基于高通量RNA-seq数据的水稻亚种特异性编码基因鉴定及长非编码RNA识别

发布时间：2018-03-10 07:12

本文选题：水稻　切入点：转录组　出处：《华中农业大学》2017年硕士论文　论文类型：学位论文

【摘要】：水稻是世界上最重要的粮食作物之一,同时也是禾本科植物研究的重要模式物种。RNA-seq技术可以得到生物体在特定时期特定组织中全部的转录本,这使得我们可以从转录组的分析中挖掘出新转录本以及新基因。本文试图从不同品种、不同组织的水稻转录组数据中挖掘粳稻日本晴和籼稻MH63、ZS97参考基因组上不存在的新转录本和新基因,尽可能全面地补充水稻的注释信息。本文采用先组装后比对的策略,通过对NCBI数据库中2012年1月-2016年4月发表的共960个样本的亚洲栽培水稻(Oryza sativa)RNA-seq数据,分籼稻(indica)、粳稻(japonica)两个亚种进行de novo组装,得到28,352条籼稻及50,648条粳稻转录本。其中籼稻有6,939条新转录本、粳稻有11,875条新转录本均未比对到水稻日本晴、MH63以及ZS97参考基因组。通过对籼、粳转录本进行相互比对,发现仅有5.1%的籼稻转录本与3%的粳稻转录本相互间有大于60%的重叠区域,这说明绝大多数的新转录本具有亚种特异性。通过开放阅读框预测及与蛋白质非冗余数据库(nr库)进行同源序列比对,从新转录本中分别预测得到3,794条籼稻及6,181条粳稻高可信度蛋白编码序列。通过对其进行功能注释,3,380条(89.1%)籼稻及5,314条(86%)粳稻蛋白编码序列可在Pfam数据库中得到比对注释,1,648条(43.4%)籼稻及2,494条(40.3%)粳稻蛋白编码序列可通过KOG注释到23个蛋白功能分类中。2,489(65.6%)条籼稻及3,795条(61.4%)粳稻蛋白编码序列有GO注释结果。715条(18.8%)籼稻及1,046条(17.0%)粳稻蛋白编码序列在KEGG代谢途径分析中得到注释。并且发现大量基因参与水稻抗病及非生物胁迫响应过程。进一步分析籼、粳稻蛋白编码基因的同源基因家族发现,2,057条(54.2%)籼稻及4,404条(71.3%)粳稻蛋白编码基因是亚种特有的。另一方面,通过对籼、粳转录本组装结果进行编码能力预测及蛋白质同源序列比对的综合策略,预测得到16,600条长非编码RNA,为水稻长非编码RNA的分析提供基础。
[Abstract]:Rice is one of the most important food crops in the world, and it is also an important model species of gramineous plants. RNA-seq technology can obtain all transcripts of organisms in specific tissues at a given time. This allows us to extract new transcripts and new genes from transcriptome analysis. The new transcripts and new genes that do not exist in the reference genome of japonica rice MH63HZS97 were excavated from rice transcriptome data of different tissues, and the annotated information of rice was supplemented as comprehensively as possible. Two subspecies of indica indica (indica indica) and japonica (japonica) were assembled by de novo from 960 Asian cultivated rice (Oryza sativa)RNA-seq) data published in NCBI database from January 2012 to April 2016, and the two subspecies were divided into two subspecies: indica indica (Indica indica) and japonica (japonica). 28,352 indica and 50,648 japonica transcripts were obtained, of which 6,939 were new transcripts in indica rice and 11,875 in japonica rice. It was found that only 5.1% indica rice transcripts and 3% japonica rice transcripts had overlapping regions greater than 60%. This indicates that most of the new transcripts are subspecies specific. From the new transcripts, 3,794 indica rice and 6,181 japonica rice high-reliability protein coding sequences were predicted. The protein coding sequences of indica rice and 5,314 japonica rice can be compared in Pfam database by means of functional annotation of 3,794 indica rice and 5,314 japonica rice protein coding sequences. The protein coding sequence of indica rice and 2,494 japonica rice can be annotated into 23 functional classification of protein by KOG. The protein coding sequences of indica rice and 3,795 rice varieties have go annotated result .715 18.8) indica rice protein coding sequence and 1,046 japonica rice protein protein coding sequence can be divided into 17. 0% japonica rice. The coding sequence was annotated in the analysis of KEGG metabolic pathway, and a large number of genes were found to be involved in the response of rice to disease resistance and abiotic stress. The homologous gene family of protein coding genes of japonica rice has found that the protein coding genes of Indica rice and 4,404 japonica rice are endemic to subspecies, on the other hand, through the analysis of indica rice, The coding ability of japonica transcripts was predicted and the integrated strategy of protein homologous sequence alignment was used to predict 16,600 long non-coding RNAs, which provided the basis for the analysis of rice long non-coding RNA.
【学位授予单位】：华中农业大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：S511

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