WRKY,轉錄因子,生物信息學,基因家族," /> 3d500期和值走势图

中國農業科學 ?? 2015, Vol. 48 ?? Issue (16): 3221-3238.doi: 10.3864/j.issn.0578-1752.2015.16.012

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蘋果WRKY基因家族生物信息學及表達分析

谷彥冰,冀志蕊,遲福梅,喬壯,徐成楠,張俊祥,董慶龍,周宗山   

  1. 中國農業科學院果樹研究所,遼寧興城 125100
  • 收稿日期:2014-12-28 出版日期:2015-08-16 發布日期:2015-08-16
  • 通訊作者: 周宗山,Tel:0429-3598268;E-mail:[email protected];董慶龍,Tel:0429-3598236;E-mail:[email protected] E-mail:[email protected]; [email protected]
  • 作者簡介:谷彥冰,Tel:0429-3598269;E-mail:[email protected]。冀志蕊,Tel:0429-3598236;E-mail:[email protected]。谷彥冰與冀志蕊為同等貢獻作者。
  • 基金資助:
    國家自然科學基金(31401852)、國家公益性行業(農業)科研專項(201203034)

Bioinformatics and Expression Analysis of the WRKY Gene Family in Apple

GU Yan-bing, JI Zhi-rui, CHI Fu-mei, QIAO Zhuang, XU Cheng-nan, ZHANG Jun-xiang, DONG Qing-long, ZHOU Zong-shan   

  1. Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng 125100, Liaoning
  • Received:2014-12-28 Online:2015-08-16 Published:2015-08-16

摘要: 【目的】鑒定蘋果(Malus domesticaBorkh.)基因組上132個WRKY基因,為研究蘋果WRKY轉錄因子在非生物和生物脅迫以及生長和發育過程中的調控作用奠定相關理論基礎,也為進一步分析蘋果WRKY基因提供信息。【方法】利用HMMER 3.0軟件,通過WRKY保守域全蛋白序列PF03106用于鑒定蘋果WRKY基因。采用WebLogo 3、DNAMAN 5.0、MapInspect、MEME和MEGA5.1等軟件對其蛋白序列進行生物信息學分析。采用RT-PCR技術檢測蘋果WRKY基因的組織表達情況。【結果】鑒定得到132個蘋果WRKY基因。分組鑒定和進化樹分析結果顯示,蘋果WRKY蛋白分為I、II和III類型,I組共有24個成員可進一步分為I-C和I-N亞組,其鋅指結構是C2H2類型(CX4CX22-23HXH)。II組含有1個WRKY區域共有79個成員,可進一步分為II-a、II-b、II-c、II-d和II-e亞組,分別有8、12、31、14和14個成員,其鋅指結構為C2H2類型(CX4-5CX23HXH)。III組共有29個成員,其鋅指結構為C2HC類型(CX7CX23-24HXC);WRKY結構域分析顯示,其高度保守,絕大多數都含有WRKYGQK七肽和鋅指結構;染色體定位分析顯示,蘋果WRKY分布于蘋果17條染色體中,呈不均勻分布。染色體1和9上分布最多,為13個;其次是染色體12,分布12個;染色體2、5和14分布最少,為4個;基因結構分析表明,MdWRKY基因家族多數由2—5個外顯子組成,基因結構進化高度保守;保守元件分析表明,MdWRKY基因家族包含10個保守元件:元件1—6為WRKY盒;元件7—10為未知盒。MdWRKY基因家族都包含有WRKY盒,I組中含有2個WRKY盒,II-a和II-b亞組中含有未知元件8,III組中含有未知元件7和9。半定量結果顯示,12個MdWRKY均在根、莖、葉、花和果中表達,且呈現出多種相對表達模式。【結論】蘋果WRKY基因家族結構高度保守,可能參與調控蘋果生長和發育等過程。

關鍵詞: 蘋果, WRKY, 轉錄因子, 生物信息學, 基因家族

Abstract: 【Objective】In this study, 132 putative WRKY proteins in the apple (Malus domestica Borkh.) genome were identified, so as to provide a basis for studying the theoretical roles of WRKY genes in the regulation of plant stress responses, growth and development, and to provide valuable information for WRKY genes cloning in apple.【Method】WRKY DNA-binding domain (PF03106) downloaded from Pfam protein families database was employed to identify WRKY genes from apple genome using HMMER 3.0. The obtained amino acid sequences were analyzed with the bioinformatics softwares, including DNAMAN 5.0, Weblogo 3, MEGA 5.1, MapInspect and MEME. RT-PCR was used to detect WRKY genes expression in different tissues of apple. 【Result】 Totally 132 apple WRKY genes were found in apple genome. The result of group identification and phylogenetic analysis revealed that apple WRKY genes were classified into Group I, Group II and Group III. Twenty-four MdWRKY proteins with two WRKY domains (group I-N and group I-C) containing CX4CX22-23HXH zinc-finger motif belonged to Group I. Seventy-nine Group II MdWRKY proteins had a single WRKY domain including CX4–5CX23HXH zinc-finger motif and could be further divided into five subgroups (Group II-a: 8 members, Group II-b: 12 members, Group II-c: 31 members, Group II-d: 14 members, and Group II-e: 14 members, respectively), whereas 29 Group III MdWRKY proteins contained a single WRKY domain with CX7CX23–24HXC zinc-finger motif. The results of domain analysis indicated that the WRKY regions contained a highly conserved heptapeptide stretch WRKYGQK at its N-terminus followed by a zinc-finger motif. Chromosome mapping analysis showed that apple WRKY genes were distributed with different densities on 17 chromosomes. The largest number of apple WRKY genes were found on chromosomes 1 and 9 (thirteen genes), followed by chromosome 12 (twelve genes). Only 4 genes located on chromosomes 2, 5 and 14. The results of gene structure analysis revealed that most of the WRKY gene contained 2-5 exons and WRKY gene structure were highly conserved in apple. Conserved motif analysis showed that the conserved motifs 1-6, which specify the WRKY domain, were observed in all apple WRKY proteins, motif 8 and motifs 7 and 9 as the unknown domain were observed in Group II-a and II-b and Group III, respectively. Two WRKY domains were assigned to Group I. RT-PCR results indicated that 12 MdWRKY genes were expressed in roots, stems, leaves, flowers and fruits at various expression levels.【Conclusion】These results suggested that MdWRKY gene family was highly and structurally conserved, and may be involved into the regulation of growth and development processes in apple.

Key words: apple, WRKY, transcription factor, bioinformatics, gene family

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