桔梗亚科的分子系统发育和生物地理学研究 -兼论细胞器基因组编码区的替代速率模式与机制

	桔梗亚科的分子系统发育和生物地理学研究 -兼论细胞器基因组编码区的替代速率模式与机制
	李春姣
导师	李德铢
关键词	桔梗亚科，浅层测序技术，系统发育基因组学，核糖体 DNA，细胞器基因组，生物地理学，编码区，替代速率，突变速率 Campanuloideae, genome skimming, phylogenomics, nuclear ribosomal DNA, organelle genome, biogeography, coding region, substitution rate, mutation rate
摘要	1. 基于浅层测序技术构建了桔梗亚科植物的系统发育关系本研究选取代表桔梗亚科 3 大分支共 43 属 197 种 379 个个体进行基因组浅层测序。从取样类群的叶绿体基因组和线粒体基因组序列数据中分别提取出 72 个和 30 个编码基因序列数据，同时提取核糖体 DNA 序列，并基于最大似然法和贝叶斯分析法进行系统发育树的构建。研究结果表明，基于叶绿体基因组数据和不同的建树方法所得桔梗亚科系统发育关系一致性很高；众多深度节点较前人的研究得到了更好的解决。研究结果充分说明利用叶绿体基因组信息来解决该亚科内系统发育关系明显要优于片段。核糖体 DNA 序列含有较少的简约信息位点，系统发育树的深度节点支持率普遍较低，不同建树方法所得系统发育关系不一致。线粒体基因组构建的系统发育树，表明桔梗亚科线粒体基因组的进化存在异质性，异质性和长枝吸引，引发了系统发育树的一些假象。有趣的是，线粒体基因组数据能够有效的解析 Platycodinae 和 Wahlenberginae 分支内部的系统发育关系。2. 桔梗亚科的生物地理学研究基于叶绿体基因组和核糖体 DNA 联合矩阵构建的高分辨和高支持率的系统发育关系，并在桔梗亚科范围内扩大种级水平取样，以桔梗亚科 43 属共 531 种为研究材料，运用最大似然法构建了该亚科更加全面的系统发育框架。基于该框架，我们采用 BEAST 和 LAGRANGE 对桔梗亚科进行了分歧时间估算以及历史生物地理的重建。结果表明桔梗亚科起源于始新世早期，其三大分支先后于始新世中期至渐新世早期在非洲、欧洲和西亚南亚形成。桔梗亚科发生了大量的物种就地分化事件，伴有部分的扩散事件。在古气候、温度、地壳运动等多种因素的影响下，该亚科形成了现有的分布格局。 3. 桔梗亚科细胞器基因组编码区替代速率模式与机制研究我们选取桔梗亚科 37 个代表属，进行叶绿体基因组和线粒体基因组的替代速率分析。一般情况下，被子植物线粒体基因组进化速率较慢，其核苷酸替代速率比叶绿体基因组慢几倍。然而，桔梗亚科 Platycodinae 和 Wahlenberginae 分支中线粒体基因组的核苷酸替代速率异常加快。桔梗亚科不同分支的线粒体基因组的替代速率呈现出前所未有的异质性，这在被子植物中较为罕见。我们从不同分支中选取代表性物种进行 RNA 编辑位点的分析，结果发现快速进化的 Platycodinae 和 Wahlenberginae 分支中的线粒体基因组的 RNA 编辑位点少于 Campanulinae 分支的，RNA 编辑位点的减少可能是由于基因组水平上由 C 到 T 的转变。另外，快速进化分支的同义替代速率与密码子第三位碱基的 GC 含量呈正相关。因此，我们推测转录本介导的重组和 GC 偏好性的基因转换可能是 Platycodinae 和 Wahlenberginae 分支中线粒体基因组替代速率显著增加的主要原因。; 1. Phylogenetic relationships of Campanuloideae based on genome skimming technology In this study, 379 individuals from 43 genera and 197 species representing three clades of the Campanuloideae were selected for genome skimming. Seventy-two and thirty protein-coding genes were extracted from the plastid genomes and mitochondrial genomes of the sampled taxa, respectively, and the ribosomal DNA sequences were extracted at the same time. The phylogenetic tree was constructed based on the Maximum Likelihood and Bayesian analysis method. The results showed that the phylogenetic relationships of the Campanuloideae subfamily obtained based on the plastid genome and different tree-building methods were highly consistent. Many deep nodes had been better resolved compared with previous studies. The results demonstrated that the using plastid genome could resolve the phylogenetic relationships of this subfamily better than molecular fragments. The ribosomal DNA sequence contained less parsimonious information sites, the supported values of deep nodes were generally low, and the phylogenetic relationships obtained by different tree-building methods were inconsistent. The phylogenetic tree constructed by the mitochondrial genome showed that there was heterogeneity in the evolution of the mitochondrial genome of Campanuloideae. The heterogeneity and the attraction of long branches caused phylogenetic artifacts. Interestingly, the respective phylogeny of Platycodinae and Wahlenberginae could be well-resolved by using the mitochondrial genes. 2. Biogeographical research on Campanuloideae Based on the phylogenetic relationships with high resolution and high support inferred from the concatenated alignments of plastome and nuclear ribosomal DNA, plus more taxa sampling of Campanuloideae, we used the Maximum Likehood to reconstruct the phylogenetic topology including 43 genera and 531 species. We alsoused the BEAST and LAGRANGE to deduce the origin time of each genera and reconstruct the historical biogeography. Our results showed that Campanuloideae originated from the early Eocene. The three clades formed in Europe, Africa, and Western and Southern Asia from the middle Eocene to the early Oligocene. Numerous within-area speciation, accompanied by some dispersal events, occurred in the this group. The present distribution pattern of the subfamily was shaped by the influence of paleoclimate, temperature, crustal movement and other factors. 3. Research on the substitution rate pattern and related mechanisms of coding region of Campanuloideae organelle genome We selected 37 representative genera to analyze the substitution rates of the plastid genome and mitochondrial genome. In general, the mitochondrial genomes of angiosperms evolve at a slower rate, and their rate of nucleotide substitution is several times slower than that of the plastid genomes. However, the rates of nucleotide substitution in the Platycodinae and Wahlenberginae clades were significantly higher.
语种	中文
	2022-08
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/151853/75215
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	李春姣. 桔梗亚科的分子系统发育和生物地理学研究 -兼论细胞器基因组编码区的替代速率模式与机制[D]. 中国科学院大学,2022.

条目包含的文件
文件名称/大小	文献类型	版本类型	开放类型	使用许可
李春姣-李春姣88374320-14df（2839KB）	学位论文		限制开放	CC BY-NC-SA	请求全文