Abstract
BackgroundThe 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.ResultsIn 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.ConclusionThis study will provide useful information to facilitate further research related to the vital roles of GhPHD gene family in plant growth and development.
Highlights
The sequencing and annotations of cotton genomes provide powerful theoretical support to unravel more physiological and functional information
Genome-wide identification of Plant homeodomain (PHD) proteins in cotton Based on the homology of protein sequences, 108, 52, and 55 PHD proteins were identified in three cotton species G. hirsutum, G. arboreum, and G. raimondii, respectively
Among 108 GhPHD proteins, 56 members belong to the Arabidopsis thaliana (At) subgenome and 52 members belong to the Dt subgenome
Summary
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. Their functional studies have not yet been carried out in cotton. Plants often face various abiotic and biotic stress conditions. Cold, drought, and salinity, whereas biotic stresses mainly come from bacteria, fungi, viruses, and insects. These abiotic and biotic stresses significantly reduce crop quality and productivity world-wide [1, 2]. Phytohormones play significant roles in regulating developmental processes and signal transduction networks, which respond to various abiotic stresses. Brassinosteroid (BR), jasmonate (JA), gibberellin (GA), salicylic acid (SA), auxin, and abscisic acid (ABA) regulate plant growth, development, stress, and defense responses [4,5,6,7,8,9,10,11], but how phytohormones mediate the growth and stress trade-off is unclear
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