木本竹基因组大小变异与演化研究

	木本竹基因组大小变异与演化研究; Variation and Evolution of Woody Bamboos Genome Size
	杨逸舟
导师	郭振华
摘要	Bambusoideae is one of the 12 subfamilies of Poaceae, with world wide distribution. It consists of three tribes, further divided into four lineages. Woody bamboos include temperate woody bamboos, neotropical woody bamboos and palaeotropical woody bamboos, allotetraploid or allohexaploid, which contain a complex evolutionary history. There are a large number of genome size variation events occurred in woody bamboos, which indicated by C value data published. Presumably, it's related to expansion of transposable elements (TEs), but lacks of specific analyses. As an important basic unit that can replicate and shift in genome autonomously, TEs have been proven to play an important role in evolution of genome like maize and wheat. Especially the Long terminal repeat retrotransposons (LTR-RTs), it’s considered to have an vital driving impact in evolution of genome size. This article is based on allohexaploid neotropical woody bamboos Bonia amplexicaulis draft genome, which has been published, further through Nanopore sequencing and Hi-C technology, obtained new chromosome-level reference genome of B.amplexicaulis. Comprehensive comparison and analysis with chromosome-level reference genome of Phyllostachys edulis, leading to deeper insight for the important role of TEs in the genome size variation of woody bamboos. Main conclusions are summarized as follows: 1. Reconstruction for evolutionary history with genome size of Bambusoideae Based on the C value data of each lineage of woody bamboos that we have obtained, and nuclear-genome internal transcribed spacer (ITS) sequences obtained based from genome skimming sequencing, and integrated with the results of fossil calibration time in TimeTree website, we reconstructed the evolutionary history of genome size within Bambusoideae finally. What's more, brownian motion models used for calculated the rates of genome size variation of ancestral branches. We found that allotetraploid temperate woody bamboos branches has a faster rate of genome size expansion than other branches, which combined with the visualization results of the Phytools R package. Contrarily, the allohexaploid palaeotropical woody bamboos branches reveals a shrinking trend. 2. Obtain and evaluation for genome of B.amplexicaulis We implemented Nanopore long-read sequencing and Hi-C technology, obtained chromosome-level genome of B.amplexicaulis. The genome was assembled into 35 chromosomes with N50 of 2.70 Mb and a total length of 850.41Mb, and 98.93% sequences are anchored to chromosomes. Different evaluations have shown that the quality of assembly obtained by Nanopore sequencing has been improved significantly compared with previous version. The Assembly results satisfied with standards of high-quality genome. 3. Annotation and comparison of TEs Completed de novo annotation and statistical analysis has been finished with EDTA pipeline for two versions of B.amplexicaulisgenome and P.edulis genome. The result
	2021-05
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74570
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	杨逸舟. 木本竹基因组大小变异与演化研究, Variation and Evolution of Woody Bamboos Genome Size[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
杨逸舟-硕士毕业论文（国科大版）47b1（2957KB）	学位论文		限制开放	CC BY-NC-SA	请求全文