Identification and characterization of long non-coding RNAs in muscle sclerosis of grass carp, Ctenopharyngodon idellus fed with faba bean meal

Long noncoding RNAs (lncRNAs) are non-protein coding transcripts which have been studied extensively in human and mouse over the past few years, and play an important role in muscle development and myogenesis. Grass carp (Ctenopharyngodon idella) fed with faba bean (Vicia faba) meal is a high-value grass carp (crisp grass carp) with firmer muscles and distinct texture. To date, the regulatory mechanism of muscle firmness increase in crisp grass carp is still unclear, especially studies about the regulation of lncRNA in muscle firmness increase. In the study, based on the muscle of crisp grass carp transcriptome sequenced, a total of 82,903,440 clean reads were generated. Among them, 4240 lncRNA transcripts corresponding to 4191 lncRNA genes were identified. The identified lncRNAs shared same characteristics with the lncRNAs in other vertebrates, including shorter length of transcripts and lower expression levels of lncRNA genes. 781 differentially expressed lncRNA genes in crisp grass carp (|log2 fold change| > 2 and FDR < 0.05) were identified, and were cis-regulates 517 neighbored protein-coding genes (cis-genes of lncRNA). GO/KEGG enrichment analysis shown that the cis-genes were significantly (P < 0.05) enriched in multiple biological process of muscle-related. More, some cis-genes of down-regulated lncRNA genes were enriched in biological process of immunity-related. These results indicating that the identified lncRNAs may be in cis-regulatory relationships. This study provides a catalog of grass carp muscle-related lncRNAs, and provides new insights into the function of lncRNAs in crisp grass carp and in muscle biological process of firmness increase for future studies.