菥蓂基因组构建与逆转录转座基因研究

	菥蓂基因组构建与逆转录转座基因研究; Genome construction and analysis of retroduplicated genes of Thlaspi arvense
	胡彦婷
导师	章成君
摘要	Thlaspi arvense, a close relative of Arabidopsis thaliana, with practical values as food and medicine, is now becoming a potential economic crop to be developed. T. arvense has strong adaptability with worldwide distribution and can thrive from sea level to above 4000m elevation in the Qinghai-Tibet Plateau (QTP), China. Its strong adaptability renders it an ideal model system for studying plants adaptation in extreme environments. Transposable elements (TEs) are one of the most abundant repeats in plant genomes and are the major driving forces in genome and gene evolution because of their ability to provide an extraordinarily versatile source of genetic variation in plants. Retrotransposons can mediate the generation of new genes (retrogenes) through the retroduplication mechanism, as well as the amplification of retrotransposons can lead to genome enlargement, which are both driving forces of genome evolution. Although there have been several preliminary recognitions got from the perspectives of phylogeography and populations biology of the adaptability of T. arvense, how the T. arvense genome evolved and adapted at a genome molecular level is largely unknown. Combined with the analysis of retrotransposons，this study on how the dynamics of retrotransposon affect the adaptive evolution of the T. arvense genome will open new ideas for understanding the adaptability of plants survived in the harsh environment. Based on single-molecule long-read sequencing, optical mapping, and chromosome conformation capture technologies, we did genome sequencing and de novo assembly of T. arvense. After constructing contig, scaffold and pseudochromosomes, and rounds of polishing and gap filling, we reported a high-quality chromosome-scale T. arvense genome, with scaffolds N50 = 59.10 Mb. Genome comparison showed that the genome size of T. arvense (est. 486 Mb) was at least twice larger than that of close relatives, where they all share the same number of chromosomes (2n=14). A total of 36,556 protein-coding genes were annotated, and the plant genome was rich in repeats, especially the long terminal repeat (LTR) retrotransposon accounting for 56.94% of the genome. Using the same repeat sequence annotation method, the comparative genomic analysis showed that the T. arvense genome was characterized by the rich contents of LTR retrotransposons, and the LTR retrotransposons have been the most recently amplified in the T. arvense genome. LTR retrotransposon began to accumulate in the T. arvense genome about 5 million years ago (MYA) and reached its peak at about 0.2 MYA. In T. arvense genome, LTR retrotransposon's Gypsy superfamily is the most abundant retrotransposons, accounting for 51.55% of the plant genome. Phylogenetic reconstruction analysis showed that athila and crm families of the Gypsy superfamily played a major role in the amplification of retrotransposons in the genome. Analysis of phylogenetic trees showed that the T. arvense and E. salsugineum were close
	2021-11
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74604
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	胡彦婷. 菥蓂基因组构建与逆转录转座基因研究, Genome construction and analysis of retroduplicated genes of Thlaspi arvense[D],2021.

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
胡彦婷-论文最终上传版132829345（9999KB）	学位论文		限制开放	CC BY-NC-SA	请求全文