两种五加科植物的叶绿体全基因组研究及其系统发育分析

发布时间：2018-06-16 04:24

本文选题：叶绿体全基因组 + 五加科　；参考：《浙江大学》2017年硕士论文

【摘要】：叶绿体是一个重要的细胞器,起源于古细菌入侵真核细胞的内共生事件,在植物光合作用中扮演了生物合成工厂的重要角色,叶绿体DNA(chloroplastDNA,cpDNA)的保守性及它的低碱基替换率则让它适用并广泛运用于植物的系统发育研究中。八角金盘(Fatsia japonica(Thunb.)Decne.et Planch.)和天胡荽(Hydrocotyle sibthorpioides Lam.)这两种五加科植物,有潜在药用价值或者本身是传统中草药,同时都具有优良的园艺价值。对其叶绿体基因组的研究可以有效补充植物界叶绿体基因组数据库,也有利于该植物相关研究以及五加科内部的属间关系研究等。本论文首次报道了这两种植物的叶绿体基因组全长序列,并基于此进行了叶绿体比较基因组学的分析和系统发育分析,取得结果如下:(1)八角金盘和天胡荽的叶绿体基因组长度分别为155,613bp和152,880bp,均具有典型的四分结构:大单拷贝区(large single-copy region,LSC)和小单拷贝区(small single-copy region,SSC)被一对反向重复区(inverted repeat,IR)分开;基因的顺序及内容与已发表的五加科植物叶绿体基因组相似。本论文也对其重复序列、简单重复序列(simple sequence repeat,SSR)、密码子使用偏性等进行了分析,为该植物的相关研究提供了基础。(2)两个叶绿体基因组的基本特征如各区域长度、GC含量、基因的组成与分布等与其他五加科植物具有相似性,同时体现了一定的个体差异,特别地,天胡荽(H.sibthorpioides)中的基因ycf15是假基因。遗传距离分析结果表现了不同植物间的差异,同时也明显地表现出群体划分倾向。(3)本论文基于22种伞形目植物叶绿体基因组中7种不同数据集和三种方法构建了系统进化树,进行了系统发育分析。结果表明天胡荽属以100%的支持率被归于五加科中,被认为位于五加科植物进化过程中的基底部,与本研究中其他五加科植物构成的"中心五加科"分支构成姐妹关系;八角金盘位于五加科AsianPalmate种团中,并被推测位于五加科的进化拓扑结构的较远端,与刺楸(Kalopanax septemlobus)和梁王茶(Metapanaxdelavayi)组成的小分支构成姐妹关系;AsianPalmate种团中的系统发育关系倾向于(((((K.septemlobus+M.delavayi)+F.japonica)+(E.senticosus+ B.hainla))+Dendropana)+ S.delavayi)。研究结果充实了整个植物界的叶绿体基因组数据库,丰富了药用植物或具有潜在药用价值植物的全基因组数据库;基于叶绿体基因组全长序列构建的系统进化树,对于目前五加科内样本数较少、属间水平上结论有限等的情况可以提供更多的系统发育数据,不同数据集进行系统进化分析的结果对以后尤其是科以下水平进化研究中的数据集的选择也具有重要的参考价值。
[Abstract]:Chloroplast is an important organelle, originated from the endosymbiosis of eukaryotic cells invaded by ancient bacteria, and plays an important role in the biosynthesis factory in plant photosynthesis. The conservation of chloroplastDNA and its low base replacement rate make it suitable and widely used in phylogenetic studies of plants. Fatsia japonicaus Thunb. Decne.et Planch.) ) Hydrocotyle sibthorpioides Lam.) These two species of Acanthopanaceae have potential medicinal value or traditional Chinese herbal medicine, and both have good horticultural value. The study of chloroplast genome can complement the chloroplast genome database of the plant and be helpful to the study of the plant and the intergeneric relationship within the family Acanthopanaceae and so on. In this paper, the full-length chloroplast genome sequences of the two plants were first reported, and based on this, the chloroplast comparative genomics and phylogenetic analysis were carried out. The results were as follows: (1) the chloroplast genome length of Acanthus and coriander were 155613bp and 152880bprespectively, with typical quaternary structure: large single-copy region LSCs and small single-copy regions SSCs were separated by a pair of reverse repeats inverted repeat IRs; The sequence and content of the genes are similar to the chloroplast genomes of the reported Acanthopanaceae plants. In this paper, the repeat sequence, simple sequence repeats, codon usage bias and so on were also analyzed, which provided the basis for the study of the plant. The basic characteristics of the two chloroplast genomes, such as the length of each region, GC content, were also analyzed. The composition and distribution of the genes were similar to those of other plants in the family Acanthopanaceae, and showed certain individual differences. In particular, the gene ycf15 in H. sibthorpioides was a pseudogene. The results of genetic distance analysis showed the difference among different plants and the tendency of population division.) in this paper, the phylogenetic tree was constructed based on 7 different data sets and 3 methods in chloroplast genome of 22 Umbellifera species. Phylogenetic analysis was carried out. The results showed that the genus coriander was attributed to the family Acanthaceae with 100% approval rate and was considered to be located at the base of the evolution process of the family Acanthaceae. The anise is located in the Asian Palmate colony of the Acanthaceae, and is presumed to be located at the far end of the evolutionary topology of the Acanthaceae. The phylogenetic relationship in Asian Palmate, which is composed of small branches of Kalopanax septemlobus and Metapanax delavayi), tends to be the same as that of K. septemlobus M. delavayi (F. japonica), E. senticosus B. hainlaa) Dendropana) S. delavayiana. The results enrich the chloroplast genome database of the whole plant world, the whole genome database of medicinal plants or plants with potential medicinal value, and the phylogenetic tree based on the full-length sequence of chloroplast genome. More phylogenetic data can be provided for the current situation where there are fewer samples and limited conclusions at the intergeneric level. The results of phylogenetic analysis of different data sets also have important reference value for the selection of data sets in the later evolutionary studies, especially at the level below the family level.
【学位授予单位】：浙江大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q943.2

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