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Background  The  WOX  ( WUSCHEL-RELATED HOMEOBOX ) gene family encodes a class of transcription factors that are unique to green plants, where they are involved in regulating the development of plant tissues and organs by determining cell fate. Although the importance of the  WOX  gene is well known, there are few studies describing their functions in cotton.    Results  In this study, 32 WOX genes were found in  Gossypium hirsutum . Phylogenetic analysis showed that WOX proteins of cotton can be divided into three clades: the ancient, intermediate, and WUS clades. The number of WOX proteins in the WUS clade was greater than the sum of the proteins in the other two clades. Our analysis revealed that 20  GhWOX  genes are distributed on 16 cotton chromosomes and that duplication events are likely to have contributed to the expansion of the  GhWOX  family. All  GhWOX  genes have introns, and each GhWOX protein contains multiple motifs. RNA-seq data and real-time PCR showed that  GhWOX13  gene subfamily is specifically expressed at a high level in cotton fibers. We also identified putative GA, NAA, and BR response elements in the promoter regions of the  GhWOX13  genes and  GhWOX13  transcripts were significantly induced by GA, NAA, and BR.    Conclusions  Our data provides a useful resource for future studies on the functional roles of cotton  WOX  genes and shows that the  GhWOX13  genes may influence cotton fiber development. Our results also provide an approach for identifying and characterizing WOX protein genes in other species.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1892-x) contains supplementary material, which is available to authorized users.

Comprehensive analysis of WOX genes uncovers that WOX13 is involved in phytohormone-mediated fiber development in cotton