Assessing Host-Pathogen Interaction Networks via RNA-Seq Profiling: A Systems Biology Approach

Abstract

RNA sequencing is a valuable tool brought about by advances in next generation sequencing (NGS) technology. Initially used for transcriptome mapping, it has grown to become one of the ‘gold standards’ for studying molecular changes that occur in niche environments or within and across infections. It employs high-throughput sequencing with many advantages over previous methods. In this chapter, we review the experimental approaches of RNA sequencing from isolating samples all the way to data analysis methods. We focus on a number of NGS platforms that offer RNA sequencing with each having their own strengths and drawbacks. The focus will also be on how RNA sequencing has led to developments in the field of host-pathogen interactions using the dual RNA sequencing technique. Besides dual RNA sequencing, this review also explores the application of other RNA sequencing techniques such as single cell RNA sequencing as well as the potential use of newer techniques like ‘spatialomics’ and ribosome-profiling in host-pathogen interaction studies. Finally, we examine the common challenges faced when using RNA sequencing and possible ways to overcome these challenges.

Molecular Interplay between Non-Host Resistance, Pathogens and Basal Immunity as a Background for Fatal Yellowing in Oil Palm (Elaeis guineensis Jacq.) Plants

“…RNA-seq became a powerful tool to study host–pathogen interactions, enlarging the horizon of opportunities for the development of early diagnosis tools, as well as for the identification of candidate genes to be employed in the development of improved genotypes resistant to a specific disease [ 23 , 24 , 25 , 26 ]. In the present study, RNA-Seq allowed not only the identification of genes/proteins differentially expressed in the leaves of FY symptomatic oil palm plants in comparison to the asymptomatic ones—either in the dry or rainy seasons— but also the identification of those differentially expressed in plants with similar FY-based phenotypes between seasons.…”