Identification, characterization, and expression analysis reveal regulatory roles of MCM genes in Patinopecten yessoensis under low-pH stress

The Yesso scallop (Patinopecten yessoensis), an ecomically important bivalve species, exhibits high susceptibility to ocean acidification. The growth retardation induced by low-pH stress poses a significant challenge for Yesso scallop aquaculture. However, the molecular mechanisms underlying this phenomenon are not well understood. Considering the pivotal role of cell proliferation in organism growth, we investigated the minichromosome maintenance (MCM) family in P. yessoensis, which are key regulators of DNA replication initiation and cell cycle regulation. In this study, we identified nine MCM genes (PyMCM2–10) in the P. yessoensis genome. These PyMCMs exhibit highly conserved sequence characteristics and typical MCM domains. Phylogenetic analysis showed that PyMCMs cluster into nine distinct clades, underscoring their strong evolutionary conservation across species homologs. Spatiotemporal expression profiling demonstrated widespread expressions of PyMCMs throughout all developmental stages and adult tissues, with particularly high levels in vigorous cell proliferation (e.g., up to 318 TPM in multicell stage and up to 202 TPM in gonad tissue). Notably, PyMCM6 exhibited consistently high expression across development and across tissues (> 44 TPM), suggesting a key regulatory role in both development and tissue maintenance. Under low-pH stress, the expressions of PyMCMs were downregulated to varying degrees, with PyMCM5 showing the most significant reduction (|log₂FC| up to 3.5), while PyMCM8 and PyMCM9 remained relatively stable. This pattern suggests a strategic response that scallops reduce DNA replication capacity (mediated by PyMCM2–7) but potentially maintain DNA repair functions (associated with PyMCM8/9 stability) to mitigate damage induced by low-pH, potentially explaining the intrinsic inhibition of cell proliferation. Quantitative real-time PCR and in situ hybridization further confirmed that low-pH stress inhibits PyMCMs expressions (p < 0.05), with the effect amplified as pH decreases. Collectively, these findings enhance our understanding of PyMCMs in regulating bivalve growth retardation under low-pH stress and provide valuable insights into the mechanisms of environmental adaptation in bivalves.