Dual RNA-Sequencing to Elucidate the Plant-Pathogen Duel

Abstract

RNA-sequencing technology has been widely adopted to investigate host responses during infection with pathogens. Dual RNA-sequencing (RNA-seq) allows the simultaneous capture of pathogen-specific transcripts during infection, providing a more complete view of the interaction. In this review, we focus on the design of dual RNAseq experiments and the application of downstream data analysis to gain biological insight into both sides of the interaction. Recent literature in this area demonstrates the power of the dual RNA-seq approach and shows that it is not limited to model systems where genomic resources are available. Sequencing costs continue to decrease and single cell transcriptomics is becoming more feasible. In combination with proteomics and metabolomics studies, these technological advances are likely to contribute to our understanding of the temporal and spatial aspects of dynamic plant-pathogen interactions. A dual approach in plantaThe interaction between plants and pathogens is an active and dynamic process that can be likened to a duel. Plants have complex defence mechanisms that can be rendered ineffective when pathogens interfere with one of the various processes required for host defence. These processes include penetration resistance, recognition by Pattern Recognition Receptors (PRRs), phytohormone signalling pathways, secretory pathways, secondary metabolite production, and plant cell death (Dou and Zhou, 2012). Until recently, transcriptomic approaches have been applied in the host and pathogen separately to obtain the gene expression profile of each organism and gain insight into infection biology or host defence mechanisms.RNA sequencing (RNA-seq) is a powerful technology that does not rely on any prior knowledge of transcripts and can generate vast quantities of data with much smaller costs involved than for older techniques such as microarrays (Pareek et al., 2011;Wilhelm and Landry, 2009). An advantage of RNA-seq in the field of plant-pathogen interactions is that both plant and pathogen transcripts can be detected simultaneously and accurately in the same sample. This tactic, known as dual RNAseq, in planta RNA-seq, simultaneous RNA-seq, or comparative RNA-seq, is a relatively new technique both in the plant and medical fields. In plants, it allows for the study of plant-pathogen interactions in herbaceous crops Kunjeti et al., 2012;Lowe et al., 2014) as well as trees (Hayden et al., 2014;Liang et al., 2014;Teixeira et al., 2014). This review outlines technical considerations for dual RNA-seq experiments, summarizes recent insights drawn from such approaches in plant-pathogen interactions, and provides an

The transcriptome of Pinus pinaster under Fusarium circinatum challenge

“…The F. circinatum transcriptome and P. pinaster de novo transcriptome assembly were combined in a single dataset to account for cross species mapping [72]. This dataset was used to map reads with Kallisto v.0.44.0 [15] with sequence bias correction and bootstrap samples set to 100.…”

“…In both instances, RNAseq reads can be assembled de novo into a transcriptome [17,83,110]. A variant of this technology is the dual RNAseq, which captures the transcriptome of the host and pathogen simultaneously, so that gene expression in both organisms may be determined [45,66,72,116].…”

A roadmap for research in octoploid strawberry

“…The paradigm of a gene-for-gene arms race has been long established, but a more accurate assessment of the durability of resistance could arise from an understanding of the selective forces operating on pathogen effectors. Dual RNA-seq technology can help uncover the dynamic interactions of pathogen and host [151][152][153] . Both the pathogen and the host transcriptomes are simultaneously captured and analyzed in silico to distinguish speciesspecific transcripts.…”

Dual species dynamic transcripts reveal the interaction mechanisms between Chrysanthemum morifolium and Alternaria alternata

“…The studies above were limited to a unilateral transcription analysis of plants under pathogenic stress. More recently, dual RNAseq has become a powerful tool for comprehensively understanding host-pathogen interactions in vivo [12], that can simultaneously capture pathogen-speci c transcripts during the infection process, provide a more complete view of interactions [13], reveal biosynthetic and metabolic pathways of crosstalk among participants, and speci cally determine the dynamic expression pro le of genes associated with hostpathogen interactions [14]. To date, the mutual in vivo attack and counterattack response between chrysanthemum and A. alternata is poorly understood.…”