存在广泛的杂交和多倍化事件,属内种间的划分存在很大困难。由于椴树属的叶绿体基因片段进化速率极低,且种类的地理分布较广,取样困难,现有的分子系统发育研究均未能很好解析种间的系统发育关系。厘清椴树属内种间的演化关系是研究该属进化历史和现代地理分布格局成因的重要基础,同时也为椴树属及其近缘类群的进化生物学、保护生物学和林木资源管理比较基因组学和功能基因组学等研究提供重要信息。本研究首次根据椴树属最新的分类修订结果,通过全面地取样,利用第二代测序技术Illumina完成了椴树属23个种50个个体的叶绿体基因组测定,通过多种方法构建了系统发育树,分析探讨了椴树属内种间的系统发育关系。此外,还对椴树属及其近缘类群的叶绿体基因组进行了比较。主要研究结果如下：1.椴树属及其近缘类群的叶绿体基因组比较分析椴树属的叶绿体基因组具有被子植物叶绿体基因组典型的四分体结构,其大小在162,250-163,001 bp之间。椴树属与同属锦葵科的棉属(Gossypium L.)和可可属(Theobroma L.)的叶绿体基因组在基因组大小、GC含量等基因组特征与结构上高度一致。椴树属编码着相同数目的113个不同的基因,包含79个蛋白质编码基因,30个tRNA基因和4个rRNA基因,且所有基因的排列顺序在这些基因组中都保持一致,整个基因组具有高度的共线性。椴树属的叶绿体基因组大小比其近缘类群的略大,主要是大单拷贝区(LSC)的非编码区中存在较长片段(100bp+)的插入/缺失造成的差异。对四种椴树属植物(Tilia amurensis Rupr., T. mandshurica Maxim., T. oliveri Szyszyl., T. paucicostata Maxim.)的叶绿体基因组比较发现,种间序列的遗传分化程度极低,在整个基因组中没有发现变异热点区。虽然椴树属叶绿体基因组包含的信息位点较少,但对四种椴树系统发育关系的重建仍得到了较高的支持。2.椴树属的叶绿体系统发育基因组学基于全叶绿体基因组序列,对23种椴树及2个外类群(滇桐Craigia yunnanensis W. W. Sm. W. E. Evans和Mortoniodendron anisophyllum (Standl.) Standl. Steyerm.)进行了系统发育重建。除全叶绿体基因组数据以外,还分别基于大单拷贝区(LSC)、小单拷贝区(SSC)、反向重复区(IR)、编码区(coding region)和非编码区(noncoding region)的序列构建了5组数据,并使用最大似然法(ML)和贝叶斯法(BI)构建系统树,结果与基于全叶绿体基因组序列分析得到的拓扑结构大体上一致,但后者在系统关系的解决程度和大部分节点的支持率上都有一定的提高。该属分为三个主要分支得到了极高的支持率。位于椴树属基部的Clade Ⅰ所揭示的种间系统关系同基于形态性状的经典分类和地理分布有明显的冲突,推断可能是杂交或不完全谱系分选导致的结果,然而对此问题的解释还需进一步的深入研究.CladeⅡ主要由分布于北美地区的椴树属植物组成,并与日本的T. kiusiana Shiras.互为姐妹群,再与我国华中地区的T.endochrysea Hand.-Mazz.形成姐妹群。Clade Ⅱ的单系性和系统发育关系得到了很高的支持,北美椴树的祖先与东亚分布的类群具有非常密切的亲缘关系,东亚-北美间断分布格局的成因还需寻找更多的证据。Clade Ⅲ可解析为10个亚分支,各个亚分支的单系性都得到强烈支持,其中欧洲的种类相对清晰,但东亚种类之间的关系未能解决。在基于叶绿体基因组重建的椴树属系统发育中,大部分的分支及亚分支存在种间关系与形态性状冲突的现象,一方面可能是由于该属频繁的杂交引起的基因渐渗或叶绿体捕获,另一方面该属也可能是一个经历了快速辐射进化的类群。椴树属的叶绿体全基因组序列虽然达162 kb,但分子进化速率低,系统发育信息位点少,这也是导致该属系统发育关系未能得到解决的原因之一。椴树属内种间的杂交、多倍化及辐射进化为澄清该属的系统发育关系带来了较大的挑战,利用叶绿体系统发育基因组学的手段构建了属内主要分支间的关系,初步形成了该属系统发育的框架,为今后对该属的深入研究奠定了基础。然而,要进一步解决该属种间的系统发育关系,澄清单系种的物种界定和杂交等问题,引入核基因数据是今后研究的必然选择。
[Abstract]:Tilia (Tilia L.) belonging to the Malvaceae (Malvaceae), including 23 species and 14 subspecies of genus Tilia. The main disjunct distribution in Europe to West Siberia and East Asian and North American temperate and subtropical areas. Most species in the genus Tilia is north temperate forest dominant tree species, has important ecological the function and economic value. Although Tilia inflorescence or infructescences with leaflike bracts large make it easily with other groups, but because of the lack of morphological classification traits effectively, and there is extensive hybridization and polyploidization events, species classification is very difficult. Because the rate of evolution of chloroplast gene fragment Tilia is very low, and the geographical distribution of species wide sampling difficulties, studies are not well resolved interspecific phylogenetic relationships of molecular phylogenetic evolution. To clarify the existing relationship of Tilia species is studied This is an important foundation for the evolution of history and modern geographical distribution pattern of the causes, but also for the genus Tilia and evolutionary biology related taxa, provide important information of biology and forest resources management and protection of comparative genomics and functional genomics research. For the first time, according to the results of the most recent taxonomic revision of the genus Tilia, through comprehensive sampling. The second generation sequencing technology Illumina completed 23 Tilia species and 50 individuals of the chloroplast genome determined by a variety of methods to construct a phylogenetic tree analysis on Tilia species phylogeny. In addition, the chloroplast genome of Tilia and its related taxa were compared. The main results are as follows: 1. Tilia and chloroplast genome related taxa comparative analysis of chloroplast genome of the genus Tilia having typical angiosperm chloroplast genome Four body structure, its size is 162250-163001 BP. Foodsaver and belong to Malvaceae Gossypium (Gossypium L.) (Theobroma L.) and Theobroma chloroplast genome in genome size, highly consistent genomic characteristics and structure of GC content. Foodsaver with 113 different genes encoding the same number, including 79 protein encoding genes, 30 tRNA genes