Annotating Long Non-Coding RNA in the Horse Transcriptome

With efforts to resolve the transcribed sequences in the equine genome, the main focus has been protein-coding RNA and their promoters. The transcription of the intergenic regions, although detected via total RNA sequencing (RNA-seq), has yet to be characterized. The most recent equine transcriptome based on RNA-seq was a prime opportunity to obtain a concurrent long non-coding RNA (lncRNA) database. This lncRNA database has a breadth of eight tissues and a depth in over twenty million reads for select tissues, providing a starting point for an equine lncRNA database. The inputs for this database are a direct continuation of the equine transcriptome pipeline developed by Mansour et al (2016) and attempt to define the uncertainty provided by the intergenic reads and three categories of novel genes with varying levels of supportive evidence. The lncRNA candidates used in this annotation were filtered using a modified pipeline from human lncRNA annotation, which removes transcripts based on size, expression, protein-coding capability and distance to the start or stop of annotated protein-coding transcripts. Our equine lncRNA database has 21,745 transcripts, demonstrating characteristics unique to lncRNA such as low expression, low exon diversity and low levels of sequence conservation to the human. These candidate lncRNA will serve as the first baseline lncRNA annotation and begin to describe the reads assigned to the intergenic space in RNA-seq experiments in the horse.