花生基因组中重复基因间基因置换的比较分析

发布时间：2019-03-17 21:42

【摘要】：花生是主要的油料和经济作物,由于其重要的经济价值,因此深入研究花生基因组结构进化与演变,具有重要的科研价值和经济意义。花生两个二倍体祖先野生种(A.duranensis和A.ipaensis)的基因测序工作完成,为花生重复基因间基因置换研究提供了基因组数据材料。课题研究以重要豆科模式植物苜蓿为外类群,对花生的两个祖先物种进行了系统的全基因组比较分析,基于同源染色体片段的基因同源共线性,统计推断了花生基因组内由多倍化事件所产生重复基因的规模,其中苜蓿12.2%(7286),花生A14.4%(5167),花生B 12.5%(5202);同时研究中对基因组间的同源关系进行了细致的相似性结构分析,构建了以苜蓿为参考,与多倍化相关的多次级基因比对列表。研究发现,加倍后物种基因内重复基因丢失是一个随机的过程,近似服从几何分布。突出地,课题研究中结合系统发育和非参数bootstrap方法建立了推断重复基因置换算法,并利用Perl、Bioperl语言集成Clustalw和PAML,实现了物种全基因组重复基因间的基因置换推断。推断结果显示,花生A基因组中有2.8%(135个),花生B基因组中有2.6%(147个)重复基因在进化过程中发生了基因置换。统计分析发现,靠近染色体端粒位置的重复基因对间更容易发生基因置换;基因置换可能更偏向于某些功能基因。课题中所建立的方法和流程能够使用于对其它物种基因组多倍化过程,及同源染色体片段间的遗传重组的探索研究,具有良好的推广性;研究产生的结果对花生基因组相关领域研究具有理论支撑作用。
[Abstract]:Peanut is a major oil and economic crop. Because of its important economic value, it is of great scientific and economic significance to study the evolution and evolution of peanut genome structure in depth. The gene sequencing of two diploid ancestor species (A.duranensis and A.ipaensis) of peanut has been completed, which provides the genomic data for the study of gene replacement between duplicated genes in peanut (Arachis hypogaea L.). In this study, alfalfa, an important leguminous model plant, was used as an outsider group to compare and analyze the whole genomes of two ancestor species of peanut, and the homologous collinearity of genes based on homologous chromosome fragments was carried out. The size of repeated genes produced by polyploidy events in peanut genome was estimated statistically, including 12.2% (7286) of alfalfa, 14.4% (5167) of peanut A and 12.5% (5202) of peanut B; At the same time, the similarity structure of homologous relationships among genomes was analyzed in detail, and a multi-level comparison list of genes related to polyploidy was constructed, which was referred to as alfalfa. It is found that the loss of repeated genes after doubling is a random process and approximately obeys geometric distribution. The inferred repeat gene replacement algorithm was established by combining phylogenetic and nonparametric bootstrap methods, and the complete genome-wide repeat gene replacement inference was realized by integrating Clustalw and PAML, with Perl,Bioperl language. The results showed that 2.8% (135) of peanut A and 2.6% (147) repeat genes of peanut B genome had been replaced during evolution. Statistical analysis showed that repeat gene pairs close to the telomere position of chromosome were more likely to occur gene replacement, and gene replacement might be more inclined to some functional genes. The methods and processes established in this paper can be used in the study of genome polyploidy of other species and genetic recombination among homologous chromosome fragments, which has a good generalization. The results of this study have a theoretical support for peanut genome-related research.
【学位授予单位】：华北理工大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S565.2;Q943.2

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