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葡萄miR169及其靶基因的生物信息学分析
作者: 方辉1 曲俊杰1 孙嘉曼1 尹玲1 潘凤英1 2* 
单位: (1 广西作物遗传改良生物技术重点开放实验室 南宁530007 2 广西农业科学院 南宁530007) 
关键词: miR169基因 靶基因 NF-YA转录因子 生物信息学 
分类号:S663.1
出版年,卷(期):页码:2017,48(8):1329-1334
摘要:

【目的】明确葡萄miR169(vvi-miR169)基因家族在葡萄生长发育及逆境胁迫响应中的重要作用,为其在葡萄分子育种和抗逆新品种选育中的应用提供参考依据。【方法】利用miRNA、Phytozome、NCBI等数据库及ClustalX 2.1、MEGA 6.0、RNAfold WebServer、psRNATarget等在线软件对vvi-miR169基因家族的序列分布、定位特征、二级结构、发育进化树和靶基因调控功能进行生物信息学分析。【结果】在miRBase中搜索到25条vvi-miR169基因同源序列,分别分布在6条染色体上,其中以位于Chr11上的序列最多,共有17条,位于Chr01、Chr04和Chr14上各有2条,而在Chr08和Chr17上各有1条。vvi-miR169基因家族成熟序列的碱基保守性很高,其前体序列均可形成稳定的二级茎环结构,且位于同一条染色体上的miR169基因序列显示出相对更近的亲缘关系。vvi-miR169基因家族共预测到21个靶基因,绝大部分miRNA都有多个靶基因,且不同miRNA具有相同的靶基因,其中有22个miRNA靶基因均含有GSVIVT01015120001(NF-YA转录因子)。【结论】vvi-miR169基因家族序列保守性较高,家族特征明显,且具有相似的调控功能;NF-YA转录因子是vvi-miR169基因家族最主要的靶基因,也是葡萄生长发育过程中抗逆境胁迫的主要调控元件。

【Objective】The important role of miR169(vvi-miR169) gene family in Vitis vinifera during the growth and stress response was clarified, which could provide reference for its application in molecular breeding and resistance breeding in Vitis vinifera. 【Method】By utilizing miRNA, Phytozome and NCBI database, ClustalX 2.1, MEGA 6, RNAfold, WebServer, psRNATarget and other online softwares, bioinformatics analysis for vvi-miR169 gene family was conducted, including its sequences, distribution characteristics, the secondary structure, phylogenetic tree and target gene regulation function. 【Result】Twenty-five vvi-miR169 homologous gene sequences which were searched in the miRBase distributed on six chromosomes. Chr11 had the most gene sequences(17 sequences) distributed on. There were two sequences on Chr01, Chr04 and Chr14, while only one on Chr08 and Chr17. Base of vvi-miR169 gene family mature sequence was of highly  conservation. Its precursor sequence could form a stable two stem loop structure, and miR169 gene sequence on the same chromosome showed close genetic relationship. It was predicted that vvi-miR169 gene family contained 21 target genes, most miRNA genes had multiple target genes, different miRNA gene shared the same targets, and 22 miRNA genes contained the same target gene of GSVIVT01015120001(transcription factor NF-YA). 【Conclusion】vvi-miR169 gene family sequences are highly conserved and characterized by obvious family features with similar regulatory function. Transcription factor NF-YA is the main target gene of vvi-miR169 gene family, and is also the main stress-resistance regulation element in the growth and development of V. vinifera.

基金项目:
国家博士后科学基金项目(2014M562497XB);广西八桂学者专项资金项目([2013]3号);广西农业科学院科技发展基金项目(桂农科2015JM28);广西农业科学院基本科研业务专项项目(桂农科2017YM33)
作者简介:
*为通讯作者,潘凤英(1985-),博士,主要从事葡萄抗病基因挖掘研究工作,E-mail:panfengying@163.com。方辉(1984-),主要从事植物功能基因组学研究工作,E-mail:fanghui2002@163.com
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