The transcriptome of equine peripheral blood mononuclear cells

PloS One
Alicja PacholewskaVidhya Jagannathan

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 cate...Continue Reading

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Citations

Oct 9, 2015·Journal of Applied Genetics·Monika Stefaniuk, Katarzyna Ropka-Molik
Aug 21, 2015·PloS One·Alicja PacholewskaVincent Gerber
Jan 22, 2017·BMC Genomics·T A MansourC T Brown
Oct 27, 2016·BMC Genomics·Alicja PacholewskaVincent Gerber
Jan 7, 2017·BMC Genomics·Alicja PacholewskaVincent Gerber
Jan 20, 2018·PloS One·B Alex MerrickGarron M Wright

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Methods Mentioned

BETA
RNA-seq
PCR
electrophoresis

Software Mentioned

Ensembl
CPC
Cuffcompare
BLASTN
Gnomon
Sequencher
GEM
Cuffquant
GeneCodes
Cufflinks

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