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棉花学报 ›› 2021, Vol. 33 ›› Issue (2): 95-111.doi: 10.11963/1002-7807.srkwxf.20210113

• 研究与进展 •    下一篇

陆地棉REM基因家族全基因组鉴定及表达分析

石荣康(),张冬梅,孙正文,刘正文,解美霞,张艳,马峙英,王省芬()   

  1. 华北作物改良与调控国家重点实验室/河北省棉花产业协同创新中心/河北省作物种质资源重点实验室/河北农业大学农学院,河北 保定071001
  • 收稿日期:2020-09-10 出版日期:2021-03-15 发布日期:2021-04-07
  • 通讯作者: 王省芬 E-mail:srk0000@126.com;cotton@hebau.edu.cn
  • 作者简介:石荣康(1996―),男,硕士研究生, srk0000@126.com
  • 基金资助:
    国家自然科学基金(31971982);河北农业大学引进人才科研专项

Genome-wide identification and expression analysis of REM gene family in Gossypium hirsutum

Shi Rongkang(),Zhang Dongmei,Sun Zhengwen,Liu Zhengwen,Xie Meixia,Zhang Yan,Ma Zhiying,Wang Xingfen()   

  1. State Key Laboratory of North China Crop Improvement and Regulation / Co-Innovation Center for Cotton Industry of Hebei Province / Key Laboratory for Crop Germplasm Resources of Hebei / College of Agronomy, Hebei Agricultural University, Baoding, Hebei 071001, China
  • Received:2020-09-10 Online:2021-03-15 Published:2021-04-07
  • Contact: Wang Xingfen E-mail:srk0000@126.com;cotton@hebau.edu.cn

摘要:

【目的】 REM (Reproductive meristem)基因家族编码一类转录因子在植物生长发育过程中发挥重要作用,但在棉花中未见报道。【方法】 基于陆地棉基因组数据和公共数据库中的转录组数据,运用生物信息学方法对陆地棉REM基因家族成员进行系统鉴定,并对该基因家族的理化性质、基因结构、组织表达特异性以及胁迫条件下的表达规律等进行分析。【结果】 陆地棉REM基因家族包含79个成员,分布在25条染色体上,可分为5个亚组。每个成员编码的蛋白质至少含有1个B3结构域,大部分定位在细胞核。基因上游2 kb序列中存在激素及胁迫响应等顺式作用元件。组织表达特性分析结果显示,大部分REM基因在胚珠或纤维中的表达量较其他组织更高。逆境胁迫下的表达分析显示,29个基因响应棉花冷、热、盐或干旱胁迫。对6个基因在纤维不同发育时期表达量进行分析,发现这些基因的表达与已发表的转录组数据基本一致。【结论】 明确了REM基因家族在基因组中的分布特征、结构特征以及系统进化特征,根据转录组数据初步揭示了该家族基因在生长发育和抗逆中的功能。

关键词: 陆地棉; REM基因家族; 生物信息学分析; 启动子; 表达分析

Abstract:

[Objective] The REM (Reproductive meristem) gene family encodes a class of transcription factors, which plays an important role in the growth and development of plants. However, it has not been reported in Gossypium hirsutum. [Methods] In this study, REM gene family were systematically identified via bioinformatics based on the third generation genomic data of G. hirsutum and the transcriptome data from public databases. The physical and chemical properties of REM protein, gene structure, gene expression patterns in different tissues and under different stresses for REM family were analyzed. [Results] REM gene family in G. hirsutum contained 79 members which distributed on 25 chromosomes and could be divided into five subfamilies. Each of REM proteins contained at least one B3 domain, and most of the members were located in the nucleus. Cis-acting elements responding to hormone and stress were located in the upstream 2 kb of genes. Gene expression analysis showed that most of the REM genes displayed higher expression in the ovules or fibers than in other tissues, and 29 REM genes responded to cold, hot, salt or drought. Expression patterns of six genes in different developmental stages detected by qRT-PCR(Quantitative real-time ploymerase chain reaction) were basically consistent with transcriptome data. [Conclusion] The distribution in the genome, gene structure, and phylogenetic characteristics of these genes were determined, and the roles of REM genes in growth, development and stress were preliminarily clarified according to transcription profile.

Key words: Gossypium hirsutum L.; REM gene family; bioinformatics analysis; promoter; expression analysis