Comparative transcriptome analysis of a lowly virulent strain of Erwinia amylovora in shoots of two apple cultivars – susceptible and resistant to fire blight

Abstract

Background Erwinia amylovora is generally considered to be a homogeneous species in terms of phenotypic and genetic features. However, strains show variation in their virulence, particularly on hosts with different susceptibility to fire blight. We applied the RNA-seq technique to elucidate transcriptome-level changes of the lowly virulent E. amylovora 650 strain during infection of shoots of susceptible (Idared) and resistant (Free Redstar) apple cultivars.ResultsThe highest number of differentially expressed E. amylovora genes between the two apple genotypes was observed at 24 h after inoculation. Six days after inoculation, only a few bacterial genes were differentially expressed in the susceptible and resistant apple cultivars. The analysis of differentially expressed gene functions showed that generally, higher expression of genes related to stress response and defence against toxic compounds was observed in Free Redstar. Also in this cultivar, higher expression of flagellar genes (FlaI), which are recognized as PAMP (pathogen-associated molecular pattern) by the innate immune systems of plants, was noted. Additionally, several genes that have not yet been proven to play a role in the pathogenic abilities of E. amylovora were found to be differentially expressed in the two apple cultivars.ConclusionsThis RNA-seq analysis generated a novel dataset describing the transcriptional response of the lowly virulent strain of E. amylovora in susceptible and resistant apple cultivar. Most genes were regulated in the same way in both apple cultivars, but there were also some cultivar-specific responses suggesting that the environment in Free Redstar is more stressful for bacteria what can be the reason of their inability to infect of this cultivar. Among genes with the highest fold change in expression between experimental combinations or with the highest transcript abundance, there are many genes without ascribed functions, which have never been tested for their role in pathogenicity. Overall, this study provides the first transcriptional profile by RNA-seq of E. amylovora during infection of a host plant and insights into the transcriptional response of this pathogen in the environments of susceptible and resistant apple plants.Electronic supplementary materialThe online version of this article (10.1186/s12864-017-4251-z) contains supplementary material, which is available to authorized users.

mRNA extraction of Xanthomonas fragariae in strawberry and validation of reference genes for the RT-qPCR for study of bacterial gene expression

“…When analysing flhF and iroN2, it was found that flhF, a flagellar biosynthesis pathway gene, was highly up-regulated, while iroN2, which encodes the TonB-dependent receptor, was down-regulated in planta. The results of the reference gyrB, ffh and pykA genes in terms of the relative gene expression analysis agree with the results obtained in preliminary analysis of the expression of flhF and iroN2 in transcriptomes obtained after RNA-seq [48]. GyrA did not make significant changes in the results obtained (data not shown).…”

“…The flhF gene was up-regulated by 231.64-fold (SE 42.01) compared with that of a pure bacterial culture; however, for the iroN2 gene, the opposite result was noted i.e., down-regulation in planta (− 16.2-fold; SE 2.072) compared to pure bacterial culture. Compared to the results of transcriptome analysis by RNA seq, the expression values of the flhF and iroN2 genes obtained in this study were similar [48].…”

Three Hfq‐dependent small RNAs regulate flagellar motility in the fire blight pathogen Erwinia amylovora

“…Two main classes of motility reported in E. amylovora include flagellar motility (Raymundo and Ries, ) and twitching motility through type IV pili (Berry et al ., ). Flagellar motility provides a means whereby the E. amylovora cells can swim through flower nectar to reach host tissues, and it has been suggested that flagella play an important role in virulence (Holtappels et al ., ; Puławska et al ., ). Like other members of the Enterobacteriaceae family, E. amylovora bears peritrichous flagella.…”

Differential gene regulatory pathways and co-expression networks associated with fire blight infection in apple (Malus × domestica)

“…Novel minor resistance alleles from domesticated apples can require less time and fewer cycles of backcrossing to develop breeding lines with improved fire blight resistance. Furthermore, highthroughput RNA-sequencing (RNA-Seq) have been used to characterize molecular mechanisms related to fire blight infection in apple cultivars 'Golden Delicious', 'Idared' and 'Free Redstar' 32,33 . RNA-Seq was used to identify transcriptome level changes in flowers of 'Golden Delicious' challenged with E. amylovora strain CFBP 1430 32 .…”