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.
Publication Date: 2015-06-24 PubMed ID: 26107351PubMed Central: PMC4481266DOI: 10.1371/journal.pone.0124375Google Scholar: Lookup
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- Journal Article
- Research Support
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- Extramural
- Research Support
- Non-U.S. Gov't
Summary
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The research article discusses a more extensive analysis of the horse genome, specifically the annotation of its protein coding regions. This was achieved through the sequencing of mRNA from multiple tissues. The findings provide a more comprehensive understanding of equine mRNA structures and protein coding variations.
Research Methodology
- The researchers acknowledged that most of the current gene annotation of the horse genome is based on in silico predictions and cross-species alignments. This means that much of what is understood about the horse genome relies on computational tools and comparisons with other species.
- To augment this, the researchers proceeded to sequence the messenger RNA (mRNA) from a pool of forty-three different tissues. When genes are expressed, they are transcribed into mRNA, which carries the code from the DNA form of the gene to the site of protein synthesis. By doing this, they aimed to use direct equine experimental evidence to expand the number of annotated equine genes.
Findings
- As a result of the sequencing, the researchers were able to derive the structures of 68,594 transcripts. Transcripts are the RNA molecules that result from genetic transcription.
- They also discovered 301,829 positions within these transcripts that had small nucleotide polymorphisms (SNPs) or small insertions and deletions (indels). These are variations in the genetic code that can have profound influences on gene function and expression.
- Interestingly, the researchers identified 780 variants that extended the open reading frame of the transcript – essentially, these are seemingly small errors in the equine reference genome. They were identified as such because they were also found as homozygous variants when resequencing the genome of the reference horse. Homozygous variants are those where both copies of a gene have the same mutation.
Significance
- The current study provides a rich resource for understanding equine mRNA structures and protein coding variants, contributing to a more nuanced understanding of the equine genome.
- This knowledge not only helps with equine genomic studies but also aids further cross-species genomic comparisons. Understanding the detailed structure and function of a closely related organism’s genome, such as a horse, can provide illuminating insights about other species, including humans.
Cite This Article
APA
Hestand MS, Kalbfleisch TS, Coleman SJ, Zeng Z, Liu J, Orlando L, MacLeod JN.
(2015).
Annotation of the Protein Coding Regions of the Equine Genome.
PLoS One, 10(6), e0124375.
https://doi.org/10.1371/journal.pone.0124375 Publication
Researcher Affiliations
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America.
- Biochemistry and Molecular Biology Department, School of Medicine, University of Louisville, Louisville, Kentucky, United States of America.
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America.
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America.
- Department of Computer Science, University of Kentucky, Lexington, Kentucky, United States of America.
- Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.
- Maxwell H. Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, Kentucky, United States of America.
MeSH Terms
- Animals
- Base Sequence
- Genome
- Horses / genetics
- Molecular Sequence Annotation
- Open Reading Frames / genetics
- RNA, Messenger / genetics
Grant Funding
- P20 GM103436 / NIGMS NIH HHS
- P20 RR016481 / NCRR NIH HHS
- R01 HG006272 / NHGRI NIH HHS
- 5P20RR016481-09 / NCRR NIH HHS
Conflict of Interest Statement
The authors have declared that no competing interests exist.
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