Investigating the influence of lncRNA-mRNA interactions on Mytilus coruscus growth using transcriptome data

Mytilus coruscus (M. coruscus) is a high-value marine aquaculture species with significant economic importance. Traditional semi-artificial seed collection methods in coastal waters are insufficient to meet current demands for improved M. coruscus varieties exhibiting desirable traits such as enhanced growth rates and larger body size. Long non-coding RNAs (lncRNAs) are known to regulate critical cellular processes, including proliferation, development, and the cell cycle. To investigate potential regulatory influences on M. coruscus growth, comparative transcriptomic analyses were performed on specimens exhibiting divergent growth phenotypes (fast-growing and slow-growing) reared under identical conditions. Foot tissue samples were aseptically collected from each group for full transcriptome sequencing. Sequencing analysis identified 91 differentially expressed long non-coding RNAs (DE-lncRNAs), comprising 55 upregulated and 36 downregulated transcripts. GO analysis showed that the target or source genes of these differentially expressed RNAs were mainly enriched in the categories of biological processes, cellular components, and molecular functions. KEGG pathway analysis revealed several signaling pathways potentially involved in growth regulation, notably TGF-beta, VEGF, Wnt, and mTOR signaling pathways. Among the identified DE-lncRNAs, MSTRG.10759.1 exhibited the highest expression levels and is predicted to regulate the BVES and RASV genes, as well as the ST13/HIP protein. Interaction network analysis of lncRNA-mRNA pairs highlighted two core target genes, PLOD1 and ANK, suggesting their potential regulatory roles in mussel growth. These findings offer new perspectives on the molecular mechanisms underlying growth in mytilids and provide foundational data for the development of molecular marker-assisted breeding strategies to produce fast-growing mussel strains.