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Home / Equine Research Bank / BMC Genomics / Tissue resolved, gene structure refined equine transcriptome...
BMC genomics2017; 18(1); 103; doi: 10.1186/s12864-016-3451-2

Tissue resolved, gene structure refined equine transcriptome.

Abstract: Transcriptome interpretation relies on a good-quality reference transcriptome for accurate quantification of gene expression as well as functional analysis of genetic variants. The current annotation of the horse genome lacks the specificity and sensitivity necessary to assess gene expression especially at the isoform level, and suffers from insufficient annotation of untranslated regions (UTR) usage. We built an annotation pipeline for horse and used it to integrate 1.9 billion reads from multiple RNA-seq data sets into a new refined transcriptome. This equine transcriptome integrates eight different tissues from 59 individuals and improves gene structure and isoform resolution, while providing considerable tissue-specific information. We utilized four levels of transcript filtration in our pipeline, aimed at producing several transcriptome versions that are suitable for different downstream analyses. Our most refined transcriptome includes 36,876 genes and 76,125 isoforms, with 6474 candidate transcriptional loci novel to the equine transcriptome. We have employed a variety of descriptive statistics and figures that demonstrate the quality and content of the transcriptome. The equine transcriptomes that are provided by this pipeline show the best tissue-specific resolution of any equine transcriptome to date and are flexible for several downstream analyses. We encourage the integration of further equine transcriptomes with our annotation pipeline to continue and improve the equine transcriptome.
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Publication Date: 2017-01-20 PubMed ID: 28107812PubMed Central: PMC5251313DOI: 10.1186/s12864-016-3451-2Google Scholar: Lookup
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  • Journal Article
  • Research Support
  • Non-U.S. Gov't
  • Research Support
  • N.I.H.
  • Extramural

Summary

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The research article presents an enhanced methodology for the interpretation of the horse transcriptome, improving the resolution of gene structures and isoforms while providing tissue-specific details.

Understanding the Necessity of the Research

  • Accurate transcriptome interpretation is essential for assessing gene expression and performing functional analysis of genetic variants. It requires a high-quality reference transcriptome.
  • The existing horse genome annotation lacks the necessary specificity and sensitivity, especially for analyzing expression at the isoform level. The current methods also have insufficient annotation of untranslated regions (UTRs).
  • These shortcomings highlight the necessity for a more refined horse transcriptome annotation, which was the primary goal of this research.

Creation of a New Transcriptome Annotation Pipeline

  • The researchers developed a new pipeline specifically for horse transcriptome annotation that integrates multiple RNA-seq datasets. Approximately 1.9 billion reads were used to build the new refined transcriptome.
  • This enhanced equine transcriptome encompasses eight different tissues from 59 individuals, which enhances the specificity of the gene structure and isoform resolution, and also provides significant tissue-specific information.
  • The pipeline uses a four-level transcript filtration, designed to create several transcriptome versions useful for different downstream analyses. This versatility is an essential aspect for wider applications.

Results and Evaluation

  • The most refined transcriptome from the application of this pipeline includes 36,876 genes and 76,125 isoforms, with 6474 potential transcriptional loci that are new to the equine transcriptome.
  • Various descriptive statistics and figures were used to showcase the quality and content of the generated transcriptome to emphasize the improvements in the method.

Conclusion and Further Improvements

  • This study’s technique resulted in the best tissue-specific resolution of any equine transcriptomes created till date and demonstrated flexibility for several downstream analyses.
  • The researchers encourage the integration of more equine transcriptomes with their annotation pipeline to continue enhancing the quality of the equine transcriptome in the future.

Cite This Article

APA
Mansour TA, Scott EY, Finno CJ, Bellone RR, Mienaltowski MJ, Penedo MC, Ross PJ, Valberg SJ, Murray JD, Brown CT. (2017). Tissue resolved, gene structure refined equine transcriptome. BMC Genomics, 18(1), 103. https://doi.org/10.1186/s12864-016-3451-2

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 18
Issue: 1
Pages: 103
PII: 103

Researcher Affiliations

Mansour, T A
  • Department of Population Health and Reproduction, University of California, Davis, Davis, USA.
  • Department of Clinical Pathology, College of Medicine, Mansoura University, Egypt, Mansoura, Egypt.
Scott, E Y
  • Department of Animal Science, University of California, Davis, Davis, USA.
Finno, C J
  • Department of Population Health and Reproduction, University of California, Davis, Davis, USA.
Bellone, R R
  • Department of Population Health and Reproduction, University of California, Davis, Davis, USA.
  • Veterinary Genetics Laboratory, University of California, Davis, Davis, USA.
Mienaltowski, M J
  • Department of Animal Science, University of California, Davis, Davis, USA.
Penedo, M C
  • Veterinary Genetics Laboratory, University of California, Davis, Davis, USA.
Ross, P J
  • Department of Animal Science, University of California, Davis, Davis, USA.
Valberg, S J
  • Large Animal Clinical Sciences, Michigan State University, College of Veterinary Medicine, East Lansing, USA.
Murray, J D
  • Department of Population Health and Reproduction, University of California, Davis, Davis, USA.
  • Department of Animal Science, University of California, Davis, Davis, USA.
Brown, C T
  • Department of Population Health and Reproduction, University of California, Davis, Davis, USA. ctbrown@ucdavis.edu.

MeSH Terms

  • Animals
  • Chromosome Mapping
  • Cluster Analysis
  • Computational Biology / methods
  • Gene Expression Profiling
  • Genome
  • Genomics / methods
  • High-Throughput Nucleotide Sequencing
  • Horses
  • Molecular Sequence Annotation
  • Organ Specificity / genetics
  • RNA Isoforms
  • Transcriptome

Grant Funding

  • K01 OD015134 / NIH HHS
  • L40 TR001136 / NCATS NIH HHS

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Citations

This article has been cited 14 times.
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