The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information. Plant homeodomain (PHD) protein family has been reported to be involved in regulating various biological processes in plants. However, their functional studies have not yet been carried out in cotton. In this study, 108, 55, and 52 PHD genes were identified in G. hirsutum, G. raimondii, and G. arboreum, respectively. A total of 297 PHD genes from three cotton species, Arabidopsis, and rice were divided into five groups. We performed chromosomal location, phylogenetic relationship, gene structure, and conserved domain analysis for GhPHD genes. GhPHD genes were unevenly distributed on each chromosome. However, more GhPHD genes were distributed on At_05, Dt_05, and At_07 chromosomes. GhPHD proteins depicted conserved domains, and GhPHD genes exhibiting similar gene structure were clustered together. Further, whole genome duplication (WGD) analysis indicated that purification selection greatly contributed to the functional maintenance of GhPHD gene family. Expression pattern analysis based on RNA-seq data showed that most GhPHD genes showed clear tissue-specific spatiotemporal expression patterns elucidating the multiple functions of GhPHDs in plant growth and development. Moreover, analysis of cis-acting elements revealed that GhPHDs may respond to a variety of abiotic and phytohormonal stresses. In this regard, some GhPHD genes showed good response against abiotic and phytohormonal stresses. Additionally, co-expression network analysis indicated that GhPHDs are essential for plant growth and development, while GhPHD genes response against abiotic and phytohormonal stresses may help to improve plant tolerance in adverse environmental conditions. This study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.

中文翻译：

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植物激素介导的植物同源域（PHD）家族对陆地棉（Gossypium hirsutum spp.）非生物胁迫的响应

棉花基因组的测序和注释为揭示更多生理和功能信息提供了强有力的理论支持。据报道，植物同源域 (PHD) 蛋白家族参与调节植物中的各种生物过程。然而，它们的功能研究尚未在棉花中进行。在这项研究中，分别在 G. hirsutum、G. raimondii 和 G. arboreum 中鉴定了 108、55 和 52 个 PHD 基因。将来自三个棉花物种、拟南芥和水稻的 297 个 PHD 基因分为五组。我们对 GhPHD 基因进行了染色体定位、系统发育关系、基因结构和保守域分析。GhPHD 基因在每条染色体上分布不均。然而，更多的 GhPHD 基因分布在 At_05、Dt_05 和 At_07 染色体上。GhPHD 蛋白描述了保守结构域，而表现出相似基因结构的 GhPHD 基因聚集在一起。此外，全基因组重复（WGD）分析表明纯化选择极大地促进了 GhPHD 基因家族的功能维持。基于 RNA-seq 数据的表达模式分析表明，大多数 GhPHD 基因显示出清晰的组织特异性时空表达模式，阐明了 GhPHD 在植物生长发育中的多种功能。此外，对顺式作用元件的分析表明，GhPHD 可能对各种非生物和植物激素胁迫做出反应。在这方面，一些 GhPHD 基因对非生物和植物激素胁迫表现出良好的反应。此外，共表达网络分析表明 GhPHDs 对植物生长发育至关重要，而 GhPHD 基因对非生物和植物激素胁迫的反应可能有助于提高植物在不利环境条件下的耐受性。这项研究将提供有用的信息，以促进与 GhPHD 基因家族在植物生长和发育中的重要作用相关的进一步研究。