The transcriptome of equine peripheral blood mononuclear cells.

Pacholewska, Alicja Elzbieta; Drögemüller, Michaela; Klukowska, Jolanta; Lanz, Simone; Hamza, Eman; Dermitzakis, Emmanouil T; Marti, Eliane Isabelle; Gerber, Vinzenz; Leeb, Tosso; Jagannathan, Vidhya (2015). The transcriptome of equine peripheral blood mononuclear cells. PLoS ONE, 10(3), e0122011. Public Library of Science 10.1371/journal.pone.0122011

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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.

Item Type:

Journal Article (Original Article)

Division/Institute:

05 Veterinary Medicine > Research Foci > Host-Pathogen Interaction
05 Veterinary Medicine > Department of Clinical Veterinary Medicine (DKV) > Equine Clinic
05 Veterinary Medicine > Department of Clinical Veterinary Medicine (DKV)
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Experimental Clinical Research
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH) > Institute of Genetics
05 Veterinary Medicine > Department of Clinical Research and Veterinary Public Health (DCR-VPH)

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Pacholewska, Alicja Elzbieta; Drögemüller, Michaela; Klukowska, Jolanta; Lanz, Simone; Hamza, Eman; Marti, Eliane Isabelle; Gerber, Vinzenz; Leeb, Tosso and Jagannathan, Vidya

Subjects:

500 Science > 570 Life sciences; biology
500 Science > 590 Animals (Zoology)
600 Technology > 610 Medicine & health
600 Technology > 630 Agriculture

ISSN:

1932-6203

Publisher:

Public Library of Science

Language:

English

Submitter:

Tosso Leeb

Date Deposited:

29 Apr 2015 11:58

Last Modified:

29 Apr 2015 11:58

Publisher DOI:

10.1371/journal.pone.0122011

PubMed ID:

25790166

BORIS DOI:

10.7892/boris.67769

URI:

https://boris.unibe.ch/id/eprint/67769

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