Comprehensive Characterization of 9,674 Rainbow Trout (Oncorhynchus mykiss) Large Intergenic Noncoding RNAs Using Next Generation Sequencing

Large intergenic noncoding RNAs (lincRNAs) are emerging in recent years as key regulators of diverse biological processes. It is still a challenge to determine the function of individual lincRNAs. Recent advances in RNA sequencing and bioinformatics methods have provided an opportunity to identify and analyze such transcripts. Rainbow trout (Oncorhynchus mykiss) is an important model organism in biomedical research, and the recently assembled genome sequences for rainbow trout will facilitate the understanding of the functional roles of non-coding RNA genes. The present study focused on the genome-wide identification of lincRNAs using RNA-Seq to sample the transcriptome across 15 rainbow trout tissues. We identified a stringent set of 9,674 intergenic lncRNAs. We found that lincRNAs in general are less conserved than protein-coding genes, strikingly tissue-specific compared with coding genes, and typically co-expressed with their neighboring genes. We also predicted that large portion of those tissue-specific lincRNAs are functionally associated with important biological processes, which indicates that they could play a key role in regulating tissue development and functionality. Taken together, our study has provided an initial rainbow trout lincRNA catalog, which will facilitate the functional analyses of lincRNAs in rainbow trout.