Identification and comparative analysis of Eriocheir sinensis microRNA transcriptome from claw muscles related molting

Molting is a critical developmental process for crustaceans, during which the claw muscles undergo periodic atrophy and restoration. The regulatory mechanism of this special muscle reshuffle around ecdysis was not clear. To investigate the molecular mechanism underlying the muscle changes in crustaceans, we used Illumina/Solexa deep sequencing technology to sequence small RNA libraries prepared from claw muscles of Eriocheir sinensis in three molting stages (inter-molt C stage, later pre-molt D3–4 stage and post molt A–B stage). The sequencing resulted in 8,054,808, 9,944,487 and 10,202,589 high-quality clean reads, corresponding to 2767, 2676, and 2891 unique miRNAs for the A–B, C and D3–4 stage samples, respectively. Bioinformatic analyses identified 1485 mature miRNAs, among which 1392 miRNAs belong to 218 miRNA families and 93 miRNAs belong to unknown families. Altogether, 115 miRNAs were differentially expressed among the three molting stages, and they were clustered into 5 subclusters according to their expression patterns. GO and KEGG analysis revealed that the predicted targets of the differentially expressed miRNAs are particularly associated with gene expression, protein degradation and synthesis, muscle atrophy and development, post-embryonic morphogenesis, and anatomical structure development. Our findings suggest that the differentially expressed miRNAs and their target genes play important roles in growth and development of crab muscles induced by molting.