基于RNA-Seq技术的栽培和野生番茄转录组分析

发布时间：2018-05-10 22:20

本文选题：番茄 + RNA-Seq　；参考：《浙江理工大学》2017年硕士论文

【摘要】：番茄生长周期短,果实营养丰富,富含多种维生素,是人们日常生活中不可或缺的一种蔬菜,另外番茄与拟南芥等模式生物的亲缘关系比较远,果实成熟周期短,因此番茄也被作为研究果实成熟的模式生物。随着对番茄需求量的逐渐增加,培育优良品种、提高产量已经成为研究者们日益关注的问题。目前,对番茄的研究主要集中在栽培和野生番茄对耐盐性、抗旱性、抗低温性、果实营养成分的差异上。基于前人对两种番茄差异性状的研究,本文主要对栽培和野生番茄在转录组水平上进行研究。通过RNA-Seq技术,对番茄的全转录组进行分析,主要工作内容如下:首先,我们对番茄转录组数据进行质量检控,并进行后续的比对、组装,组装之后得到388666个转录本,并对转录本的长度分布情况进行了统计分析。另外,不同组织中转录本的表达量相差很大,表达量高的转录本主要集中在花、果实、根和营养组织中。其次,我们分析了栽培和野生番茄的差异表达基因。预测得到126个上调的差异表达基因和87个下调的差异表达基因。对差异表达基因进行GO功能注释和Pathway分析,从而确定这些差异表达基因的功能和生物学途径,其主要富集在光收集复合物、质膜聚光复杂度、淀粉和蔗糖代谢、亚麻酸代谢,生物合成氨基酸等。另外,我们还对各个组织中的差异表达基因进行GO注释,从而确定不同组织中差异表达基因的功能。最后,我们预测了554个差异表达长非编码RNA和426个mRNA,并进行了统计分析。通过构建长非编码RNA和mRNA的共表达网络,进一步筛选出与长非编码RNA相关的mRNA,并对这些mRNA进行功能注释,其功能主要集中在对生物的刺激做出反应、肽酶抑制剂的活动等,从而推测这些长非编码RNA的调控功能。除此之外,我们还预测了番茄的新转录本,每个新转录本都包含至少一个外显子和一个蛋白编码区域,其具体功能还需要进一步研究。
[Abstract]:Tomato is an indispensable vegetable in people's daily life because of its short growth cycle, rich in nutrition and rich in multivitamins. In addition, tomato has a long relationship with model organisms such as Arabidopsis thaliana, and the fruit ripening cycle is short. Therefore, tomato is also used as a model organism to study fruit ripening. With the increasing demand for tomato, the cultivation of good varieties and the increase of yield have become increasingly concerned by researchers. At present, the research on tomato is mainly focused on the difference of salt tolerance, drought resistance, low temperature resistance and fruit nutrition between cultivated and wild tomato. Based on the previous studies on the differences between the two tomato species, the transcriptome level of cultivated and wild tomato was studied in this paper. The main work of this paper is as follows: firstly, we checked the quality of tomato transcriptome data and compared them with each other. After assembling, we got 388666 transcripts. The length distribution of transcripts was analyzed statistically. In addition, the expression of the transcripts in different tissues varied greatly, and the high expression transcripts were mainly concentrated in flowers, fruits, roots and nutritious tissues. Secondly, we analyzed the differentially expressed genes between cultivated and wild tomato. 126 up-regulated differentially expressed genes and 87 down-regulated differentially expressed genes were predicted. Go functional annotation and Pathway analysis were performed to determine the functional and biological pathways of these differentially expressed genes, which were mainly concentrated in light collection complex, plasma membrane aggregation complexity, starch and sucrose metabolism, and linolenic acid metabolism. Biosynthetic amino acids, etc. In addition, we annotated the differentially expressed genes in different tissues to determine the function of differentially expressed genes in different tissues. Finally, 554 differentially expressed RNA and 426 mRNAs were predicted and analyzed statistically. By constructing the coexpression network of long non-coding RNA and mRNA, the mRNAs related to long non-coding RNA were screened out, and the function of these mRNA was annotated. The functions of these mRNAs were mainly focused on the responses to biological stimuli, the activities of peptidase inhibitors and so on. Therefore, the regulatory functions of these long non-coding RNA were speculated. In addition, we predicted the new transcripts of tomato. Each new transcript contains at least one exon and one protein coding region, and its function needs further study.
【学位授予单位】：浙江理工大学
【学位级别】：硕士
【学位授予年份】：2017
【分类号】：Q943.2

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