Integration of small RNAs and mRNAs by high-throughput sequencing reveals a complex regulatory network in Chinese sea cucumber, Russian sea cucumber and their hybrids.

The body wall of the sea cucumber is an important tissue with high nutritional value. In this study, the parents of Apostichopus japonicus were derived from Russia (R) and China (C). We examined the transcriptional profiles in the body wall from F1 hybrids (CR and RC) and purebreds (CC and RR) at 9 months. In total, 34.07 G clean data were obtained from the transcriptome, 100,870 unigenes were identified, and 26,483 unigenes were annotated. Based on edgeR, 1097-4,587differentially expressed genes (DEGs) were identified. In total, 50.72 M clean data were obtained from the small RNA libraries, and 202 miRNAs were identified, including 7 known miRNAs and 195 novel miRNAs. In total, 175 miRNAs were identified as significantly differentially expressed miRNAs (diffmRNAs). Additionally, 3538 target genes were predicted, and 2243 genes were annotated in NR, COG, GO and KEGG. Furthermore, the relationships between the small RNAs and transcripts were identified, and the novel miRNA functions were predicted by integrating the small RNAs and transcriptome. According to the saponins content, RR was lower than other lines. DEGs involved in the biosynthesis of saponins were identified, including 23 DEGs involved in glycosyl, 21 DEGs involved in P450s, 5 DEGs involved in transferases and 15 DEGs involved in OSCs, from these, gdp-l-fucose, fucTcpa2 and cyp17A1 may affect the differences in the saponins development of the body wall in RR purebreds. In addition, miRNA_11347 and miRNA_32095 was associated in saponins. Our study provides fundamental information regarding the molecular mechanism of the heterosis of the sea cucumber and may suggest strategies for the selection of rapidly growing and highly nutritive strains of sea cucumber in aquaculture.