Genome-wide identification of the monovalent cation/proton antiporter (CPA) superfamily and expression analysis in tomato

The cation/proton antiporter (CPA) superfamily, crucial for regulating Na+, K+, and pH equilibrium in plant cells, plays an essential role in plant growth and stress adaptation. However, limited research has been conducted on the CPA gene superfamily in tomatoes. In this study, a total of 31 SlCPA members were identified in the tomato genome, comprising 18 cation/H+ exchangers (SlCHXs), 7 Na+/H+ exchangers (SlNHXs), and 6 K+ efflux antiporters (SlKEAs). A comprehensive analysis encompassing their chromosomal locations, gene structures, phylogenetic relationships, collinearity, tissue-specific expression profiles, and responses to abiotic stress was undertaken. Collinearity and phylogenetic analyses unveiled two groups, represented by Solyc08g081810, Solyc01g008190, Solyc12g056160, and Solyc06g060630, Solyc08g078880, suggesting potential redundancy resulting from duplication events. Tissue-specific expression analysis revealed SlNHXs and SlKEAs expression at multiple developmental stages, while SlCHXs were predominantly expressed during early flower and fruit development, indicating their likely involvement in these processes. Salt treatment notably induced the expression of SlSOS1 (Solyc01g005020) and Solyc04g056600, implicating their role in responding to salt stress. Under drought stress, the expression of Solyc01g005020 and Solyc08g081820 was also significantly induced, supported by promoter element analyses indicating the presence of drought response-related cis-elements like ABRE and MYB binding sites. This study establishes a foundation for further elucidating the gene functions of individual members within the tomato SlCPA family.