| Summary: | Multidrug and Toxic Compound Extrusion (MATE) proteins are essential transporters that extrude metabolites and participate in plant development and the detoxification of toxins. Little is known about the <i>MATE</i> gene family in the Solanaceae, which includes species that produce a broad range of specialized metabolites. Here, we identified and analyzed the complement of <i>MATE</i> genes in pepper (<i>Capsicum annuum</i>) and potato (<i>Solanum tuberosum</i>). We classified all <i>MATE</i> genes into five groups based on their phylogenetic relationships and their gene and protein structures. Moreover, we discovered that tandem duplication contributed significantly to the expansion of the pepper <i>MATE</i> family, while both tandem and segmental duplications contributed to the expansion of the potato <i>MATE</i> family, indicating that <i>MATEs</i> took distinct evolutionary paths in these two Solanaceous species. Analysis of ω values showed that all potato and pepper <i>MATE</i> genes experienced purifying selection during evolution. In addition, collinearity analysis showed that <i>MATE</i> genes were highly conserved between pepper and potato. Analysis of <i>cis</i>-elements in <i>MATE</i> promoters and <i>MATE</i> expression patterns revealed that MATE proteins likely function in many stages of plant development, especially during fruit ripening, and when exposed to multiple stresses, consistent with the existence of functional differentiation between duplicated <i>MATE</i> genes. Together, our results lay the foundation for further characterization of pepper and potato <i>MATE</i> gene family members.
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