TY - JOUR
T1 - Annotation of the protein coding regions of the equine genome
AU - Hestand, Matthew S.
AU - Kalbfleisch, Theodore S.
AU - Coleman, Stephen J.
AU - Zeng, Zheng
AU - Liu, Jinze
AU - Orlando, Ludovic Antoine Alexandre
AU - MacLeod, James N.
PY - 2015
Y1 - 2015
N2 - 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.
AB - 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.
U2 - 10.1371/journal.pone.0124375
DO - 10.1371/journal.pone.0124375
M3 - Journal article
C2 - 26107351
AN - SCOPUS:84939213635
SN - 1932-6203
VL - 10
JO - PLoS Computational Biology
JF - PLoS Computational Biology
IS - 6
M1 - e0124375
ER -