An Equine Long Non-Coding RNA Database Complimenting the Most Recent Equine Transcriptome

To date, efforts to resolve the transcribed sequences in the equine genome have primarily focused on protein-coding RNA and their promoters. Transcribed intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet to be characterized in the horse. The most recent equine transcriptome based on RNA-seq was a prime opportunity for the development of a concurrent long non-coding RNA (lncRNA) database. This preliminary lncRNA dataset was developed from the eight tissues used in above equine transcriptome. The lncRNA used in this annotation are filtered using a modified pipeline from human lncRNA annotation, which removes transcripts based on size, expression, protein coding capability and distances to the start or stop of genes. An additional filter involved local de novo assembly of the equine transcriptome in regions characterized specifically in the horse as “complex loci”. These regions have conflicting annotations by various equine transcriptomes and have been reconstructed de novo to obtain the most accurate sequence at that locus. Preliminary data, post filtering by expression, length and overlap with genes from the recent equine annotation as well as NCBI and ENSEMBL databases has resulted in a lncRNA database with 24,189 transcripts, with a mean expression of 7 transcripts per million (TPM) across all eight tissues. This database will serve as a baseline for lncRNA annotation and begin to describe the reads assigned to the intergenic space in RNA-seq experiments.