水稻CO39基因组的组装注释与分析

发布时间：2018-02-06 03:29

本文关键词： 籼稻CO39(Oryza sativa L.CO39) 全基因组测序基因组组装与注释单核苷酸多态性结构变异　出处：《福建农林大学》2017年硕士论文　论文类型：学位论文

【摘要】：水稻是最重要的粮食作物之一,世界上有一半的人口以水稻为主食。随着人口的不断增加,急需提高水稻总产量以满足人类生存的需求。然而水稻的生长发育会受到各种逆境的胁迫,且不同水稻品种对逆境具有不同的感抗能力。前期研究表明籼型水稻品种CO39易感稻瘟病,但能抗各种非生物逆境胁迫,如高温。因此,CO39已被用作多个水稻遗传群体的亲本材料。但有关CO39品种基因组序列的组装及其注释的研究尚未见报道。本文应用二代基因组DNA测序技术,首先对籼稻品种CO39基因组进行深度测序,然后进行组装与注释,获得如下结果。1.基于参考基因组组装后的CO39基因组一致性序列为356Mb,其中包含69.8Mb的N和61Mb大小未定位的contigs序列。一致性序列覆盖cDNA长度90%以上的占40%,覆盖cDNA长度70%以上的占62%,覆盖cDNA长度50%以上的占到了 73%。2.基因组注释发现在CO39基因组中3,244个可信度较高的基因有相应的功能注释,也挖掘出2,111,981个SNPs。同时构建了数据库CO39 基因组数据库(http://localhost/snp2gene/snp.php),用于保存 CO39基因组序列、注释和高质量的SNPs数据,以方便其他研究人员的应用。3.SVs分析结果表明,CO39基因组中有40,980个长度大于100bp的长片段Indels,69.5Mb大小的插入序列,50.4Mb大小的缺失片段。分析SNPs对编码基因的影响以及SVs的变异情况,发现抗稻瘟病基因LOC_Os09g15840的编码区上没有任何碱基的突变且该基因也不属于缺失片段。4.从公共数据库中下载50份水稻品种的基因组重测序数据,分别以水稻品种9311、日本晴和CO39基因组为参考基因组进行拼接组装,比较50份水稻品种基因组的组装效果。结果发现其中5个水稻品种以CO39为参考基因组的组装效果显著优于以日本晴和9311为参考基因组的组装效果,进一步说明了 CO39基因组作为其他水稻品种基因组DNA重测序序列组装的参考基因组的可靠性。本文组装注释并分析了水稻籼型品种CO39的基因组,为以CO39为亲本的水稻遗传群体的比较基因组学研究奠定了基础,也为水稻不同品种基因组DNA序列的组装与注释提供了参考。
[Abstract]:Rice is one of the most important food crops. Half of the world's population feeds on rice. There is an urgent need to increase the total yield of rice to meet the needs of human survival. However, the growth and development of rice will be subjected to various stresses. Early studies showed that indica rice variety CO39 was susceptible to blast, but could resist various abiotic stresses, such as high temperature. CO39 has been used as a parent material for many rice genetic populations. However, studies on genome sequence assembly and annotation of CO39 varieties have not been reported. The second generation genomic DNA sequencing technique has been used in this paper. First, the CO39 genome of indica rice was deeply sequenced, then assembled and annotated. The following results were obtained. 1. The consensus sequence of CO39 genome based on reference genome assembly was 356Mb. There are 69.8 Mb N and 61Mb unlocated contigs sequences, 40% of which cover cDNA length above 90%. The number of those who covered the length of cDNA more than 70% accounted for 62%, and those that covered the length of cDNA more than 50% accounted for 73.2. the genome annotation was found in the genome of CO39 3. The 244 more reliable genes had functional annotations and mined 2,111. 981 SNPs. At the same time, we built the database CO39 genome database http: / / / localhost / snp2gene/ snp.php / http: / / localhost / snp2gene/ snp.php. Used to preserve CO39 genomic sequences, annotations, and high-quality SNPs data to facilitate the application of other researchers. 3. SVs analysis results show that there are 40 in the Co39 genome. There were 980 insertion sequences in the size of 69.5Mb with a length of more than 100bp. The effect of SNPs on the coding gene and the variation of SVs were analyzed. It was found that there was no base mutation in the coding region of rice blast resistance gene LOC_Os09g15840 and that the gene did not belong to the deletion fragment. 4. Download 50 rice varieties genes from public database. Group resequenced data. The rice varieties 9311, Nippon genome and CO39 genome were used as reference genomes respectively. The results showed that the assembly effect of 5 rice varieties using CO39 as reference genome was significantly better than that of Nippon Fine and Japanese 9311 reference genomes. . Further explanation. The reliability of CO39 genome as the reference genome of DNA resequencing sequence assembly of other rice varieties. The genome of rice indica variety CO39 was annotated and analyzed in this paper. It lays a foundation for comparative genomics of rice genetic populations with CO39 as parent, and provides a reference for the assembly and annotation of genomic DNA sequences of different rice varieties.
【学位授予单位】：福建农林大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q943.2;S511

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