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Home / Equine Research Bank / PLoS One / The transcriptome of equine peripheral blood mononuclear cel...
PloS one2015; 10(3); e0122011; doi: 10.1371/journal.pone.0122011

The transcriptome of equine peripheral blood mononuclear cells.

Abstract: Complete transcriptomic data at high resolution are available only for a few model organisms with medical importance. The gene structures of non-model organisms are mostly computationally predicted based on comparative genomics with other species. As a result, more than half of the horse gene models are known only by projection. Experimental data supporting these gene models are scarce. Moreover, most of the annotated equine genes are single-transcript genes. Utilizing RNA sequencing (RNA-seq) the experimental validation of predicted transcriptomes has become accessible at reasonable costs. To improve the horse genome annotation we performed RNA-seq on 561 samples of peripheral blood mononuclear cells (PBMCs) derived from 85 Warmblood horses. The mapped sequencing reads were used to build a new transcriptome assembly. The new assembly revealed many alternative isoforms associated to known genes or to those predicted by the Ensembl and/or Gnomon pipelines. We also identified 7,531 transcripts not associated with any horse gene annotated in public databases. Of these, 3,280 transcripts did not have a homologous match to any sequence deposited in the NCBI EST database suggesting horse specificity. The unknown transcripts were categorized as coding and noncoding based on predicted coding potential scores. Among them 230 transcripts had high coding potential score, at least 2 exons, and an open reading frame of at least 300 nt. We experimentally validated 9 new equine coding transcripts using RT-PCR and Sanger sequencing. Our results provide valuable detailed information on many transcripts yet to be annotated in the horse genome.
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Publication Date: 2015-03-19 PubMed ID: 25790166PubMed Central: PMC4366165DOI: 10.1371/journal.pone.0122011Google Scholar: Lookup
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  • Journal Article
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  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research focused on enriching the genomic information of horses by using RNA sequencing. The researchers conducted this on 561 sample cells from 85 Warmblood horses and found several new isoforms and horse-specific transcripts, some of which were confirmed in further testing.

Introduction: The Importance of the Study

  • The research is focused on enhancing our understanding of the horse genome, primarily because much of the current data is based on extrapolation from comparable species and lacks experimental substantiation. A significant portion of the existing equine genes are single-transcript, pointing to the necessity of discovering alternative isoforms of known genes.
  • Modern technological advancements like RNA sequencing (RNA-seq) have made it feasible to experimentally validate the predicted transcriptomes at a reasonable cost. As such, the researchers applied this technique to improve the horse genome annotation.

Methodology: How the Study Was Carried Out

  • The researchers obtained their RNA-seq data from 561 samples of Peripheral Blood Mononuclear Cells (PBMCs), collected from 85 Warmblood horses.
  • The gathered sequence reads were mapped and used to assemble an updated transcriptome.

Results: Insights and Discoveries

  • The new assembly revealed numerous alternative isoforms pertaining to known or predicted genes. This confirms the existence of (previously unidentified) alternative gene variants, contributing to the advancement of horse genomics.
  • Newly identifiable transcripts associated with none of the horse genes annotated in public databases amounted to 7,531. Among these, 3,280 did not match any sequence in the NCBI EST database, suggesting they may be unique to horses.
  • These unknown transcripts were then classified as coding and noncoding based on their coding potential scores. Out of these, 230 showed promising features – high coding potential score, at least 2 exons, and an open reading frame of at least 300 nucleotides – that suggested they were protein-coding.
  • Nine new equine coding transcripts were experimentally validated through RT-PCR and Sanger sequencing.

Conclusion: Understanding the Significance of the Work

  • The researchers’ efforts to reannotate the horse genome have yielded important findings. Through RNA sequencing, they unveiled numerous alternative isoforms and potentially horse-specific transcripts, enhancing our understanding of horse genomics.
  • By uncovering and validating new equine coding transcripts, this study adds value to the currently sparse horse genome database. These results may further encourage research in this field, thereby contributing to the development of drug discovery, and diagnosis and treatment of horse diseases.

Cite This Article

APA
Pacholewska A, Drögemüller M, Klukowska-Rötzler J, Lanz S, Hamza E, Dermitzakis ET, Marti E, Gerber V, Leeb T, Jagannathan V. (2015). The transcriptome of equine peripheral blood mononuclear cells. PLoS One, 10(3), e0122011. https://doi.org/10.1371/journal.pone.0122011

Publication

PloS one
ISSN: 1932-6203
NlmUniqueID: 101285081
Country: United States
Language: English
Volume: 10
Issue: 3
Pages: e0122011
PII: e0122011

Researcher Affiliations

Pacholewska, Alicja
  • Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Drögemüller, Michaela
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Klukowska-Rötzler, Jolanta
  • Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland; Division of Pediatric Hematology/Oncology, Department of Pediatrics, Bern University Hospital, Bern, Switzerland.
Lanz, Simone
  • Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland.
Hamza, Eman
  • Clinical Immunology Group, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, Switzerland.
Dermitzakis, Emmanouil T
  • Department of Genetic Medicine and Development, University of Geneva Medical School, Geneva, Switzerland; Institute of Genetics and Genomics in Geneva, Swiss Institute of Bioinformatics, Geneva, Switzerland.
Marti, Eliane
  • Clinical Immunology Group, Department of Clinical Research and Veterinary Public Health, University of Bern, Bern, Switzerland.
Gerber, Vincent
  • Swiss Institute of Equine Medicine, Vetsuisse Faculty, University of Bern and Agroscope, Bern, Switzerland.
Leeb, Tosso
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.
Jagannathan, Vidhya
  • Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland.

MeSH Terms

  • Animals
  • Chromosome Mapping
  • Female
  • Gene Expression Profiling
  • Horses / blood
  • Horses / genetics
  • Leukocytes, Mononuclear / metabolism
  • Male
  • Molecular Sequence Annotation
  • RNA, Messenger / genetics
  • RNA, Messenger / metabolism
  • Sequence Analysis, RNA

Conflict of Interest Statement

The authors have declared that no competing interests exist.

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