猕猴桃属叶绿体基因组进化及其系统发育关系重建
发布时间：2018-10-29 09:47
【摘要】：猕猴桃属植物存在普遍的杂交渐渗现象,其属下分类一直以来都存在争议,因此,该属植物的系统发育关系有待于进一步揭示。随着测序技术的快速发展,叶绿体基因组被广泛用于植物物种的系统发育关系研究。相较于编码区而言,叶绿体基因组非编码区序列更有利于解析低分类阶元植物物种系统发育关系。为获得更多猕猴桃叶绿体基因组相关数据,本研究对毛花猕猴桃(Actinidia eriantha)、软枣猕猴桃(Actinidiaarguta)和狗枣猕猴桃(Actinidiakolomikta)进行了叶绿体全基因组的测定与注释。分析与比较了已经测得的九个猕猴桃属植物叶绿体基因组结构,同时通过比对寻找叶绿体基因间隔区变异位点,开发了叶绿体基因间隔区内具有多态性位点的分子标记,对猕猴桃属植物属内系统发育关系进行重建。主要研究结果如下:(1)毛花猕猴桃、软枣猕猴桃和狗枣猕猴桃叶绿体基因组均为环状双链DNA,总长度在156,484-157,425bp之间,有典型的4个区域:一对反向重复区长度在23,892-24,226bp之间,大的单拷贝区域长度在88,093-88,639bp之间,小的单拷贝区域长度在20,475-20,579bp之间。三个基因组均编码113个不同的基因,包括79个蛋白编码基因,30个tRNA基因和4个rRNA基因,其中有16个基因在重复区有一个拷贝,一个基因(trnfM-CAU)在大的单拷贝区域有一个拷贝。毛花猕猴桃、软枣猕猴桃和狗枣猕猴桃三个叶绿体基因组中包含的重复序列总数目依次为39、25、33;软枣猕猴桃叶绿体基因组的重复序列中不存在60bp以下的重复序列。使用位点模型检测到ycf2,accD和一个遗传系统基因rpl20在猕猴桃的进化过程中经历了正选择作用。(2)利用mVISTA对叶绿体基因组序列一致性差异进行比较分析,共检测到24个基因间隔区序列存在较大差异。选择其中4个基因间隔区区间:rps16-trnQ(UUG)、ndhC-trnV(UAC)、ndhF-rpl32 和 trnE(UUC)-trnT(GGU)进行引物设计,用于猕猴桃属植物的系统发育关系重建。研究结果显示四个基因间隔区的序列更好地揭示了猕猴桃系统发育关系;除了支持净果组作为一个独立进化分支外,其他3个组(斑果组、星毛组和糙毛组)都不成单系;现有的猕猴桃分类系统有待于进一步完善。
[Abstract]:There is a general phenomenon of hybrid infiltration in Actinidia, and the classification of Actinidia has always been controversial. Therefore, the phylogenetic relationship of Actinidia needs to be further revealed. With the rapid development of sequencing, chloroplast genome is widely used to study phylogenetic relationship of plant species. Compared with the coding region, the sequence of chloroplast genome noncoding region is more favorable to the phylogenetic relationship of plant species with low taxonomic order. In order to obtain more relevant data of chloroplast genome of Actinidia chinensis, the whole chloroplast genome of Actinidia (Actinidia eriantha), soft date kiwifruit (Actinidiaarguta) and dog jujube kiwifruit (Actinidiakolomikta) were determined and annotated in this study. The chloroplast genome structure of nine kiwifruit plants was analyzed and compared. At the same time, a molecular marker with polymorphic loci in chloroplast spacer region was developed by comparing and searching for variation sites in chloroplast spacer region. The phylogenetic relationship of genus Actinidia was reconstructed. The main results were as follows: (1) the chloroplast genomes of Actinidia chinensis, Actinidia chinensis and Actinidia angustifolia were all circular double-stranded DNA, with total length of 156484-157425bp. There are four typical regions: the length of a pair of reverse repeat regions is between 23892-24226bp, the length of large single copy region is between 88093-88639bp, and the length of small single copy region is between 20475-20579bp. The three genomes all encode 113 different genes, including 79 protein coding genes, 30 tRNA genes and 4 rRNA genes, 16 of which have a copy in the repeat region. A gene (trnfM-CAU) has a copy in a large single copy region. The total number of repeats contained in the chloroplast genomes of Actinidia deliciosa, Actinidia chinensis and Actinidia angustifolia was 390.2533, and the repeat sequence of Actinidia chinensis chloroplast genome did not contain the repeat sequence below 60bp. The site model was used to detect the positive selection of ycf2,accD and a genetic system gene rpl20 in the evolution of kiwifruit. (2) the difference of chloroplast genome sequence consistency was analyzed by mVISTA. A total of 24 gene spacer sequences were detected. Rps16-trnQ (UUG), ndhC-trnV (UAC), ndhF-rpl32 and trnE (UUC)-trnT (GGU) were selected for primer design to reconstruct phylogenetic relationship of Actinidia. The results showed that the sequence of the four spacers better revealed the phylogenetic relationship of kiwifruit, except for supporting the net fruit group as an independent evolutionary branch, none of the other three groups (fruiting group, stellate group and strigose group) were single. The existing kiwifruit classification system needs to be further improved.
