Comparative microRNAs expression profiles analysis during embryonic development of common carp, Cyprinus carpio.

MicroRNAs (miRNAs) play important roles in biological processes by regulating specific gene expression. Limited miRNAs information is available on embryonic development in common carp (Cyprinus carpio) so far. In this study, six important embryonic development stages of C. carpio were collected to perform a times-series of small RNA-seq experiments from cleavage, blastocyst, gastrulation, organ formation, hatching stage to 1 day post-hatching larva. The expression profiles of miRNAs were identified and differentially expressed miRNAs (DEMs) were screened out based on pairwise comparison. A mean of 12,744,989 raw reads and 9,888,123 clean reads were obtained from each library. A total of 2565 miRNAs were identified. 68 of 204 DEMs were overlapped with stage-specific miRNAs, in which 15 were known miRNAs and seemed to play a key role in embryogenesis. Additionally, time-course expression reveals several intriguing fluctuations during embryogenesis. Numerous signaling pathways were identified in embryonic development, including the phototransduction, hippo signaling pathway, Wnt, melanogenesis, histidine metabolism and fatty acid biosynthesis. The results would provide new insight into the roles of miRNAs in embryonic development, and would help us to advance the understanding of miRNA-mediated mechanisms in embryonic development of fish. Unlabelled Image • It provides the first miRNAs expression profile of six embryonic stages in C. carpio. • We screened the stage specific miRNAs and differentially expressed miRNAs (DEMs). • 15 known DEMs seemed to play important roles in embryogenesis. • The specifically expressed miRNAs-mRNA interaction is crucial for mechanisms. • Many pathways related to embryonic development were identified. [ABSTRACT FROM AUTHOR]