Genome-wide identification and expression analysis of Gossypium RING-H2 finger E3 ligase genes revealed their roles in fiber development, and phytohormone and abiotic stress responses

RING-H2 finger E3 ligase (RH2FE3) genes encode cysteine-rich proteins that mediate E3 ubiquitin ligase activity and degrade target substrates. The roles of these genes in plant responses to phytohormones and abiotic stresses are well documented in various species, but their roles in cotton fiber development are poorly understood. To date, genome-wide identification and expression analyses of Gossypium hirsutum RH2FE3 genes have not been reported. We performed computational identification, structural and phylogenetic analyses, chromosomal distribution analysis and estimated Ka/Ks values of G. hirsutum RH2FE3 genes. Orthologous and paralogous gene pairs were identified by all-versus-all BLASTP searches. We predicted cis-regulatory elements and analyzed microarray data sets to generate heatmaps at different development stages. Tissue-specific expression in cotton fiber, and hormonal and abiotic stress responses were determined by quantitative real time polymerase chain reaction (qRT-PCR) analysis. We investigated 140 G. hirsutum, 80 G. arboreum, and 89 G. raimondii putative RH2FE3 genes and their evolutionary mechanisms and compared them with orthologs in Arabidopsis and rice. A domain-based analysis of the G. hirsutum RH2FE3 genes predicted conserved signature motifs and gene structures. Chromosomal localization showed the genes were distributed across all G. hirsutum chromosomes, and 60 duplication events (4 tandem and 56 segmental duplications) and 98 orthologs were detected. cis-elements were detected in the promoter regions of G. hirsutum RH2FE3 genes. Microarray data and qRT-PCR analyses showed that G. hirsutum RH2FE3 genes were strongly correlated with cotton fiber development. Additionally, almost all the identified genes were up-regulated in response to phytohormones (brassinolide, gibberellic acid (GA), indole-3-acetic acid (IAA), and salicylic acid (SA)) and abiotic stresses (cold, heat, drought, and salt). The genome-wide identification, comprehensive analysis, and characterization of conserved domains and gene structures, as well as phylogenetic analysis, cis-element prediction, and expression profile analysis of G. hirsutum RH2FE3 genes and their roles in cotton fiber development and responses to plant hormones and abiotic stresses are reported here for the first time. Our findings will contribute to the genome-wide analysis of putative RH2FE3 genes in other species and lay a foundation for future physiological and functional research on G. hirsutum RH2FE3 genes.