桃WRKY基因家族全基因组鉴定和表达分析

doi:10.16288/j.yczz.15-235

遗传 ›› 2016, Vol. 38 ›› Issue (3): 254-270.doi: 10.16288/j.yczz.15-235

桃WRKY基因家族全基因组鉴定和表达分析

谷彦冰, 冀志蕊, 迟福梅, 乔壮, 徐成楠, 张俊祥, 周宗山, 董庆龙

中国农业科学院果树研究所,兴城 125100

收稿日期:2015-05-27 修回日期:2015-12-30 出版日期:2016-03-20 发布日期:2016-03-20
通讯作者: 董庆龙,助理研究员,研究方向:果树分子生物学.
周宗山,研究员,研究方向:果树病理学. E-mail:dong19850412@163.com zszhouqrj@163.com
作者简介:谷彦冰,硕士研究生,专业方向:果树分子病理学.E-mail: guyanbing2010@126.com冀志蕊,助理研究员,研究方向:果树分子病理学.E-mail:xinyu_jzr@163.com.谷彦冰和冀志蕊为并列第一作者.
基金资助:
国家自然科学基金项目(编号:31401852)和农业部公益性行业项目(编号:201203034)资助

Genome-wide identification and expression analysis of the WRKY gene family in peach

Yanbing Gu, Zhirui Ji, Fumei Chi, Zhuang Qiao, Chengnan Xu, Junxiang Zhang, Zongshan Zhou, Qinglong Dong

Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, China

Received:2015-05-27 Revised:2015-12-30 Online:2016-03-20 Published:2016-03-20
Supported by:
Supported by the National Natural Science Foundation of China (No; 31401852) and Special Fund for Agro-scientific Research in the Public Interest (No; 201203034)

摘要/Abstract

摘要： WRKY转录因子是植物中最大的转录调控家族之一,在生物和非生物胁迫以及植物生长和发育过程中起着重要调控作用.本文利用HMMER 3.0软件,使用WRKY保守域全蛋白序列(Pfam数据库编号:PF03106)鉴定桃(Prunus persica L.)基因组中的WRKY基因;利用DNAMAN 5.0,WebLogo 3,MEGA5.1,MapInspect和MEME等软件对其蛋白序列进行生物信息学分析.本文共鉴定得到61个桃WRKY基因.进化树分析结果显示,桃WRKY蛋白分为Ⅰ,Ⅱ和Ⅲ类型,类型Ⅰ分为Ⅰ-C亚组和Ⅰ-N亚组,类型Ⅱ分为Ⅱ-a,II-b,II-c,II-d和II-e亚组.WRKY结构域分析显示,WRKY结构域高度保守,绝大多数都含有WRKYGQK七肽和锌指结构.染色体定位分析显示,桃WRKY基因分布于8条染色体中,呈不均匀分布.内含子和外显子结构分析表明,WRKY基因结构进化高度保守.保守元件分析表明,桃WRKY基因家族包含5个保守元件,元件1,2和3为WRKY盒,元件4,5为未知盒.桃WRKY基因家族都包含有WRKY盒,类型Ⅰ中含有2个WRKY盒;II-d亚组中含有未知元件5.半定量和荧光定量PCR结果显示,16个WRKY基因均在桃的根,茎,叶,花和果中表达,但其相对表达水平不同.

关键词: 桃, WRKY, 转录因子, 基因家族, 表达分析

Abstract: The WRKY transcription factors are one of the largest families of transcriptional regulators and play diverse regulatory roles in biotic and abiotic stresses, plant growth and development processes. In this study, the WRKY DNA-binding domain (Pfam Database number: PF03106) downloaded from Pfam protein families database was exploited to identify WRKY genes from the peach (Prunus persica 'Lovell') genome using HMMER 3.0. The obtained amino acid sequences were analyzed with DNAMAN 5.0, WebLogo 3, MEGA 5.1, MapInspect and MEME bioinformatics softwares. Totally 61 peach WRKY genes were found in the peach genome. Our phylogenetic analysis revealed that peach WRKY genes were classified into three Groups: Ⅰ, Ⅱ and Ⅲ. The WRKY N-terminal and C-terminal domains of Group Ⅰ (group I-N and group I-C) were monophyletic. The Group Ⅱ was sub-divided into five distinct clades (groupⅡ-a, Ⅱ-b, Ⅱ-c, Ⅱ-d and Ⅱ-e). Our domain analysis indicated that the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK at its N-terminus followed by a zinc-finger motif. The chromosome mapping analysis showed that peach WRKY genes were distributed with different densities over 8 chromosomes. The intron-exon structure analysis revealed that structures of the WRKY gene were highly conserved in the peach. The conserved motif analysis showed that the conserved motifs 1, 2 and 3, which specify the WRKY domain, were observed in all peach WRKY proteins, motif 5 as the unknown domain was observed in group Ⅱ-d, two WRKY domains were assigned to GroupⅠ. SqRT-PCR and qRT-PCR results indicated that 16 PpWRKY genes were expressed in roots, stems, leaves, flowers and fruits at various expression levels. Our analysis thus identified the PpWRKY gene families, and future functional studies are needed to reveal its specific roles.

Key words: peach, WRKY, transcription factor, expression analysis, gene family

谷彦冰, 冀志蕊, 迟福梅, 乔壮, 徐成楠, 张俊祥, 周宗山, 董庆龙. 桃WRKY基因家族全基因组鉴定和表达分析[J]. 遗传, 2016, 38(3): 254-270.

Yanbing Gu, Zhirui Ji, Fumei Chi, Zhuang Qiao, Chengnan Xu, Junxiang Zhang, Zongshan Zhou, Qinglong Dong. Genome-wide identification and expression analysis of the WRKY gene family in peach[J]. HEREDITAS(Beijing), 2016, 38(3): 254-270.

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桃WRKY基因家族全基因组鉴定和表达分析

Genome-wide identification and expression analysis of the WRKY gene family in peach

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