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Background  In plants, Calcium (Ca 2+ ) acts as a universal messenger in various signal transduction pathways, including responses to biotic and abiotic stresses and regulation of cellular and developmental processes. The Ca 2+ /cation antiporter (CaCA) superfamily proteins play vital roles in the transport of Ca 2+  and/or other cations. However, the characteristics of these superfamily members in  Saccharum  and their evolutionary and functional implications have remained unclear.    Results  A total of 34  CaCA  genes in  Saccharum spontaneum , 5  CaCA  genes in  Saccharum  spp. R570, and 14  CaCA  genes in  Sorghum bicolor  were identified and characterized. These genes consisted of the H + /cation exchanger (CAX), cation/Ca 2+  exchanger (CCX), EF-hand / CAX (EFCAX), and Mg 2+ /H +  exchanger (MHX) families, among which the CCX and EFCAX could be classified into three groups while the CAX could be divided into two groups. The exon/intron structures and motif compositions suggested that the members in the same group were highly conserved. Synteny analysis of  CaCAs  established their orthologous and paralogous relationships among the superfamily in  S. spontaneum , R570, and  S. bicolor . The results of protein-protein interactions indicated that these CaCA proteins had direct or indirect interactions. Quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis demonstrated that most members of  Saccharum CaCA  genes exhibited a similar expression pattern in response to hormonal (abscisic acid, ABA) treatment but played various roles in response to biotic ( Sporisorium scitamineum ) and abiotic (cold) stresses. Furthermore,  ScCAX4 , a gene encoding a cytoplasm, plasma membrane and nucleus positioning protein, was isolated from sugarcane. This gene was constitutively expressed in different sugarcane tissues and its expression was only induced at 3 and 6 h time points after ABA treatment, however was inhibited and indued in the whole process under cold and  S. scitamineum  stresses, respectively.    Conclusions  This study systematically conducted comparative analyses of  CaCA  superfamily genes among  S. spontaneum , R570, and  S. bicolor , delineating their sequence and structure characteristics, classification, evolutionary history, and putative functions. These results not only provided rich gene resources for exploring the molecular mechanism of the  CaCA  superfamily genes but also offered guidance and reference for research on other gene families in  Saccharum .    Supplementary Information  The online version contains supplementary material available at 10.1186/s12864-021-07828-3.

The CaCA superfamily genes in Saccharum: comparative analysis and their functional implications in response to biotic and abiotic stress