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Background  Plant NADPH oxidase (NOX), also known as respiratory burst oxidase homolog (rboh), encoded by the  rboh  gene, is a key enzyme in the reactive oxygen species (ROS) metabolic network. It catalyzes the formation of the superoxide anion (O 2  •− ), a type of ROS. In recent years, various studies had shown that members of the plant  rboh  gene family were involved in plant growth and developmental processes as well as in biotic and abiotic stress responses, but little is known about its functional role in upland cotton.    Results  In the present study, 26 putative  Ghrboh  genes were identified and characterized. They were phylogenetically classified into six subfamilies and distributed at different densities across 18 of the 26 chromosomes or scaffolds. Their exon-intron structures, conserved domains, synteny and collinearity, gene family evolution, regulation mediated by  cis -acting elements and microRNAs (miRNAs) were predicted and analyzed. Additionally, expression profiles of  Ghrboh  gene family were analyzed in different tissues/organs and at different developmental stages and under different abiotic stresses, using RNA-Seq data and real-time PCR. These profiling studies indicated that the  Ghrboh  genes exhibited temporal and spatial specificity with respect to expression, and might play important roles in cotton development and in stress tolerance through modulating NOX-dependent ROS induction and other signaling pathways.    Conclusions  This comprehensive analysis of the characteristics of the  Ghrboh  gene family determined features such as sequence, synteny and collinearity, phylogenetic and evolutionary relationship, expression patterns, and  cis -element- and miRNA-mediated regulation of gene expression. Our results will provide valuable information to help with further gene cloning, evolutionary analysis, and biological function analysis of cotton  rboh s.

Comprehensive analysis of the Gossypium hirsutum L. respiratory burst oxidase homolog (Ghrboh) gene family