本文選題：椴樹屬　切入點：錦葵科　出處：《云南大學(xué)》2016年博士論文　論文類型：學(xué)位論文

【摘要】：椴樹屬(Tilia L.)隸屬于錦葵科(Malvaceae),包括了23個種和14個亞種。椴樹屬植物主要間斷分布于歐洲至西西伯利亞-東亞和北美洲的溫帶和亞熱帶地區(qū)。椴樹屬中大部分物種是北溫帶森林的優(yōu)勢樹種,具有重要的生態(tài)功能和經(jīng)濟價值。雖然椴樹屬的花序或果序上具大型的葉狀苞片使其很容易與其他類群區(qū)別,但因為缺乏有效的形態(tài)分類性狀,且存在廣泛的雜交和多倍化事件,屬內(nèi)種間的劃分存在很大困難。由于椴樹屬的葉綠體基因片段進化速率極低,且種類的地理分布較廣,取樣困難,現(xiàn)有的分子系統(tǒng)發(fā)育研究均未能很好解析種間的系統(tǒng)發(fā)育關(guān)系。厘清椴樹屬內(nèi)種間的演化關(guān)系是研究該屬進化歷史和現(xiàn)代地理分布格局成因的重要基礎(chǔ),同時也為椴樹屬及其近緣類群的進化生物學(xué)、保護生物學(xué)和林木資源管理比較基因組學(xué)和功能基因組學(xué)等研究提供重要信息。本研究首次根據(jù)椴樹屬最新的分類修訂結(jié)果,通過全面地取樣,利用第二代測序技術(shù)Illumina完成了椴樹屬23個種50個個體的葉綠體基因組測定,通過多種方法構(gòu)建了系統(tǒng)發(fā)育樹,分析探討了椴樹屬內(nèi)種間的系統(tǒng)發(fā)育關(guān)系。此外,還對椴樹屬及其近緣類群的葉綠體基因組進行了比較。主要研究結(jié)果如下：1.椴樹屬及其近緣類群的葉綠體基因組比較分析椴樹屬的葉綠體基因組具有被子植物葉綠體基因組典型的四分體結(jié)構(gòu),其大小在162,250-163,001 bp之間。椴樹屬與同屬錦葵科的棉屬(Gossypium L.)和可可屬(Theobroma L.)的葉綠體基因組在基因組大小、GC含量等基因組特征與結(jié)構(gòu)上高度一致。椴樹屬編碼著相同數(shù)目的113個不同的基因,包含79個蛋白質(zhì)編碼基因,30個tRNA基因和4個rRNA基因,且所有基因的排列順序在這些基因組中都保持一致,整個基因組具有高度的共線性。椴樹屬的葉綠體基因組大小比其近緣類群的略大,主要是大單拷貝區(qū)(LSC)的非編碼區(qū)中存在較長片段(100bp+)的插入/缺失造成的差異。對四種椴樹屬植物(Tilia amurensis Rupr., T. mandshurica Maxim., T. oliveri Szyszyl., T. paucicostata Maxim.)的葉綠體基因組比較發(fā)現(xiàn),種間序列的遺傳分化程度極低,在整個基因組中沒有發(fā)現(xiàn)變異熱點區(qū)。雖然椴樹屬葉綠體基因組包含的信息位點較少,但對四種椴樹系統(tǒng)發(fā)育關(guān)系的重建仍得到了較高的支持。2.椴樹屬的葉綠體系統(tǒng)發(fā)育基因組學(xué)基于全葉綠體基因組序列,對23種椴樹及2個外類群(滇桐Craigia yunnanensis W. W. Sm. W. E. Evans和Mortoniodendron anisophyllum (Standl.) Standl. Steyerm.)進行了系統(tǒng)發(fā)育重建。除全葉綠體基因組數(shù)據(jù)以外,還分別基于大單拷貝區(qū)(LSC)、小單拷貝區(qū)(SSC)、反向重復(fù)區(qū)(IR)、編碼區(qū)(coding region)和非編碼區(qū)(noncoding region)的序列構(gòu)建了5組數(shù)據(jù),并使用最大似然法(ML)和貝葉斯法(BI)構(gòu)建系統(tǒng)樹,結(jié)果與基于全葉綠體基因組序列分析得到的拓?fù)浣Y(jié)構(gòu)大體上一致,但后者在系統(tǒng)關(guān)系的解決程度和大部分節(jié)點的支持率上都有一定的提高。該屬分為三個主要分支得到了極高的支持率。位于椴樹屬基部的Clade Ⅰ所揭示的種間系統(tǒng)關(guān)系同基于形態(tài)性狀的經(jīng)典分類和地理分布有明顯的沖突,推斷可能是雜交或不完全譜系分選導(dǎo)致的結(jié)果,然而對此問題的解釋還需進一步的深入研究.CladeⅡ主要由分布于北美地區(qū)的椴樹屬植物組成,并與日本的T. kiusiana Shiras.互為姐妹群,再與我國華中地區(qū)的T.endochrysea Hand.-Mazz.形成姐妹群。Clade Ⅱ的單系性和系統(tǒng)發(fā)育關(guān)系得到了很高的支持,北美椴樹的祖先與東亞分布的類群具有非常密切的親緣關(guān)系,東亞-北美間斷分布格局的成因還需尋找更多的證據(jù)。Clade Ⅲ可解析為10個亞分支,各個亞分支的單系性都得到強烈支持,其中歐洲的種類相對清晰,但東亞種類之間的關(guān)系未能解決。在基于葉綠體基因組重建的椴樹屬系統(tǒng)發(fā)育中,大部分的分支及亞分支存在種間關(guān)系與形態(tài)性狀沖突的現(xiàn)象,一方面可能是由于該屬頻繁的雜交引起的基因漸滲或葉綠體捕獲,另一方面該屬也可能是一個經(jīng)歷了快速輻射進化的類群。椴樹屬的葉綠體全基因組序列雖然達162 kb,但分子進化速率低,系統(tǒng)發(fā)育信息位點少,這也是導(dǎo)致該屬系統(tǒng)發(fā)育關(guān)系未能得到解決的原因之一。椴樹屬內(nèi)種間的雜交、多倍化及輻射進化為澄清該屬的系統(tǒng)發(fā)育關(guān)系帶來了較大的挑戰(zhàn),利用葉綠體系統(tǒng)發(fā)育基因組學(xué)的手段構(gòu)建了屬內(nèi)主要分支間的關(guān)系,初步形成了該屬系統(tǒng)發(fā)育的框架,為今后對該屬的深入研究奠定了基礎(chǔ)。然而,要進一步解決該屬種間的系統(tǒng)發(fā)育關(guān)系,澄清單系種的物種界定和雜交等問題,引入核基因數(shù)據(jù)是今后研究的必然選擇。
[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.

【學(xué)位授予單位】：云南大學(xué)
【學(xué)位級別】：博士
【學(xué)位授予年份】：2016
【分類號】：Q943.2

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