Integrated full-length transcriptome and microRNA sequencing approaches reveal sex-related RNAs in Collichthys lucidus

Collichthys lucidus is an important economical fish species and shows sex dimorphism on the growth rate. However, there is lack of research on sex-related mechanism of C. lucidus. To better understand the sex-related molecular mechanisms in C. lucidus, full length transcriptome sequencing and microRNA sequencing were performed. In this study, 36,364,007 subreads reads and 71,687 high-quality isoforms with an average length of 2936.42 bp were generated from a pooled library of 13 tissues in C. lucidus. We obtained 40,643 high-quality non-redundant transcripts that covered 12,477 annotated gene loci and 5,884 novel transcripts. Moreover, we identified 1,376 lncRNAs and 2,576 transcript factors, among which 13 transcript factors were sex-related genes. Furthermore, 171 differentially expressed miRNAs (DE-miRNAs) were identified between ovary and testis, and the regulatory networks between DE-miRNAs, DE-mRNA and lncRNA were established. Functional enrichment analysis revealed that the target genes of the DE-miRNAs were significantly enriched in p53 signaling pathway, PI3K-Akt signaling pathway and TGF-beta signaling pathway. Sex-related miRNAs were identified and the expression of miR-430c-3p and miR-430f-3p were specifically in the gonad compared to other tissues, and significantly upregulated in the testis compared with the ovary. We provide the first comprehensive full-length transcriptome and miRNA profile resource for the gender of C. lucidus that might lay a foundation for further researches on the sex determination in C. lucidus.