and 4 rRNA genes, and all the genes sequence in the genome are consistent, the whole genome has a high degree of synteny. The chloroplast genome size of the genus Tilia is slightly larger than its relatives, is mainly the large single copy region (LSC) has a long fragment the non encoding region (100bp+) insertion / deletions caused. The difference of four kinds of plants in the genus Tilia (Tilia amurensis Rupr., T. mandshurica Maxim., T. oliveri Szyszyl., T. paucicostata Maxim.) based on Chloroplast The group found that the degree of genetic differentiation between sequences is very low, no mutation hotspots found throughout the genome. Although Tilia chloroplast genome contains less informative sites, but the reconstruction of the relationship between the four Linden phylogeny has chloroplast support.2. system is the high development of genomics linden tree full of chloroplast based on the genomic sequence, 23 kinds of Tilia and 2 outgroup (Craigia yunnanensis W. W. Sm. Craigia W. E. Evans and Mortoniodendron anisophyllum (Standl.) Standl. Steyerm.) by phylogenetic reconstruction. In addition to the chloroplast genome data are based on the large single copy region (LSC), a small single copy region (SSC), reverse repeat region (IR), encoding region (coding region) and non encoding region (noncoding region) sequence constructed 5 sets of data, and use the method of maximum likelihood (ML) and Bayesian method (BI) system The whole tree, and chloroplast genome sequence analysis based on the topological structure of the general consensus, but the latter in solving the relation degree of the system and most of the nodes on the support rate has improved to some extent. It is divided into three main branches have a high support rate. A system Clade is located in linden tree is based the Department I revealed there was a conflict with the classical classification and geographical distribution of morphological traits based on hybridization may be inferred or incomplete lineage sorting result, however, this problem still need to explain further in-depth study of.Clade II is mainly composed of distributed in North American plants of the genus Tilia, and T. in Japan kiusiana Shiras. is the sister group to form a sister group of.Clade and China's central region T.endochrysea Hand.-Mazz. single system development and system relations have very high support, North America Linden ancestors and East Asian distribution groups have very close genetic relationship, East Asia North America disjunct distribution pattern causes the need to look for more evidence of.Clade III can be resolved into 10 sub branches, sub branches of monophyly are strongly supported by the European species, the relationship between the East Asian species but failed to clear. Between the solution. Based on the reconstruction of the chloroplast genome of Tilia system development, there is relationship between species and morphological traits, most of the branches and sub branches of the conflict phenomenon, on the one hand may be caused by the frequent hybridization introgression or chloroplast capture, on the other hand, this genus may also be an experienced the rapid evolution of the radiation group. The whole genome sequence of Tilia chloroplast although up to 162 KB, but the rate of molecular evolution, phylogenetic information site less, which leads to the phylogenetic relationship One of the reasons to solve not been. Linden interspecific hybridization, the great challenge of polyploidization and radiation evolution system of the genus to clarify phylogenetic relationships, the development of genomics using chloroplast system means to construct relationship between main branches within the genus, the initial formation of the system development framework for the future. Research on the genus basis. However, to further solve the relationship between the development of the system between the species, clarify the monophyletic species definition and hybridization, introducing nuclear gene data is inevitable in future research.

【学位授予单位】：云南大学
【学位级别】：博士
【学位授予年份】：2016
【分类号】：Q943.2

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