Screening and identification of microRNAs during larval metamorphic development of Chinese mitten crab Eriocheir sinensis

MicroRNAs (miRNAs) represent a class of endogenous small non-coding RNAs with 18–25 nucleotides that are involved in diverse biological processes. In the present study, differentially expressed miRNAs in four different metamorphic stages of Eriocheir sinensis were comprehensively detected and validated from high-throughput sequencing miRNA data sets. We identified and characterized 597 known miRNAs and 901 novel miRNAs from the four small RNA libraries. We also demonstrated the evolutionary conservation of miRNAs from Chinese mitten crab with those from other species. Analyses of miRNA expression profiles during brachyurization development of the Chinese mitten crab revealed that 86 mature miRNAs were dysregulated, 47 of which were significantly differentially expressed. The results of real-time quantitative PCR analyses for a few selected miRNAs were similar to those of deep sequencing analyses. Intriguingly, the results of Gene Ontology annotation and KEGG pathway analyses indicated that miRNA gene clusters and families were consistently dysregulated at four different metamorphic stages, although they were enriched at various levels. Functional enrichment analysis revealed the versatile physiological roles (over six signal pathways) of these miRNAs. The results suggest that these miRNAs might play potential key roles in the regulation of gene expression in the brachyurization development of the Chinese mitten crab. Particularly, miR-2a-3p, miR-305-5p, miR-263a-5p and miR-7-5p may play major regulatory roles in the metamorphosis of E. sinensis.