Genome-Wide Discovery of Long Non-Coding RNAs in Rainbow Trout and Their Potential Roles in Muscle Growth and Quality

The ENCODE project revealed that ~70% of the human genome is transcribed. While only 1-2% of the RNAs encode for proteins, the rest are non-coding RNAs. LncRNAs form a diverse class of non-coding RNAs that are longer than 200nt. Evidences are emerging that lncRNAs play critical roles in various cellular processes including regulation of gene expression, development, immunity and diseases, and their expression is tightly regulated. LncRNAs usually show low levels of gene expression and sequence conservation, which make their computational identification in genomes difficult.

In this study, about two billion Illumina sequence reads (including data used in annotating the trout genome and de novo assembling a transcritpome reference) were mapped to the genome reference using the TopHat and Cufflinks software. Transcripts shorter than 200 base-pairs, with more than 100 amino acid ORF, or with significant homologies to the NCBI nr-protein database were removed. In addition, a computational pipeline was used to filter the remaining transcripts based on a protein-coding-score test and similarity to other non-coding RNAs. More than 70,000 lncRNAs were identified, a small percentage of them matched known lncRNAs in other species. RNA-Seq expression profiling identified differentially expressed lncRNAs in rainbow trout families showing variations in muscle yield and quality traits. Some of the differentially expressed lncRNAs may be involved in regulating protein-coding genes associated with muscle traits. In addition, lncRNAs showed tissue specific patterns of expression. The rainbow trout lncRNAs identified and characterized in this study provide a valuable resource for functional genome research in salmonids.