Genome-wide landscape of microsatellites and their association with gene architecture and transcriptomic features in Perna viridis

The Asian green mussel ( Perna viridis ), an economically and ecologically significant bivalve, is recognised for its role as a filter feeder and sentinel species in coastal ecosystems. Despite its significance, the functional integration of repetitive DNA elements, particularly simple sequence repeats (SSRs), within its genome remains poorly understood. Here, we present a chromosome-level analysis of SSR distribution in Perna viridis , integrating genome organisation, functional annotation, and tissue-specific transcriptomics. A total of 268,715 SSR loci were identified, showing strong depletion in coding regions, modest enrichment in intronic and intergenic compartments, and substantial but slightly depleted representation in promoter regions. Integration with transcriptomic data revealed that 58.0% of strongly differentially expressed genes contained SSRs, with 50.8% associated with promoter-localised repeats. Functional enrichment analysis showed that SSR-associated genes are enriched in stress response, signalling, immunity, and detoxification pathways, with promoter SSRs preferentially linked to regulatory gene classes (up to 74.5%). Despite this, SSR density per gene was broadly distributed across functional categories, with the highest loads in stress-responsive (6.67), signalling (6.73), and detoxification genes (7.0). Together, these findings indicate a structured functionally constrained distribution of microsatellites within genomic regions associated with regulatory and adaptive processes in Perna viridis . The genome-wide SSR resource and associated functional annotations generated in this study provide a valuable foundation for future genetic improvement, environmental monitoring, and functional genomics in Perna viridis .