Annotation of the protein coding regions of the equine genome

Matthew S. Hestand, Theodore S. Kalbfleisch, Stephen J. Coleman, Zheng Zeng, Jinze Liu, Ludovic Orlando, James N. MacLeod

Research output: Contribution to journalArticlepeer-review

21 Scopus citations


Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons.

Original languageEnglish
Article numbere0124375
JournalPLoS ONE
Issue number6
StatePublished - Jun 24 2015

Bibliographical note

Publisher Copyright:
© 2015 Hestand et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

ASJC Scopus subject areas

  • General


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