Fire blight disease reactome: RNA-seq transcriptional profile of apple host plant defense responses to Erwinia amylovora pathogen infection.

Tim Kamber,Thomas Wicker,Brion Duffy,Theo H. M. Smits,Joël F. Pothier,Jan P. Buchmann

doi:10.1038/srep21600

Abstract

The molecular basis of resistance and susceptibility of host plants to fire blight, a major disease threat to pome fruit production globally, is largely unknown. RNA-sequencing data from challenged and mock-inoculated flowers were analyzed to assess the susceptible response of apple to the fire blight pathogen Erwinia amylovora. In presence of the pathogen 1,080 transcripts were differentially expressed at 48 h post inoculation. These included putative disease resistance, stress, pathogen related, general metabolic, and phytohormone related genes. Reads, mapped to regions on the apple genome where no genes were assigned, were used to identify potential novel genes and open reading frames. To identify transcripts specifically expressed in response to E. amylovora, RT-PCRs were conducted and compared to the expression patterns of the fire blight biocontrol agent Pantoea vagans strain C9-1, another apple pathogen Pseudomonas syringae pv. papulans, and mock inoculated apple flowers. This led to the identification of a peroxidase superfamily gene that was lower expressed in response to E. amylovora suggesting a potential role in the susceptibility response. Overall, this study provides the first transcriptional profile by RNA-seq of the host plant during fire blight disease and insights into the response of susceptible apple plants to E. amylovora.

Highlights

Plants have developed an arsenal of defense responses elicited by biotic and abiotic stresses
The reads were filtered from primer and polyA + sequences resulting in 1,991,992 and 6,138,188 reads, of which 47.1% and 47.5% respectively could be aligned to the apple genome sequence
The differentially expressed transcripts were assigned to cellular component, biological processes and molecular function according to the gene ontologies (GO) (Fig. 2)

Summary

Introduction

Plants have developed an arsenal of defense responses elicited by biotic and abiotic stresses. The specific recognition of pathogen effectors (Avr) by disease resistance (R) proteins leads to the induction of a hypersensitive response (local cell death) at the infection site and inhibition or growth stop of the pathogen. DspA/E physically interacts with four serine/threonine receptor kinases of apple, designated as DspE-interacting proteins[16] Beside these well characterized virulence factors, novel insights into host-specificity, evolutionary aspects, and core genes were provided by comparative genomic approaches of sequenced E. amylovora strains[17,18,19,20,21]. CDNA amplified fragment length polymorphism or suppression subtractive cDNA hybridization techniques to identify genes involved in the E. amylovora–Malus interaction[22,23,24] These studies gave first insights into this host-pathogen interaction, but are not reflecting the whole genome-wide transcriptional changes. Previously unknown genes in the apple genome could be assigned and ORFs were detected in the genomes of M. × domestica and Prunus persica

Methods

Results

Conclusion