Annotation of the protein coding regions of the equine genome

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

doi:10.1371/journal.pone.0124375

Annotation of the protein coding regions of the equine genome

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

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Abstract

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 language	English
Article number	e0124375
Journal	PLOS ONE
Volume	10
Issue number	6
Number of pages	13
ISSN	1932-6203
DOIs	https://doi.org/10.1371/journal.pone.0124375
Publication status	Published - 2015

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title = "Annotation of the protein coding regions of the equine genome",

abstract = "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.",

author = "Hestand, {Matthew S.} and Kalbfleisch, {Theodore S.} and Coleman, {Stephen J.} and Zheng Zeng and Jinze Liu and Orlando, {Ludovic Antoine Alexandre} and MacLeod, {James N.}",

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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.

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DO - 10.1371/journal.pone.0124375

M3 - Journal article

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SN - 1932-6203

VL - 10

JO - PLoS Computational Biology

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Annotation of the protein coding regions of the equine genome

Abstract

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