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Background  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.    Results  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.    Conclusion  This study will provide useful information to facilitate further research related to the vital roles of  GhPHD  gene family in plant growth and development.

Response of phytohormone mediated plant homeodomain (PHD) family to abiotic stress in upland cotton (Gossypium hirsutum spp.)