Genome-Wide Identification of Mitochondrial Calcium Uniporter Family Genes in the Tomato Genus and Expression Profilings Under Salt Stress

The mitochondrial calcium uniporter (MCU) is a key channel controlling mitochondrial Ca²⁺ homeostasis, yet its role in plant stress responses remains unclear. Using the tomato pan-genome, this study identified 66 MCU genes across 12 tomato species and grouped them into two distinct evolutionary subfamilies. Phylogenetic, collinearity, and selection pressure analyses revealed that <i>MCU</i> genes are evolutionarily conserved and have undergone strong purifying selection. In addition, one MCU gene located on chromosome 6 appears to have originated before the divergence of monocots and dicots, indicating an ancient evolutionary trajectory. Gene structure and conserved motif analyses confirmed their structural conservation, while promoter cis-element analysis suggested that <i>MCU</i> genes are widely involved in light and hormone responsiveness. Expression profiling under salt stress showed that multiple <i>MCU</i> genes are differentially regulated in a time-dependent manner: <i>SolycMCU1</i> and <i>SolycMCU2</i> respond rapidly at early stages, whereas <i>SolycMCU5</i> and <i>SolycMCU6</i> are upregulated during middle and late phases. These results highlight the functional diversification of <i>MCU</i> genes in tomato under salt stress. This study provides the first comprehensive evolutionary and functional analysis of the tomato MCU gene family, offering insights into their stress-regulatory mechanisms and potential use in breeding salt-tolerant tomatoes.