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.

MicroRNAs (miRNAs) 通过调节特定基因表达在生物过程中发挥重要作用。到目前为止，关于鲤鱼（Cyprinus carpio）胚胎发育的 miRNA 信息有限。在这项研究中，C. carpio 的六个重要胚胎发育阶段收集了从卵裂、胚泡、原肠胚形成、器官形成、孵化阶段到孵化后 1 天的一系列小 RNA-seq 实验。鉴定miRNA的表达谱，并基于成对比较筛选出差异表达的miRNA（DEM）。从每个文库中获得了 12,744,989 个原始读数和 9,888,123 个干净读数的平均值。共鉴定出 2565 个 miRNA。204 个 DEM 中有 68 个与阶段特异性 miRNA 重叠，其中 15 个是已知的 miRNA，似乎在胚胎发生中起关键作用。此外，时间过程表达揭示了胚胎发生过程中的几个有趣的波动。在胚胎发育过程中发现了许多信号通路，包括光转导、河马信号通路、Wnt、黑色素生成、组氨酸代谢和脂肪酸生物合成。该结果将为 miRNA 在胚胎发育中的作用提供新的见解，并有助于我们进一步了解 miRNA 介导的鱼类胚胎发育机制。