【学位授予单位】：中国科学院武汉植物园
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q943.2
本文编号：2297351
[Abstract]:There is a general phenomenon of hybrid infiltration in Actinidia, and the classification of Actinidia has always been controversial. Therefore, the phylogenetic relationship of Actinidia needs to be further revealed. With the rapid development of sequencing, chloroplast genome is widely used to study phylogenetic relationship of plant species. Compared with the coding region, the sequence of chloroplast genome noncoding region is more favorable to the phylogenetic relationship of plant species with low taxonomic order. In order to obtain more relevant data of chloroplast genome of Actinidia chinensis, the whole chloroplast genome of Actinidia (Actinidia eriantha), soft date kiwifruit (Actinidiaarguta) and dog jujube kiwifruit (Actinidiakolomikta) were determined and annotated in this study. The chloroplast genome structure of nine kiwifruit plants was analyzed and compared. At the same time, a molecular marker with polymorphic loci in chloroplast spacer region was developed by comparing and searching for variation sites in chloroplast spacer region. The phylogenetic relationship of genus Actinidia was reconstructed. The main results were as follows: (1) the chloroplast genomes of Actinidia chinensis, Actinidia chinensis and Actinidia angustifolia were all circular double-stranded DNA, with total length of 156484-157425bp. There are four typical regions: the length of a pair of reverse repeat regions is between 23892-24226bp, the length of large single copy region is between 88093-88639bp, and the length of small single copy region is between 20475-20579bp. The three genomes all encode 113 different genes, including 79 protein coding genes, 30 tRNA genes and 4 rRNA genes, 16 of which have a copy in the repeat region. A gene (trnfM-CAU) has a copy in a large single copy region. The total number of repeats contained in the chloroplast genomes of Actinidia deliciosa, Actinidia chinensis and Actinidia angustifolia was 390.2533, and the repeat sequence of Actinidia chinensis chloroplast genome did not contain the repeat sequence below 60bp. The site model was used to detect the positive selection of ycf2,accD and a genetic system gene rpl20 in the evolution of kiwifruit. (2) the difference of chloroplast genome sequence consistency was analyzed by mVISTA. A total of 24 gene spacer sequences were detected. Rps16-trnQ (UUG), ndhC-trnV (UAC), ndhF-rpl32 and trnE (UUC)-trnT (GGU) were selected for primer design to reconstruct phylogenetic relationship of Actinidia. The results showed that the sequence of the four spacers better revealed the phylogenetic relationship of kiwifruit, except for supporting the net fruit group as an independent evolutionary branch, none of the other three groups (fruiting group, stellate group and strigose group) were single. The existing kiwifruit classification system needs to be further improved.
【学位授予单位】：中国科学院武汉植物园
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q943.2
【参考文献】
相关期刊论文 前8条
1 杨丽;赵韩生;彭镇华;董丽莉;高志民;;竹子叶绿体基因组SSR分子标记的开发及其应用[J];热带亚热带植物学报;2014年03期
2 王博;高磊;苏应娟;王艇;;基于叶绿体基因组全序列分析真叶植物叶绿体基因的适应性进化[J];中山大学学报(自然科学版);2012年03期
3 黄宏文;;猕猴桃驯化改良百年启示及天然居群遗传渐渗的基因发掘[J];植物学报;2009年02期
4 姜正旺,王圣梅,张忠慧,黄宏文;猕猴桃属花粉形态及其系统学意义[J];植物分类学报;2004年03期
5 徐小彪,张秋明;中国猕猴桃种质资源的研究与利用[J];植物学通报;2003年06期
6 何子灿,钟扬,刘洪涛,唐先华,叶力,黄德世,徐立铭;中国猕猴桃属植物叶表皮毛微形态特征及数量分类分析[J];植物分类学报;2000年02期
7 梁畴芬;论猕猴桃属植物的分布[J];广西植物;1983年04期
8 梁畴芬;猕猴桃属新的分类群[J];广西植物;1982年01期
，本文编号：2297351
本文链接：https://www.wllwen.com/shoufeilunwen/benkebiyelunwen/2297351.html
