The transcriptional landscape of Rhizoctonia solani AG1-IA during infection of soybean as defined by RNA-seq.

Tanya R Copley,Raj Duggavathi,Suha Jabaji,Rita Grosch

doi:10.1371/journal.pone.0184095

Abstract

Rhizoctonia solani Kühn infects most plant families and can cause significant agricultural yield losses worldwide; however, plant resistance to this disease is rare and short-lived, and therefore poorly understood, resulting in the use of chemical pesticides for its control. Understanding the functional responses of this pathogen during host infection can help elucidate the molecular mechanisms that are necessary for successful host invasion. Using the pathosystem model soybean-R. solani anastomosis group AG1-IA, we examined the global transcriptional responses of R. solani during early and late infection stages of soybean by applying an RNA-seq approach. Approximately, 148 million clean paired-end reads, representing 93% of R. solani AG1-IA genes, were obtained from the sequenced libraries. Analysis of R. solani AG1-IA transcripts during soybean invasion revealed that most genes were similarly expressed during early and late infection stages, and only 11% and 15% of the expressed genes were differentially expressed during early and late infection stages, respectively. Analyses of the differentially expressed genes (DEGs) revealed shifts in molecular pathways involved in antibiotics biosynthesis, amino acid and carbohydrate metabolism, as well as pathways involved in antioxidant production. Furthermore, several KEGG pathways were unique to each time point, particularly the up-regulation of genes related to toxin degradation (e.g., nicotinate and nicotinamid metabolism) at onset of necrosis, and those linked to synthesis of anti-microbial compounds and pyridoxine (vitamin B6) biosynthesis 24 h.p.o. of necrosis. These results suggest that particular genes or pathways are required for either invasion or disease development. Overall, this study provides the first insights into R. solani AG1-IA transcriptome responses to soybean invasion providing beneficial information for future targeted control methods of this successful pathogen.

Highlights

Rhizoctonia foliar blight (RFB) or aerial blight first appeared in Louisiana, U.S.A. in the 1950s on soybean (Glycine max (L.) Merr.) [1]
Alignment with TopHat2 showed that less than 1% of reads aligned to the soybean genome, indicating that the membrane method developed for leaf infection was effective and sufficient for extracting highly purified R. solani RNA during biological interactions
Principal component analysis (PCA) revealed tight clustering of all control samples and no outliers, irrespective of time of harvest, and clear separation of the soybean-R. solani interaction samples (Fig 3A). This was further supported by hierarchical cluster analysis (HCA) and heatmap analysis of the top 40% differentially expressed genes (Fig 3B)

Summary

Introduction

Rhizoctonia foliar blight (RFB) or aerial blight first appeared in Louisiana, U.S.A. in the 1950s on soybean (Glycine max (L.) Merr.) [1]. Recent outbreaks of the disease in Brazil and in the southern states of the U.S.A. have caused yield losses of 30–60% [2,3,4]. RNA-seq of R. solani during soybean infection

Methods

Results

Discussion

Conclusion