多重基因组学数据在草莓属种间关系鉴别中的应用

	多重基因组学数据在草莓属种间关系鉴别中的应用; The Application of Multiple Genomics Data in the Identification of Fragaria Interspecific Relationships
	贾乔雅
导师	章成君，朱安丹
摘要	The genus Fragaria belongs to the family Rosaceae (Rosoideae subfamily) , and they are the perennial evergreen plants with high economic value in horticulture. Hybridization and polyploidization events have great impacts on the speciation and diversification of Fragaria species. However, the early molecular techniques for evaluation the interspecific relationships of Fragaria are mainly based on the limited chloroplast genes and a few nuclear genes, resulting in less informative sites and limited resolution , making it difficult to identify the phylogenetic relationships from different ploidy species with Fragaria. Benefit from the development of the high-throughput sequencing technologies, it is feasible to obtain data from different genomic sources, optimize the technical evaluation scheme, and apply it to a more accurate identification among the species in a single genus. This study aims to construct the reliable phylogenetic relationships among Fragaria by establishing the molecular evaluation systems from three data sets: chloroplast genomes, mitochondrial protein-coding genes and nuclear single copy genes . This research developed a framework for comparative analysis based on multiple genomic data, and thereby identified the interspecies relationships of the Fragaria. The main results are as follows: 1. Acquisition and analysis of multi-genomic data We collected and sequenced 18 species covering more than 85% of all species in the genus Fragaria, and used Novoplasty and other bioinformatic softwares to assemble and annotate the mitochondrial and chloroplast genomes of all the 31 individuals, generating 31 complete chloroplast genomes, 15 complete mitochondrial genomes and 16 mitochondrial draft genomes. All the protein coding genes from chloroplast genomes and mitochondria genomes were annotated. Moreover, a total of 92 nuclear single copy genes were selected according to the genomic data from three diploid Fragaria species and the transcriptomic data from 15 Fragaria species. 2. Establishment of a molecular evaluation system based on multi-genomic data and its application in the identification of phylogenetic relationships within Fragaria Statistical models such as maximum likelihood (ML) were used to construct phylogenies based on the 156 kb chloroplast genomes, 30 mitochondrial protein coding genes, and 92 nuclear single-copy genes. Based on the bootstrap value, all ploidy, diploid and tetraploid, diploid and octoploid data were used to analyze the relationship between the species in Fragaria, and a more reliable analysis system was established. By comparing the advantages and disadvantages of the different sources of genomic data and the consistency of the phylogenetic trees of different data sets, we preliminary analyzed the relationship within Fragaria: (1) Fragaria is roughly divided into three branches, named the vesca clade (A clade), the Fragaria iinumae clade (B clade) and the Chinese clade (C clade); (2) In the Chinese clade
	2020-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74136
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	贾乔雅. 多重基因组学数据在草莓属种间关系鉴别中的应用, The Application of Multiple Genomics Data in the Identification of Fragaria Interspecific Relationships[D],2020.

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