Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing

Vertebrate genomes encode thousands of non-coding RNAs including short non-coding RNAs (such as microRNAs) and long non-coding RNAs (lncRNAs). Chicken (Gallus gallus) is an important model organism for developmental biology, and the recently assembled genome sequences for chicken will facilitate the understanding of the functional roles of non-coding RNA genes during development. The present study concerns the first systematic identification of lncRNAs using RNA-Seq to sample the transcriptome during chicken muscle development. A computational approach was used to identify 281 new intergenic lncRNAs in the chicken genome. Novel lncRNAs in general are less conserved than protein-coding genes and slightly more conserved than random non-coding sequences. The present study has provided an initial chicken lncRNA catalog and greatly increased the number of chicken ncRNAs in the non-protein coding RNA database. Furthermore, the computational pipeline presented in the current work will be useful for characterizing lncRNAs obtained from deep sequencing data. ► The first systematic identification of lncRNAs during chicken muscle development was reported. ► Using the computational approach, 281 new lncRNAs were identified in the chicken genome. ► The novel lncRNAs are slightly more conserved than random noncoding sequences. ► The presented pipeline will be useful for characterizing lncRNAs from deep sequencing data.sd