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| 基于转录组数据的蔷薇类和天南星科系统发育基因组学研究; Phylogenomics of Rosids and Araceae Using Transcriptome Data | |
| 赵磊 | |
| Thesis Advisor | 李德铢，伊廷双 |
| Abstract | Phylogenomics is a new cross-discipline between phylogenetics and genomics, which applies large-scale genomic data to resolve phylogenetic relationships, and infer the function of DNA or protein sequences based on the built phylogenetic framework to deeply understand scientific issues such as the mechanism of molecular evolution. The genomic datasets are from plastome, mitochondrial genome and nuclear genome. Phylogenetic studies on plastid and mitochondrial gene loci or genomes have played an important role in resolving relationships at different taxonomic levels. However, plastome and mitochondrial genomes are generally uniparental inheritance, and are accompanied by horizontal gene transfer in some cases. In recent years, the cost of high-throughput sequencing has been greatly reduced, which provides a good opportunity for us to use genomic and transcriptome sequences to study phylogenetic relationships. The main purpose of the study is to explore the applications of transcriptome data to resolve some controversial phylogenetic relationships in Rosids and Araceae, and address the diversification of major lineages of Araceae based on the newly-built phylogenetic framework. The main results are as follows: 1. Phylogenomics of Rosids Rosids are one of two major lineages of eudicots, which contain 17 orders, 140 families and ca. 70,000 species. Here, we employed nuclear sequences from 36 nuclear genomes and 27 transcriptomes (one newly sequenced) to address the phylogenetic relationships of rosids. Using coalescence and concatenation methods, phylogenetic analyses of 891 single or low copy orthologous genes from 63 species representing 14 orders produced similar topologies except the placement of Zygophyllales. Through comprehensive analyses, we found that missing data and gene tree heterogeneity were potential reasons for the conflicting results. Phylogenetic analysis using concatenation method could produce wrong topology in case of large missing data and high gene tree heterogeneity. Our results provide new insights into the rosid relationships: the Myrtales-Geraniales clade is sister to the remaining orders within the rosids; Zygophyllales is the basal to an “expanded” malvid clade; the COM clade is not monophyletic, which belongs to malvids instead of fabids; fabids only include the nitrogen-fixing clade that further resolved into the Fabales-Fagales clade, and the Rosales-Cucurbitales clade. Overall, our phylogenomic analyses provide valuable insights into the phylogenetic relationship of rosids, and suggest that coalescence methods, e.g., ASTRAL-II, are more efficient than concatenation methods in dealing with the problem of large amount of missing data and high gene tree heterogeneity. 2. Phylogenomics and Diversification of Araceae Polyploidy, or whole genome duplication (WGD) and shift of sexual systems are widely regarded as key innovations promoting plant diversification. However, the hypotheses are still very controversial as the case |
| 2020-08 | |
| Document Type | 学位论文 |
| Identifier | http://ir.kib.ac.cn/handle/151853/74222 |
| Collection | 昆明植物所硕博研究生毕业学位论文 |
| Recommended Citation GB/T 7714 | 赵磊. 基于转录组数据的蔷薇类和天南星科系统发育基因组学研究, Phylogenomics of Rosids and Araceae Using Transcriptome Data[D],2020. |
| Files in This Item: | ||||||
| File Name/Size | DocType | Version | Access | License | ||
| 赵磊-赵磊 博士毕业论文 正版4e7ad（7010KB） | 学位论文 | 限制开放 | CC BY-NC-SA | Application Full Text | ||
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