Abstract：[Objective]Transposableelementsareamajordriverof genomeevolution，yetthefunctionsofthegaggenefamilyin uplandcotonremainunclear.Thisstudyaimedtoidentifymembersofthegaggenefamilyinuplandcotonandanalyze their structuralcharacteristics，evolutionaryelationshipsandexpresionpates toexploretheirpotentialolesinottongrowth， development，andstressresponses.[Methods]BasedontheTM-1reference genomeofuplandcotton，gaggenefamilyembers were identified using HMMER software，NCBI-CDDdatabaseandthePfamdatabase.Bioinformaticstoolswereemployed to analyze theirphysicochemical properties，subcellularlocalization，andchromosomaldistribution.Phylogenetictrees were constructed using ClustalXand MEGA X.Cis-acting elements in promoter regions were predicted using PlantCARE website， andLTRtransposon distribution wasanalyzed with RepeatMaskerandLTR_retriever.Transcriptomedata and quantiative real-time polymerase chainreaction were performedtoanalysis theexpressionpaterns and functionsof gag genes.[Results]A total of 166gag genes was identified in uplandcoton with significantly more genes inthe A sub-genome than in the D sub-genome.Phylogeneticanalysisdividedthefamilyintotwomajorsubfamilies（ninesubgroups）withdiversegenestructures， mostofwhich are located inLTR transposons.Promoter analysis revealed abundant cis-acting elements relatedtocoton growth，development，hormoneresponses，and stressadaptation.Expresionprofilingshowedthatcertaingenes，suchas

Ghir_A09Go13490and Ghir_D04G004460，werehighly expressed inspecifictisses（e.g.，ovules，fibers）orunderstre conditions（e.g，hightemperature，saltstress）.Conclusion]hegaggenefamilyexhibitssignificantdiversityinuplandcotton with its evolutionclosely linkedtoLTRtransposonactivity.Somemembersmayplayroles inabioticstressresponsesandseed development， offering potential targets for cotton genetic improvement.

Keywords： Gossypium hirsutum L.; gag gene; bioinformatics; expression pattern

转座子活动是生物基因组进化的重要驱动力，转座子不均等扩增调控同源基因转录、剪接和翻译，进而影响棉种谱系的特异分化。转座子是首次在玉米中发现可以在基因组中移动的DNA遗传元件。转座子总共分为2大类，一类是通过RNA转座，采用“复制和粘贴”机制进行转座，被称为反转录转座子，另一类是通过“剪切和粘贴\"的DNA转座子。反转录转座子进一步分为长末端重复（longterminalrepeat，LTR）反转录转座子和非LTR反转录转座子。LTR反转录转座子主要分为Copia 类和Gypsy类，其中某些Gypsy类成员含有编码包膜蛋白的env基因，被称为内源性逆转录病毒（endogenousretrovirus，ERV）。LTR在侧翼两端生成1段 4～6 bp的短重复序列，称为靶点重复位点（target siteduplication，TSD），可作为转座子注释鉴定的重要特征。LTR中间的编码区包含1个或多个开放阅读框，包含gag（groupspecificantigen，编码结构蛋白）和pol（编码逆转录酶等）2个基因，借助宿主体系进行转录，这种方式与逆转录病毒相似。逆转录病毒基因组结构由3部分组成，分别是基因gag（编码结构蛋白）pol（编码各种酶，如逆转录酶和整合酶）和env（编码包膜蛋白），虽然逆转录类病毒的基因组结构高度多样化，但都包含gag基因和pol基因[3]。从进化上分析，逆转录病毒可能是由Gypsy类型的LTR逆转录转座子进化而来的[4]。

目前对动物gag基因的研究较多，其中主要涉及ERV。ERV通过逆转录过程将其序列整合进宿主基因组，并具有转录活性，且在宿主基因组中不断扩张，ERV可以通过孟德尔遗传在代际之间进行垂直传播。逆转录病毒在人类和动物中的研究比较多[5，例如ERVK伴随着雀形目鸟类辐射性物种分化而在这些鸟类基因组中积累，其残留的序列可能作为顺式调控元件影响鸣禽大脑基因表达。……