保护基因组学方法在蒜头果物种保护中的应用

	保护基因组学方法在蒜头果物种保护中的应用; Application of conservation genomics approach to the conservation of Malania oleifera
	姚刚
导师	马永鹏
摘要	The sixth great extinction of species is now underway, making conservation actions to save endangered species globally urgent, and population-level conservation genomics research is and will continue to provide the necessary scientific basis and strong support for conservation actions. As of October 31, 2021, the published genomes of threatened angiosperms represent less than 5% of the currently published angiosperm genomes. Progress in genomic studies of Plant species with extremely small populations(PSESP) has been very slow, which has severely hampered conservation genomics research and limited the science of conservation practice. In this paper, the genome quality of Malania oleifera, a Plant species with extremely small populations with important economic value, was firstly improved based on high-throughput chromosome conformation capture (Hi-C). At the same time, the whole genome resequencing and the application of conservation genomics methods covering 165 samples from 17 populations in the whole range of M. oleifera were used as a reference genome to analyze the formation and maintenance mechanisms of "small populations" of M. oleifera and to provide a reference for the effective formulation of conservation strategies for garlic nuts. The main results and conclusions of this paper are as follows. (1) After several attempts and explorations, high-purity DNA large fragments were obtained from yellowing Malania oleifera leaves, and the quality of the previous reference genome sketch was enhanced with the help of chromosome high-throughput capture technology and third-generation single-molecule sequencing technology, and the results showed that the new version of the genome was significantly improved in both completeness and accuracy. Among them, Contig N50 increased from 1.2 Mb to 4.9 Mb, Scaffold N50 increased from 4.6 Mb to 112.6 Mb, the number of gaps in the genome decreased from 1710 to 514, and the sequence mount rate reached 98.2%. (2) The M. oleifera originated in the late Cretaceous (-87.85 million years), corrected by 1.1 million years compared to previous results; it is the result of no new paleopolyploidization events in recent history. (3) The main results of conservation genomics are as follows: (i) Whole-genome resequencing of 165 samples and a series of conservation genomics analyses identified 43413408 genome-wide variants, which were filtered for downstream analysis including 250362 SNPs. (ii) the highest population polymorphism was in the BM1 (π=0.00656) and ND (π=0.00568) populations and the lowest was in the JM (π=0.00211) and NP (π=0.00206) populations, and the DX population was the most differentiated from the other populations, and the Mantel test for geographic distance and genetic differentiation coefficient indicated that as geographic distance increased, the more distant the genetic relationship . (iii) The population structure was analyzed using three methods and three types of loci, and the results showed that th
	2021-11
文献类型	学位论文
条目标识符	http://ir.kib.ac.cn/handle/151853/74501
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	姚刚. 保护基因组学方法在蒜头果物种保护中的应用, Application of conservation genomics approach to the conservation of Malania oleifera[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
姚刚-2021-11-30保护基因组学方（4349KB）	学位论文		限制开放	CC BY-NC-SA	请求全文