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Background  Transcription factors operate as important switches of transcription networks, and NAC (NAM, ATAF, and CUC) transcription factors are a plant-specific family involved in multiple biological processes. However, this gene family has not been systematically characterized in cotton.    Results  Here we identify a large number of genes with conservative NAC domains in four cotton species, with 147 found in  Gossypium arboreum , 149 in  G. raimondii , 267 in  G. barbadense  and 283 in  G. hirsutum . Predicted membrane-bound  NAC  genes were also identified. Phylogenetic analysis showed that cotton NAC proteins clustered into seven subfamilies and homologous protein pairs showed similar characteristics. Evolutionary property analysis revealed that purifying selection of  NAC  genes occurred between diploid and polyploid cotton species, and variation analysis showed  GhNAC  genes may have been subjected to selection and domestication. NAC proteins showed extensive transactivation and this was dependent on the C-terminus. Some development and stress related cis-elements were enriched in the promoters of  GhNAC  genes. Comprehensive expression analysis indicated that 38  GhNAC  genes were candidates for involvement in fiber development, and 120 in stress responses. Gene co-expression network analysis revealed relationships between fiber-associated  NAC  genes and secondary cell wall (SCW) biosynthesis genes.    Conclusions   NAC  genes were identified in diploid and tetraploid cotton, revealing new insights into their evolution, variation and homology relationships. Transcriptome analysis and co-expression network indicated roles for  GhNAC  genes in cotton fiber development and stress response, and NAC genes may prove useful in molecular breeding programmes.    Electronic supplementary material  The online version of this article (10.1186/s12870-018-1367-5) contains supplementary material, which is available to authorized users.

Comprehensive analysis of NAC transcription factors uncovers their roles during fiber development and stress response in cotton