棉花学报2025，Vol.37Issue(3)：185-193,9.DOI:10.11963/cs20250020
陆地棉gag基因家族的鉴定与分析
Identification and analysis of the gag gene family in Gossypium hirsutum L
摘要
Abstract
[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.关键词
陆地棉/gag基因/生物信息学/表达模式Key words
Gossypium hirsutum L./gag gene/bioinformatics/expression pattern引用本文复制引用
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..陆地棉gag基因家族的鉴定与分析[J].棉花学报,2025,37(3):185-193,9.基金项目
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) （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) （2022BKF273）
