摘要
【目的】转座子是基因组进化的重要驱动力,但陆地棉中gag基因家族的功能尚未明确。本研究旨在鉴定陆地棉中的gag基因家族成员,分析其结构特征、进化关系及表达模式,为探究其在棉花生长发育和逆境响应中的功能奠定基础。【方法】基于陆地棉遗传标准系TM-1基因组,利用HMMER软件、NCBI-CDD数据库和Pfam数据库鉴定gag基因家族成员;通过生物信息学工具分析其理化性质、亚细胞定位和染色体分布;利用ClustalX和MEGA X构建系统进化树;通过PlantCARE分析启动子顺式作用元件及结合RepeatMasker和LTR_retriever分析LTR转座子的分布特征;利用转录组数据和实时定量聚合酶链式反应分析部分gag基因的表达模式,探索gag基因的功能。【结果】鉴定出陆地棉166个gag基因,其中A亚组基因数量多于D亚组。系统进化分析显示,该家族可分为2大类(9个亚类),基因结构多样。大多数Ghgag基因存在于LTR转座子。启动子分析发现大量与生长发育、激素响应及逆境胁迫相关的顺式作用元件。表达模式表明,部分基因在特定组织(如胚珠、纤维)或逆境(高温、盐胁迫)中较高水平表达,如Ghir_A09G013490和Ghir_D04G004460。【结论】gag基因家族在陆地棉中具有结构和功能多样性,其进化与LTR转座子活动密切相关。部分成员可能参与非生物胁迫响应及胚珠发育调控,为棉花遗传改良提供了潜在靶点。
[Objective]Transposable elements are a major driver of genome evolution,yet the functions of the gag gene family in upland cotton remain unclear.This study aimed to identify members of the gag gene family in upland cotton and analyze their structural characteristics,evolutionary relationships,and expression patterns to explore their potential roles in cotton growth,development,and stress responses.[Methods]Based on the TM-1 reference genome of upland cotton,gag gene family members were identified using HMMER software,NCBI-CDD database and the Pfam database.Bioinformatics tools were employed to analyze their physicochemical properties,subcellular localization,and chromosomal distribution.Phylogenetic trees were constructed using ClustalX and MEGA X.Cis-acting elements in promoter regions were predicted using PlantCARE website,and LTR transposon distribution was analyzed with RepeatMasker and LTR_retriever.Transcriptome data and quantiative real-time polymerase chain reaction were performed to analysis the expression patterns and functions of gag genes.[Results]A total of 166 gag genes was identified in upland cotton with significantly more genes in the A sub-genome than in the D sub-genome.Phylogenetic analysis divided the family into two major subfamilies(nine subgroups)with diverse gene structures,most of which are located in LTR transposons.Promoter analysis revealed abundant cis-acting elements related to cotton growth,development,hormone responses,and stress adaptation.Expression profiling showed that certain genes,such as Ghir_A09G013490 and Ghir_D04G004460,were highly expressed in specific tissues(e.g.,ovules,fibers)or under stress conditions(e.g.,high temperature,salt stress).[Conclusion]The gag gene family exhibits significant diversity in upland cotton,with its evolution closely linked to LTR transposon activity.Some members may play roles in abiotic stress responses and seed development,offering potential targets for cotton genetic improvement.
作者
王旭明
赵夏夏
布热比亚·亚合普
翟亚巍
杨高峰
郭志刚
马云珍
张友平
Wang Xuming;Zhao Xiaxia;Burabiye Yakup;Zhai Yawei;Yang Gaofeng;Guo Zhigang;Ma Yunzhen;Zhang Youping(Agricultural and Rural Affairs Bureau of Kashgar,Kashgar,Xinjiang 844000,China;People's Government of Kashgar City Pahataikeli Township,Kashgar,Xinjiang 844000,China;Institute of Cotton Research,Chinese Academy of Agricultural Sciences,Anyang,Henan 455000,China)
出处
《棉花学报》
北大核心
2025年第3期185-193,I0003-I0006,共13页
Cotton Science
基金
喀什地区科技计划项目《喀什市帕哈太克里乡稻区新水稻品种适应性筛选试验》(ks2022076)
新疆维吾尔自治区科技特派员创新创业项目《海水稻良种良法试验示范推广》(2022BKF273)。
关键词
陆地棉
GAG基因
生物信息学
表达模式
Gossypium hirsutum L.
gag gene
bioinformatics
expression pattern
