Genome-Wide Analysis Reveals Expansion and Positive Selection of Monocarboxylate Transporter Genes Linked to Enhanced Salinity and Ammonia Tolerance in Sinonovacula constricta

Our previous genome analysis of <i>Sinonovacula constricta</i> revealed an expansion of the monocarboxylate transporter gene family, which is crucial for metabolic dynamic balance and intracellular pH regulation. To further elucidate the role of these expanded <i>MCT</i> genes in response to variable environmental conditions, we conducted a comprehensive genome-wide identification, phylogenetic evolution and expression analysis. In this study, 16 sodium-coupled monocarboxylate transporter genes (designated as <i>ScSMCTs</i>) and 54 proton-coupled monocarboxylate transporter genes (designated as <i>ScMCTs</i>) were identified from the <i>S. constricta</i> genome. The results of gene number comparison indicated significant expansion of <i>ScSMCTs</i> and <i>ScMCTs</i> in mollusks compared to vertebrates, likely due to tandem repeats and dispersed duplications in <i>S. constricta</i>. The syntenic analysis demonstrated that the razor-clam <i>MCT</i> genes had the highest number of homologous gene pairs with <i>Meretrix meretrix</i>. The phylogenetic tree showed that <i>MCT</i> and <i>SMCT</i> proteins were distinctly clustered in two large branches. Moreover, positive selection analysis revealed three positive selection sites in the <i>MCT</i> amino acid sequences sites. Multi-transcriptome analyses and the temporal expression patterns displayed that <i>ScSMCTs</i> and <i>ScMCTs</i> play distinct roles in response to salinity and ammonia stressors. It is worth noting that the majority of these genes involved in abiotic stresses belong to <i>MCTs</i>. Overall, our findings revealed the important roles of <i>ScSMCTs</i> and <i>ScMCTs</i> under abiotic stress, and provided valuable information for the evolution of this family in mollusks, as well as a theoretical basis for the further study of the mechanism and function of this gene family in <i>S. constricta</i>.