Transcriptome analysis provides insights into differentially expressed long noncoding RNAs between the testis and ovary in golden pompano (Trachinotus blochii)

The golden pompano (Trachinotus blochii) is a warm water fish that is widely distributed in tropical and subtropical waters. T. blochii is one of the most important economic species in China where it is produced in marine cage culture; however, few studies have been performed on the mechanism of sex determination and differentiation, and there are no obvious morphological differences between males and females. To further understand the role of long non-coding RNAs (lncRNAs) in sex determination and gonadal development of T. blochii, we conducted a tran-scriptome analysis of T. blochii ovaries and testes. In this study, a total of 530,128,262 clean reads were produced from six cDNA libraries, after stringent filtering. The RNA-seq analysis yielded 13,509 novel lncRNAs, 2621 novel mRNAs, and 18,683 known mRNA transcripts with 4909 and 10,410 differentially expressed lncRNAs and mRNAs. The Gene Ontology (GO) enrichment patterns between the lncRNAs and mRNAs were different. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis confirmed that some of the differentially expressed mRNAs and target genes of the lncRNAs were mainly associated with several sex determination and gonadal development signaling pathways, including the GnRH signaling pathway, the Wnt signaling pathway, and the insulin signaling pathway. The lncRNA-mRNA co-expression network analysis showed that the lncRNA TCONS_00083175 may play a key role in the T. blochii sex differentiation. The findings broaden our understanding of lncRNAs and gonad genetics, and provide new insight into the function of lncRNAs in sex differentiation and highlight a key lncRNA for future studies.