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棉花学报 ›› 2021, Vol. 33 ›› Issue (2): 112-123.doi: 10.11963/1002-7807.dllxgh.20210119

• 研究与进展 • 上一篇    下一篇

陆地棉Nudix基因家族的全基因组鉴定及表达分析

窦玲玲1(),孙亚如2(),赵琴1,田瑞洁1,康洋洋1,朱怡然1,杨蕾蕾1,王彩虹3,冯宇3,王文博1,肖光辉3,*()   

  1. 1.咸阳师范学院化学与化工学院,陕西 咸阳712000
    2.河南大学生命科学学院,河南 开封475004
    3.陕西师范大学生命科学学院,西安710119
  • 收稿日期:2020-09-22 出版日期:2021-03-15 发布日期:2021-04-07
  • 通讯作者: 肖光辉 E-mail:xjyldll@126.com;syrfighting123@163.com;guanghuix@snnu.edu.cn
  • 作者简介:窦玲玲(1987―),女,博士, xjyldll@126.com|孙亚如(1995―),女,硕士, syrfighting123@163.com
  • 基金资助:
    国家自然科学基金面上项目(31600223);棉花生物学国家重点实验室开放课题(CB2019A03);陕西省自然科学基金青年项目(2019JQ-062);陕西省科协青年托举人才计划(20190205);2020年陕西省大学生创新创业训练计划项目(S202010722071);2020年咸阳师范学院综合类科研基金项目(XSYK20002)

Genome-wide identification and expression analysis of Nudix gene family in upland cotton

Dou Lingling1(),Sun Yaru2(),Zhao Qin1,Tian Ruijie1,Kang Yangyang1,Zhu Yiran1,Yang Leilei1,Wang Caihong3,Feng Yu3,Wang Wenbo1,Xiao Guanghui3,*()   

  1. 1. School of Chemistry and Chemical Engineering, Xianyang Normal University, Xianyang, Shaanxi 712000, China
    2. School of Life Sciences, Henan University, Kaifeng, Henan 475004, China
    3. College of Life Sciences, Shaanxi Normal University, Xi’an 710119, China;
  • Received:2020-09-22 Online:2021-03-15 Published:2021-04-07
  • Contact: Xiao Guanghui E-mail:xjyldll@126.com;syrfighting123@163.com;guanghuix@snnu.edu.cn

摘要:

【目的】 Nudix是一类能够催化各种核苷二磷酸衍生物水解的酶,具有维持遗传物质稳定,响应逆境胁迫等生物学功能。本研究旨在对陆地棉Nudix基因进行全基因组分析,为深入研究Nudix基因家族参与棉纤维生长发育调控机制提供参考。【方法】 通过生物信息学方法对陆地棉基因组(ZJU_v2.1)的Nudix基因进行全基因组鉴定,并系统分析Nudix基因家族成员的理化性质、序列特征、基因复制、系统进化和表达情况。【结果】 从陆地棉基因组中共鉴定到76个GhNudix基因,经聚类分析将其分为7个亚组(Clade Ⅰ、Ⅱ、Ⅲ、Ⅳ、Ⅴ、Ⅵ和Ⅶ)。基因复制分析表明,片段重复是陆地棉GhNudix基因家族成员扩增的主要原因。转录组数据表明GhNudix基因的表达不但有组织特异性而且有时间特异性。其中在纤维发育的起始和伸长阶段高调表达的GhNudix基因主要分布在Clade Ⅰ和Ⅱ;且大部分Clade Ⅰ和Ⅱ亚组的GhNudix基因启动子含有响应生长素和赤霉素的顺式作用元件,由此推测Clade Ⅰ和Ⅱ亚组的GhNudix基因在陆地棉纤维的起始和伸长阶段发挥作用。【结论】 陆地棉GhNudix基因家族的全基因组鉴定和分析,为后续研究其在棉纤维发育中的作用机制提供参考。

关键词: 陆地棉; Nudix基因; 系统进化; 表达分析

Abstract:

[Objective] Nudix hydrolases, which catalyze the hydrolysis of nucleoside diphosphate derivatives, play an important role in maintaining the stability of genetic material and responding to biotic and abiotic stresses. The purpose of this study is to conduct a genome-wide analysis of the Nudix genes in Gossypium hirsutum and to provide a reference for further functional study of the Nudix genes associated with cotton fiber development. [Methods] Through bioinformatics methods, the whole-genome identification of the Nudix genes was carried out in G. hirsutum genome (ZJU_v2.1), and the physicochemical properties, sequence characteristics, gene duplication, phylogenetic evolution and expression profiles of the GhNudix gene families were systematically analyzed. [Results] A total of 76 GhNudix genes were identified from the G. hirsutum genome and were further divided into seven subgroups by phylogenetic analysis (Clade Ⅰ, Ⅱ, Ⅲ, Ⅳ, Ⅴ, Ⅵ and Ⅶ). Gene duplication analysis showed that segmental duplication was the main force for the amplification of GhNudix genes in G. hirsutum. According to transcriptome data, GhNudix genes expressed with not only tissue-specificity, but also time-specificity. GhNudix genes, which highly expressed during the initial and elongation stages of fiber development, mainly distributed in Clade Ⅰ and Ⅱ; most of the GhNudix promoters of the Clade Ⅰ and Ⅱ subgroups contain cis-elements that respond to auxin and gibberellin. Therefore, we speculated that the GhNudix genes of Clade Ⅰ and Ⅱ subgroups play roles in the initiation and elongation of upland cotton fibers. [Conclusions] Genome-wide identification and analysis of the GhNudix gene family in G. hirsutum will provide a reference for the follow-up study of its biological mechanism in cotton fiber development.

Key words: Gossypim hirsutum; Nudix gene; phylogenetic analysis; expression analysis