基于浅层基因组数据的核心十字花科系统发育基因组学研究

	基于浅层基因组数据的核心十字花科系统发育基因组学研究; Resolving Robust Phylogenomics of Core Brassicaceae Using Genome Skimming Data
	刘良敏
导师	李德铢
摘要	Brassicaceae (or Cruciferae) is consist of ca. 3,977 species in 351 genera, it has traditionally been known as a natural group, which is an economically and scientifically important family globally distributed, including oilseed rape and the model plant, Arabidopsis thaliana. Much molecular data have been used in phylogenetic studies, and as a result, the number of tribes in the family had been expanded to 52 tribes. However, the relationships among major clades and tribes of Brassicaceae are still controversial due to the complex evolutionary history and the fact that previous studies were based on either incomplete taxon sampling or sequence data. With the development of sequencing technologies and decline of sequencing cost, the complete plastomes are increasingly used for phylogenetic analyses, obtained from genome skimming sequencing through multiple types of molecular materials. Here, we focus on reconstructing the phylogenetic relationships within core Brassicaceae based on complete plastid genomes and nrDNA sequences (18S-26S), and analyses of genome size evolution were further explored. Main conclusions are summarized as the following: 1. Phylogenetic relationships among the core Brassicaceae Our framework of core Brassicaceae represented the most comprehensive sampling and the best resolved framework to date, in which many intertribal relationships were clarified with strong support. We investigated the core Brassicaceae phylogenetics using 222 plastomes from 201 taxa, including 106 plastomes assembled from newly sequenced genome skimming data. The sampling represented 71 genera from 61.5% tribes and four unassigned species, as well as three species from the basal Aethionemeae as outgroups. Phylogenies reconstructed from four plastid datasets under different partitions and tree inference strategies are consistent with the circumscriptions of core Brassicaceae, in which three well-supported lineages Ⅰ, Ⅱ and Ⅲ (abbreviated as LI, LII, and LIII thereafter) were revealed, with LⅠ sister to LⅡ + LⅢ. Of these, LⅠ includes 13 tribes and 2 species unassigned to any tribe, the LⅡ comprises 11 tribes and two unassigned species (Conringia planisiliqua and Schrenkiella parvula), and the LⅢ consists of seven tribes. In this study, largely congruent topologies and long-controversial deep relationships were well-resolved with strong statistical support. For example, the monophyly of the newly delimitated LⅡ was strongly supported by three different partition strategies, concatenated versus coalescent methods under Bayesian and Maximum likelihood analyses. This lineage comprised 11 tribes, including four tribes previously unassigned to any lineage, i.e., Biscutelleae was the earliest diverging clade, and Cochlearieae was sister to Megacarpaeeae + Anastaticeae. Within LⅡ, the inter-tribal relationships were also well-resolved, except that conflicting position of Orychophragmus was detected among different datasets. In LⅢ, Shehbazia was resolved as a m
	2020-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74155
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	刘良敏. 基于浅层基因组数据的核心十字花科系统发育基因组学研究, Resolving Robust Phylogenomics of Core Brassicaceae Using Genome Skimming Data[D],2020.

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