Structural annotation of equine protein-coding genes determined by mRNA sequencing.
Abstract: The horse, like the majority of animal species, has a limited amount of species-specific expressed sequence data available in public databases. As a result, structural models for the majority of genes defined in the equine genome are predictions based on ab initio sequence analysis or the projection of gene structures from other mammalian species. The current study used Illumina-based sequencing of messenger RNA (RNA-seq) to help refine structural annotation of equine protein-coding genes and for a preliminary assessment of gene expression patterns. Sequencing of mRNA from eight equine tissues generated 293,758105 sequence tags of 35 bases each, equalling 10.28 gbp of total sequence data. The tag alignments represent approximately 207 × coverage of the equine mRNA transcriptome and confirmed transcriptional activity for roughly 90% of the protein-coding gene structures predicted by Ensembl and NCBI. Tag coverage was sufficient to refine the structural annotation for 11,356 of these predicted genes, while also identifying an additional 456 transcripts with exon/intron features that are not listed by either Ensembl or NCBI. Genomic locus data and intervals for the protein-coding genes predicted by the Ensembl and NCBI annotation pipelines were combined with 75,116 RNA-seq-derived transcriptional units to generate a consensus equine protein-coding gene set of 20,302 defined loci. Gene ontology annotation was used to compare the functional and structural categories of genes expressed in either a tissue-restricted pattern or broadly across all tissue samples.
© 2010 The Authors, Journal compilation © 2010 Stichting International Foundation for Animal Genetics.
Publication Date: 2010-11-26 PubMed ID: 21070285DOI: 10.1111/j.1365-2052.2010.02118.xGoogle Scholar: Lookup
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- Journal Article
- Research Support
- N.I.H.
- Extramural
- Research Support
- Non-U.S. Gov't
- Research Support
- U.S. Gov't
- Non-P.H.S.
Summary
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The article is about a study aiming to refine the gene structure for horses using RNA sequencing. Sequencing of mRNA was used to help generate comprehensive gene data and to assess gene expression patterns in horse tissue.
Objective of Research
- The ultimate goal of this study was to refine the structural annotation of equine protein-coding genes. This is important because the available data concerning these genes are primarily based on predictive models derived from sequence analysis or the extraction of gene structures from other mammalian species. By refining these models, the researchers hoped to provide a more accurate gene map specific to the horse species.
Method
- The team conducted sequencing of mRNA from eight equine tissues. This step generated 293,758105 sequence tags, each 35 bases long, resulting in 10.28 gbp (giga base pairs) of total sequence data.
- Tag alignment, resulted in roughly 207 × coverage of the equine mRNA transcriptome and confirmed transcriptional activity for about 90% of the protein-coding gene structures that were predicted by Ensembl and the National Center for Biotechnology Information (NCBI).
Results
- The sequence tag coverage was sufficient to refine the structural annotation for 11,356 of the predicted genes.
- An additional 456 transcripts with exon/intron features, not listed by Ensembl or NCBI, were also identified.
- Information on the location and intervals for the protein-coding genes predicted using the Ensembl and NCBI annotation pipelines were combined with 75,116 RNA-seq-derived transcriptional units. This combination resulted in a consensus equine protein-coding gene set of 20,302 defined loci features.
Use of Gene Ontology Annotation
- The researchers used Gene ontology annotation to make comparisons between the functional and structural categories of genes. This method was applied to genes that showed expression either in a tissue-restricted pattern or broadly across all tissue samples.
Cite This Article
APA
Coleman SJ, Zeng Z, Wang K, Luo S, Khrebtukova I, Mienaltowski MJ, Schroth GP, Liu J, MacLeod JN.
(2010).
Structural annotation of equine protein-coding genes determined by mRNA sequencing.
Anim Genet, 41 Suppl 2, 121-130.
https://doi.org/10.1111/j.1365-2052.2010.02118.x Publication
Researcher Affiliations
- Department of Veterinary Science, Maxwell H. Gluck Equine Research Center, University of Kentucky, Lexington, KY 40546, USA.
MeSH Terms
- Animals
- Female
- Gene Expression
- Horses / genetics
- Male
- Molecular Sequence Annotation
- Organ Specificity
- Proteins / genetics
- RNA, Messenger / genetics
- Sequence Analysis, RNA
Grant Funding
- P20 RR16481 / NCRR NIH HHS
Citations
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