Annotation of the Equine mRNA Transcriptome

We have investigated the structural annotation of equine protein coding genes in three studies.  Known and predicted gene loci in EquCab2 were analyzed with RNA-seq reads from a pool of 43 different equine tissues.  A total of 26,542 transcript structures were defined with three or more exons, representing 18,284 gene loci.  Broadly expressed mRNA transcripts were prioritized by the experimental design, since tissue-restricted variants were less likely to be detected in the pooled sample.  A separate study of six individual tissues identified an additional 428 loci with RNA-seq read alignments consistent with multiple exon mRNAs, all of which had been previously unannotated in EquCab2.  The majority are homologues of known protein-coding genes annotated in other species, but the set also includes several genes that appear to be unique to equids.  Finally, 76 genes not currently on the equine gene list were localized to a set of genomic DNA contigs constructed using 2x100 paired-end gDNA reads from Twilight that failed to align to EquCab2.  Taken together, these data provide a baseline of equine protein-coding gene structure.