Histone deacetylases (HDACs) catalyze histone deacetylation and suppress gene transcription during various cellular processes. Within the superfamily of HDACs, RPD3/HDA1-type HDACs are the most studied, and it is reported that RPD3 genes play crucial roles in plant growth and physiological processes. However, there is a lack of systematic research on the RPD3/HDA1 gene family in cotton. In this study, genome-wide analysis identified 9, 9, 18, and 18 RPD3 genes in Gossypium raimondii, G. arboreum, G. hirsutum, and G. barbadense, respectively. This gene family was divided into 4 subfamilies through phylogenetic analysis. The exon-intron structure and conserved motif analysis revealed high conservation in each branch of the cotton RPD3 genes. Collinearity analysis indicated that segmental duplication was the primary driving force during the expansion of the RPD3 gene family in cotton. There was at least one presumed cis-element related to plant hormones in the promoter regions of all GhRPD3 genes, especially MeJA- and ABA-responsive elements, which have more members than other hormone-relevant elements. The expression patterns showed that most GhRPD3 genes had relatively high expression levels in floral organs and performed higher expression in early-maturity cotton compared with late-maturity cotton during flower bud differentiation. In addition, the expression of GhRPD3 genes could be significantly induced by one or more abiotic stresses as well as exogenous application of MeJA or ABA. Our findings reveal that GhRPD3 genes may be involved in flower bud differentiation and resistance to abiotic stresses, which provides a basis for further functional verification of GhRPD3 genes in cotton development and a foundation for breeding better early-maturity cotton cultivars in the future.

中文翻译：

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棉花RPD3 / HDA1基因家族的全基因组鉴定和表达模式分析。

组蛋白脱乙酰基酶（HDAC）在各种细胞过程中催化组蛋白脱乙酰基化并抑制基因转录。在HDAC的超家族中，对RPD3 / HDA1型HDAC的研究最多，据报道RPD3基因在植物生长和生理过程中起着至关重要的作用。但是，目前对棉花的RPD3 / HDA1基因家族缺乏系统的研究。在这项研究中，全基因组分析分别确定了雷蒙氏棉，植物棉，陆地棉和巴巴德氏棉中的9个，9个，18个和18个RPD3基因。通过系统进化分析将该基因家族分为4个亚家族。外显子-内含子结构和保守基序分析显示，棉花RPD3基因的每个分支都具有高度保守性。共线性分析表明，节段重复是棉花RPD3基因家族扩增过程中的主要驱动力。在所有GhRPD3基因的启动子区域中，至少有一种与植物激素有关的顺式元素，尤其是MeJA和ABA响应元件，其成员比其他与激素相关的元件更多。表达模式表明，大多数GhRPD3基因在花器官分化过程中在花器官中具有相对较高的表达水平，并在早熟棉中表达高于晚熟棉。另外，一种或多种非生物胁迫以及外源施用MeJA或ABA可显着诱导GhRPD3基因的表达。