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Background  WUSCHEL-related homeobox (WOX) family members play significant roles in plant growth and development, such as in embryo patterning, stem-cell maintenance, and lateral organ formation. The recently published cotton genome sequences allow us to perform comprehensive genome-wide analysis and characterization of WOX genes in cotton.    Results  In this study, we identified 21, 20, and 38 WOX genes in  Gossypium arboreum  (2n = 26, A 2 ),  G. raimondii  (2n = 26, D 5 ), and  G. hirsutum  (2n = 4x = 52, (AD) t ), respectively. Sequence logos showed that homeobox domains were significantly conserved among the WOX genes in cotton,  Arabidopsis , and rice. A total of 168 genes from three typical monocots and six dicots were naturally divided into three clades, which were further classified into nine sub-clades. A good collinearity was observed in the synteny analysis of the orthologs from At and Dt (t represents tetraploid) sub-genomes. Whole genome duplication (WGD) and segmental duplication within At and Dt sub-genomes played significant roles in the expansion of WOX genes, and segmental duplication mainly generated the WUS clade. Copia and Gypsy were the two major types of transposable elements distributed upstream or downstream of WOX genes. Furthermore, through comparison, we found that the exon/intron pattern was highly conserved between  Arabidopsis  and cotton, and the homeobox domain loci were also conserved between them. In addition, the expression pattern in different tissues indicated that the duplicated genes in cotton might have acquired new functions as a result of sub-functionalization or neo-functionalization. The expression pattern of WOX genes under different stress treatments showed that the different genes were induced by different stresses.    Conclusion  In present work, WOX genes, classified into three clades, were identified in the upland cotton genome. Whole genome and segmental duplication were determined to be the two major impetuses for the expansion of gene numbers during the evolution. Moreover, the expression patterns suggested that the duplicated genes might have experienced a functional divergence. Together, these results shed light on the evolution of the WOX gene family, and would be helpful in future research.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-017-1065-8) contains supplementary material, which is available to authorized users.

Genome-wide analysis of WOX genes in upland cotton and their expression pattern under different stresses