Identification and characterization of microRNAs in the spleen of common carp immune organ

MicroRNAs (miRNAs) play an important role in the regulation of many fundamental biological processes in eukaryotes; however, miRNAs associated with immune functions in the common carp have not been reported. In this study, a small-RNA cDNA library was constructed from the spleen of the common carp. A total of 10,603,456 high-quality clean reads, representing 293,603 unique sequences, were obtained from the small-cDNA library using the Solexa sequencing. By the bioinformatic analysis, 194 conserved miRNAs and 12 novel miRNAs were identified in the carp spleen. The abundant miRNAs principally belong to 30 miRNA gene families such as let-7, mir-10, mir-15, mir-30, and so on. The conservation analysis showed that 23 families were present both in protostomes and deuterostomes, 46 families were conserved only in vertebrates, and 5 families (mir-430, mir-722, mir-724, mir-734, and mir-738) were identified only in fish species. Furthermore, GO enrichment analysis and KEGG pathway analysis suggested that miRNAs expressed in the spleen of common carp are involved in immune system development, lymphoid organ development, lymphocyte activation, immune response, B cell receptor signaling pathway, T cell receptor signaling pathway, Fc gamma R-mediated phagocytosis, Toll-like receptor signaling pathway, and so on. This study described the miRNA transcriptome in spleen tissue for the first time in the common carp. The results expand the number of known common carp miRNAs and provides a meaningful framework to understand the common carp immune system and defense mechanisms.