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Background   MYB  transcription factors are a kind of DNA binding protein that can specifically interact with the promoter region. Members of  MYB  TFs are widely involved in plant growth and development, secondary metabolism, stress response, and hormone signal transduction. However, there is no report of comprehensive bioinformatics analysis on the MYB family of  Casuarina equisetifolia .    Results  In this study, bioinformatics methods were used to screen out 182  MYB  transcription factors from the  Casuarina equisetifolia  genome database, including 69 1R-MYB, 107 R2R3-MYB, 4 R1R2R3-MYB, and 2 4R-MYB. The  C. equisetifolia  R2R3-MYB genes were divided into 29 groups based on the phylogenetic topology and the classification of the  MYB  superfamily in  Arabidopsis thaliana , while the remaining  MYB  genes (1R-MYB, R1R2R3-MYB, and 4R-MYB) was divided into 19 groups. Moreover, the conserved motif and gene structure analysis shown that the members of the  CeqMYB s were divided into the same subgroups with mostly similar gene structures. In addition, many conserved amino acids in the R2 and R3 domains of  CeqMYB s by WebLogo analysis, especially tryptophan residues (W), with 3 conserved W in R2 repeat and 2 conserved W in R3 repeat. Combining promoter and GO annotation analysis, speculated on the various biological functions of  CeqMYB s, thus 32  MYB  genes were selected to further explore its response to salt stress by using qPCR analysis technique. Most  CeqMYB  genes were differentially regulated following multiple salt treatments.    Conclusions  Seven genes ( CeqMYB164 ,  CeqMYB4 ,  CeqMYB53 ,  CeqMYB32 ,  CeqMYB114, CeqMYB71  and  CeqMYB177 ) were assigned to the “response to salt stress” by GO annotation. Among them, the expression level of CeqMYB4 was up-regulated under various salt treatments, indicating  CeqMYB4  might participated in the response to salt stress. Our results provide important information for the biological function of  C. equisetifolia , as well as offer candidate genes for further study of salt stress mechanism.    Supplementary Information  The online version contains supplementary material available at 10.1186/s12870-021-03083-6.

Genome-wide analysis of MYB transcription factors and their responses to salt stress in Casuarina equisetifolia