Identification of miRNA-mRNA interaction networks in the thymus of large yellow croaker (Larimichthys crocea) from juvenile to adult stages

The thymus serves as a central lymphoid organ essential for T-cell maturation and adaptive immunity across jawed vertebrates. However, post-transcriptional regulatory mechanisms governing thymic development and involution remain poorly characterized in teleost fish. This study systematically analyzed the miRNA-mRNA interaction networks in the thymus of large yellow croaker ( Larimichthys crocea ) spanning juvenile (4 months post-fertilization, mpf) to adult stage (28 mpf). Small RNA sequencing identified 515 conserved and 396 novel miRNAs, among which 94 novel miRNAs and 155 known miRNAs exhibited significant differential expression during thymic development. Conserved thymic enrichment was observed for miR-181 family members, miR-125b-5p and miR-205–5p. Additionally, the analysis uncovered teleost-adapted miRNAs, such as novel-4540, novel-14694 and novel-15524. Target prediction revealed 3153, 1609, and 12 negatively regulated miRNA-mRNA pairs in 16 vs 4 mpf, 28 vs 4 mpf, and 28 vs 16 mpf comparisons, respectively. Functional enrichment analyses linked target mRNAs to T-cell development pathways and involution-related processes. Despite morphological involution at 28 mpf, stable expression of key genes and miRNAs, such as cd3 , miR-181 family, and miR-205–5p, indicated preserved T-cell production. The results unveil evolutionarily conserved and teleost-adapted post-transcriptional networks driving thymic ontogeny, providing foundational insights into teleost immunity and strategies for enhancing disease resilience. • Identifying conserved and novel miRNAs. • Conserved thymic enrichment‌ of miR-181 family, miR-125b-5p and miR-205-5p. • miRNA-mRNA profiles during different development stage were constructed.