Comprehensive assessment of a miRNA-mRNA regulatory network in Meretrix meretrix: Implications for metabolism and autophagy across divergent growth rates

MicroRNAs (miRNAs) are a class of non-coding RNAs that modulate gene expression at the post-transcriptional level. Characterized by their dynamic expression patterns, miRNAs play a crucial role in regulating a multitude of biological processes, including metabolism and autophagy. For fishermen, enhancing the growth performance of the Asian hard clam, Meretrix meretrix, is vital for increasing yields and their income. To elucidating the regulatory mechanisms underlying clam growth, a comparative analysis of the miRNA and mRNA transcriptomes was undertaken for M. meretrix specimens exhibiting disparate growth rates. The results showed that a total of 32 differentially expressed miRNAs (DEMs) and 1049 differentially expressed mRNAs (DEGs) were identified. Furthermore, an integrated miRNA-mRNA expression analysis enabled the identification of 459 differentially predicted target genes (DETGs) associated with the DEMs. A significant enrichment in multiple functional categories related to metabolism and autophagy was observed among the DETGs. We constructed an intricate regulatory network that encompasses the metabolic and autophagy pathways influenced by 11 pivotal DEMs and 15 DETGs, which differ across the growth rates of M. meretrix. The results indicate that variations in growth rates elicit complex responses in both miRNA and mRNA expression, profoundly influencing the metabolic and autophagy processes within M. meretrix.