Abstract
RNA-seq has emerged as an important technology for measuring gene expression in peripheral blood samples collected from humans and other vertebrate species. In particular, transcriptomics analyses of whole blood can be used to study immunobiology and develop novel biomarkers of infectious disease. However, an obstacle to these methods in many mammalian species is the presence of reticulocyte-derived globin mRNAs in large quantities, which can complicate RNA-seq library sequencing and impede detection of other mRNA transcripts. A range of supplementary procedures for targeted depletion of globin transcripts have, therefore, been developed to alleviate this problem. Here, we use comparative analyses of RNA-seq data sets generated from human, porcine, equine, and bovine peripheral blood to systematically assess the impact of globin mRNA on routine transcriptome profiling of whole blood in cattle and horses. The results of these analyses demonstrate that total RNA isolated from equine and bovine peripheral blood contains very low levels of globin mRNA transcripts, thereby negating the need for globin depletion and greatly simplifying blood-based transcriptomic studies in these two domestic species.
Highlights
It is increasingly recognised that new technological approaches are urgently required for infectious disease diagnosis, surveillance, and management in burgeoning domestic animal populations as livestock production intensifies across the globe (Thornton, 2010; Nabarro and Wannous, 2014; Animal Task Force, 2016)
In light of our RNA-seq data analyses, we propose that globin mRNA transcript depletion is not a pre-requisite for transcriptome profiling of bovine and equine peripheral blood samples
This observation greatly simplifies the laboratory and bioinformatics workflows required for RNA-seq studies of whole blood collected from domestic cattle and horses
Summary
It is increasingly recognised that new technological approaches are urgently required for infectious disease diagnosis, surveillance, and management in burgeoning domestic animal populations as livestock production intensifies across the globe (Thornton, 2010; Nabarro and Wannous, 2014; Animal Task Force, 2016) In this regard, new strategies have emerged that leverage peripheral blood gene expression to study host immunobiology and to identify panels of RNA transcript biomarkers that can be used as specific biosignatures of infection by particular pathogens for Bovine and Equine Globin Transcripts both animal and human infectious disease (Ramilo and Mejias, 2009; Mejias and Ramilo, 2014; Chaussabel, 2015; Ko et al, 2015; Holcomb et al, 2017). For humans, more than 70% of peripheral blood mRNA transcripts are derived from the haemoglobin subunit alpha 1, subunit alpha 2 and subunit beta genes (HBA1, HBA2, and HBB) (Wu et al, 2003; Field et al, 2007; Mastrokolias et al, 2012)
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