浙工商大测序鉴定病毒侵染的番茄miRNA谱

番茄是一种重要的经济蔬菜作物，当前的番茄品种并没有对黄瓜花叶病毒(CMV)形成自然抗性或耐受性，因此，该病毒感染可能导致灾难性的作物损失。micrornA(miRNA)在植物发育和应激反应过程中起重要调节作用。虽然目前已有可获得番茄基因组信息的数据库，但已经确定的番茄miRNA的数量有限。

浙江工商大学冯俊丽副研究员领衔的研究小组与联川生物技术总监郎秋蕾博士率领的科研团队联手对黄瓜花叶病毒(CMV)感染的番茄miRNA谱及miRNA调控的靶基因进行深入研究，研究成果发表在近期的Planta上。

针对黄瓜花叶病毒(CMV)感染的和对照的番茄，研究人员分别构建了两个独立的小RNA文库，并进行高通量测序(小RNA测序项目由联川生物承担完成)。基于测序分析和发夹结构的预测，共有50个植物miRNA和273个潜在候选的miRNA(PC-miRNA)在番茄中被首次鉴定出来，其中12个植物miRNA和80个PC-miRNA分别来自一个前体序列的3p和5p链。

对比分析表明，79个miRNA(包括15个新发现的西红柿miRNA)和40个PC-miRNA在两个库之间存在差异表达，同时一些新发现的番茄miRNA和PC-miRNA的表达模式通过qRT-PCR方法得到进一步验证。

对于一些已知的和新发现的番茄miRNA的潜在靶基因，研究人员通过降解组测序(降解组测序项目由联川生物承担完成)进行了预测，靶基因注释表明，它们参与多种生物学过程，包括转录调控和病毒抗性。这些靶基因转录本GO分析表明，在受CMV-Fny(一种已深入研究的CMV病毒株)感染的西红柿中，与防御响应和光合作用相关的基因，受影响最为严重。

此项研究新发现了许多番茄miRNA，有助于研究人员对miRNA介导调控网络的深入理解，并为病毒致病机制提供了新见解。

原文摘要：

Identification of microRNAs and their targets in tomato infected with Cucumber mosaic virus based on deep sequencing

Junli Feng, Shasha Liu, Mengna Wang, Qiulei Lang, Chunzhi Jin

MicroRNAs (miRNAs) play important regulatory roles in plant development and stress responses. Tomato is an economically important vegetable crop in the world with publicly available genomic information database, but only a limited number of tomato miRNAs have been identified. In this study, two independent small RNA libraries from mock and Cucumber mosaic virus (CMV)-infected tomatoes were constructed, respectively, and sequenced with a high-throughput Illumina Solexa system. Based on sequence analysis and hairpin structure prediction, a total of 50 plant miRNAs and 273 potentially candidate miRNAs (PC-miRNAs) were firstly identified in tomato, with 12 plant miRNAs and 82 PC-miRNAs supported by both the 3p and 5p strands. Comparative analysis revealed that 79 miRNAs (including 15 new tomato miRNAs) and 40 PC-miRNAs were differentially expressed between the two libraries, and the expression patterns of some new tomato miRNAs and PC-miRNAs were further validated by qRT-PCR. Moreover, potential targets for some of the known and new tomato miRNAs were identified by the recently developed degradome sequencing approach, and target annotation indicated that they were involved in multiple biological processes, including transcriptional regulation and virus resistance. Gene ontology analysis of these target transcripts demonstrated that defense response- and photosynthesis-related genes were most affected in CMV-Fny-infected tomatoes. Because tomato is not only an important crop but also is a genetic model for basic biology research, our study contributes to the understanding of miRNAs in response to virus infection.

作者：联川生物