【摘要】：花生是主要的油料和經(jīng)濟(jì)作物,由于其重要的經(jīng)濟(jì)價(jià)值,因此深入研究花生基因組結(jié)構(gòu)進(jìn)化與演變,具有重要的科研價(jià)值和經(jīng)濟(jì)意義。花生兩個(gè)二倍體祖先野生種(A.duranensis和A.ipaensis)的基因測(cè)序工作完成,為花生重復(fù)基因間基因置換研究提供了基因組數(shù)據(jù)材料。課題研究以重要豆科模式植物苜蓿為外類群,對(duì)花生的兩個(gè)祖先物種進(jìn)行了系統(tǒng)的全基因組比較分析,基于同源染色體片段的基因同源共線性,統(tǒng)計(jì)推斷了花生基因組內(nèi)由多倍化事件所產(chǎn)生重復(fù)基因的規(guī)模,其中苜蓿12.2%(7286),花生A14.4%(5167),花生B 12.5%(5202);同時(shí)研究中對(duì)基因組間的同源關(guān)系進(jìn)行了細(xì)致的相似性結(jié)構(gòu)分析,構(gòu)建了以苜蓿為參考,與多倍化相關(guān)的多次級(jí)基因比對(duì)列表。研究發(fā)現(xiàn),加倍后物種基因內(nèi)重復(fù)基因丟失是一個(gè)隨機(jī)的過(guò)程,近似服從幾何分布。突出地,課題研究中結(jié)合系統(tǒng)發(fā)育和非參數(shù)bootstrap方法建立了推斷重復(fù)基因置換算法,并利用Perl、Bioperl語(yǔ)言集成Clustalw和PAML,實(shí)現(xiàn)了物種全基因組重復(fù)基因間的基因置換推斷。推斷結(jié)果顯示,花生A基因組中有2.8%(135個(gè)),花生B基因組中有2.6%(147個(gè))重復(fù)基因在進(jìn)化過(guò)程中發(fā)生了基因置換。統(tǒng)計(jì)分析發(fā)現(xiàn),靠近染色體端粒位置的重復(fù)基因?qū)﹂g更容易發(fā)生基因置換;基因置換可能更偏向于某些功能基因。課題中所建立的方法和流程能夠使用于對(duì)其它物種基因組多倍化過(guò)程,及同源染色體片段間的遺傳重組的探索研究,具有良好的推廣性;研究產(chǎn)生的結(jié)果對(duì)花生基因組相關(guān)領(lǐng)域研究具有理論支撐作用。
[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.
【學(xué)位授予單位】：華北理工大學(xué)
【學(xué)位級(jí)別】：碩士
【學(xué)位授予年份】：2017
【分類號(hào)】：S565.2;Q943.2

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