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Background  Among CESA-like gene superfamily, the cellulose synthase-like D ( CSLD ) genes are most similar to cellulose synthase genes and have been reported to be involved in tip-growing cell and stem development. However, there has been no genome-wide characterization of this gene subfamily in cotton. We thus sought to analyze the evolution and functional characterization of CSLD proteins in cotton based on fully sequenced cotton genomes.    Results  A total of 23 full-length CSLD proteins were identified in  Gossypium raimondii ,  Gossypium arboreum  and  Gossypium hirsutum.  The phylogenetic tree divided the CSLD proteins into five clades with strong support: CSLD1, CSLD2/3, CSLD4, CSLD5 and CSLD6. The total expression of  GhCSLD  genes was the highest in androecium & gynoecium (mostly contributed by  CSLD1  and  CSLD4 ) compared with other  CSL  genes.  CSLD1  and  CSLD4  were only highly expressed in androecium & gynoecium (A&G), and showed tissue-specific expression. The total expression of  CSLD2/3, 5 and 6  was highest in the specific tissues. These results suggest that  CSLD  genes showed the different pattern of expression. Cotton CSLD proteins were subjected to different evolutionary pressures, and the CSLD1 and CSLD4 proteins exhibited episodic and long-term shift positive selection. The predicted three-dimensional structure of GrCSLD1 suggested that GrCSLD1 belongs to glycosyltransferase family 2. The amino acid residues under positive selection in the CSLD1 lineage are positioned in a region adjacent to the class-specific region (CSR), β1-strand and transmembrane helices (TMHs) in the GrCSLD1structure.    Conclusion  Our results characterized the CSLD proteins by an integrated approach containing phylogeny, transcriptional profiling and 3D modeling. The study added to the understanding about the importance of the CSLD family and provide a useful reference for selecting candidate genes and their associations with the biosynthesis of the cell wall in cotton.    Electronic supplementary material  The online version of this article (doi:10.1186/s12870-017-1063-x) contains supplementary material, which is available to authorized users.

Evolution, gene expression profiling and 3D modeling of CSLD proteins in cotton