RNA-seq of 43 Equine Tissues Improves Transcriptome Annotation

Initial protein-coding gene annotation of the horse genome was based on in silico predictions and a limited number of equine EST and mRNA sequences. In 2010, equine gene annotation was improved using next-generation sequencing of mRNA from eight tissues (1). The earlier stage of RNA-seq technology limited this dataset to 35 bp reads. Taking this analysis to the next step, we have now analyzed a pool of forty-three different equine mRNA samples with 75 bp single and paired-end RNA-seq reads. This more robust primary dataset combined with better computational methods have enabled an improved structural annotation of the equine mRNA transcriptome. A primary objective is to define the major transcript structures at each equine gene locus, and thereby eliminate ambiguities that result from trying to illustrate exon boundaries from multiple mRNA isoforms within a single consensus gene model. A second objective is to present these data in a user friendly manner using custom track formats that are viewable in the UCSC Genome Browser. Taken together, we hope to provide a resource of equine mRNA structures that will be useful for tissue- or disease-specific transcriptional comparisons.

1) Coleman SJ et al. 2010. Structural annotation of equine protein-coding genes determined by mRNA sequencing. Anim Genet. 41 Suppl 2:121-30.