高山大黄属“温室植物”基因组的组装与注释

	高山大黄属“温室植物”基因组的组装与注释
	匡田辉
导师	孙航
关键词	高山，温室植物，基因组，组装，注释 Alpine, Greenhouse-Plant, Genome, Assembly, Annotation
摘要	青藏高原生物长期受低温、低氧、强紫外线辐射等极端的高原环境条件的影响，适应性进化出了诸多特殊的功能性状，来确保自身的生存和繁衍。虽然动物对青藏高原极端环境的适应机制已有报道，但是青藏高原植物特别是野生植物适应性基因组学机制的研究还十分匮乏。我们选取2种具有显著耐高寒和强紫外线辐射适应性状的高山“温室植物”作为研究对象，进行了全基因组的测序、组装和注释，为在组学层面解析其适应性机制提供基础。主要结果如下： 1) 塔黄(Rheum nobile)基因组组装大小为1.36Gbp，Contig N50为9.0Mbp，BUSCO评估值为93.6%；苞叶大黄(Rheum alexandrae)基因组组装大小为2.04Gbp，ContigN50为36.3Mbp，BUSCO评估值为94.1%。 2) 塔黄基因组注释基因共58950个，重复区域1002.07Mbp；苞叶大黄共注释基因61463个，重复区域1665.64Mbp。 3）塔黄和苞叶大黄基因组中Tekay、Althila、CRM以及Retand等LTR亚家族成员数远远多于戟叶酸模。塔黄和苞叶大黄基因组中IKeros和SIRE亚家族成员数远远少于戟叶酸模，甚至出现了Alesia亚家族的缺失。重复元件的种类在3个基因组中存在差别，这种重复元件的扩张或者丢失可能与其适应性相关。 4) 对重复元件的进化分析发现，相比于戟叶酸模基因组，塔黄和苞叶大黄基因组中LTR在基因附近区域存在富集现象，这可能是自然选择的结果。这些插入为塔黄和苞叶大黄适应高山环境提供了优势，可能是适应高山环境的一种的机制。 5) 对塔黄、苞叶大黄以及其他多个石竹目物种的基因家族分析显示，塔黄基因组中全部基因可聚类为54788个基因家族，苞叶大黄基因组中全部基因则可聚类为61463个基因家族。基于单拷贝基因构建系统发育树显示，塔黄和苞叶大黄聚为一个分支，并与荞麦属物种聚类。塔黄和苞叶大黄起源于8.809 Ma，这可能是适应青藏高原隆升所致。; Faced with extreme plateau environmental conditions such as low temperature, hypoxia, and strong ultraviolet radiation for a long time, the organisms on the Qinghai-Tibet Plateau (QTP) have adaptively evolved many special functional traits to ensure their own survival and reproduction. Although the adaptation mechanism of animals to the extreme environment of the QTP has been reported, the research on the adaptive genomics mechanism of QTP plants, especially wild plants, is still very scarce. We selected two alpine "greenhouse plants" with remarkable alpine tolerance and strong ultraviolet radiation adaptability as research objects, and sequenced, assembled and annotated their whole genomes, which provide a basis for further analyzing their adaptive mechanisms at the omics level. The main results are as follows: (1) We assembled genomes of these two species. For Rheum nobile, its genome size is about 1.36 Gbp and its Contig N50 size is about 9.0 Mpb. For R. alexandrae, its genome size is about 2.04 Gbp and its contig N50 is about 36.3 Mbp. We also programmed BUSCO assessment about assemblies of these two species. The BUSCO value of R. nobile and R. alexandrae are 93.6% and 94.1%, respectively. (2) The annotation results of R. nobile show that it has 58950 genes and its repeat regions size is about 1002.07 Mbp. R. alexandrae has 61463 genes and its repeats regions is about 1665.56 Mbp. (3) The numbers of LTR subfamily members such as Tekay, Althila, CRM and Retand in the genomes of R. nobile and R. alexandrae are far more than those of Rumex hastatus. The numbers of IKEros and SIRE subfamily members in the genomes of R. nobile and R. alexandrae are far less than those of Rumex hastatus, and even the deletion of the Alesia subfamily appeared. The types of repetitive elements differ among the three genomes, and the expansion or loss of repetitive elements may be related to their adaptability. (4) Based on the evolutionary analysis of repetitive elements, it was found that LTRs in the genomes of R. nobile and R. alexandrae have more members in the upstream and downstream of genes compared with the genomes of Rumex hastatus. The enrichment of LTRs in the regions near the genes may be the result of natural selection. These insertions provide advantages for the adaptation of R. nobile and R. alexandrae to the alpine environment. (5) We performed gene family analysis by combining R. nobile, R. alexandrae with some other species genome data. We identified 54788 and 61463 gene families in R. nobile and R. alexandrae, respectively. The construction of phylogenetic tree based on single-copy gene showed that R. nobile and R. alexandrae were clustered into one clade and clustered with Fagopyrum tataricum. R. nobile and R. alexandrae diverge in 8.809 Ma, which was likely caused by the uplift of the QTP.
语种	中文
	2022-05
学位授予单位	中国科学院大学
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/75139
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	匡田辉. 高山大黄属“温室植物”基因组的组装与注释[D]. 中国科学院大学,2022.

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