Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

Dataset Information

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

ABSTRACT: The aim of our study was to decipher differences in the response of a lowly virulent E. amylovora strain to infection of susceptible and resistant apple cultivars at the transcriptome level. For this purpose, we applied an RNA-seq technique to see the global changes in gene expression of E. amylovora while interacting with two apple cultivars at two time points after inoculation of shoots. Additionally, we compared transcriptomes of E. amylovora growing on a microbiological medium and in planta to elucidate transcriptional changes in bacterial cells induced by the host plant environment.

INSTRUMENT(S): Illumina MiSeq

ORGANISM(S): Erwinia amylovora

SUBMITTER: Joanna Pulawska

PROVIDER: E-MTAB-5630 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:Molecular events regulating apple fruit ripening and sensory quality are largely unknown. Such knowledge is essential for genomic-assisted apple breeding and postharvest quality management. In this study, a parallel transcriptome profile analysis, scanning electron microscopic (SEM) examination and systematic physiological characterization were performed on two apple cultivars, Honeycrisp (HC) and Cripps Pink (CP), which have distinct ripening features and texture attributes. Systematic physiological characterization of fruit ripening based on weekly maturity data indicated substantial differences in fruit crispness and firmness at comparable ripening stages. SEM images of fruit cortex tissues prepared from fruits with equivalent maturity suggested that the cell wall thickness may contribute to the observed phenotypes of fruit firmness and crispness. A high-density long-oligo apple microarray consisting of duplex 190,135 cross-hybridization-free 50-70-mer isothermal probes, and representing 23,997 UniGene clusters, was manufactured on a Nimblegen array platform. Transcriptome profiling identified a total of 1793 and 1209 UniGene clusters differentially expressed during ripening from cortex tissues of HC and CP, respectively. UniGenes implicated in hormone metabolism and response, cell wall biosynthesis and modification and those encoding transcription factors were among the prominent functional groups. Between the two cultivars, most of the identified UniGenes were similarly regulated during fruit ripening; however, a short list of gene families or specific family members exhibited distinct expression patterns between the two cultivars, which may represent candidate genes regulating cultivar-specific apple fruit ripening patterns and quality attributes. Using a single color labeling system, a total of 24 microarray slides were utilized, one for each cortex tissue sample, for transcriptome profiling analysis. 2 cultivars x 3 developmental stages x 4 biological replicates.

Dataset Information

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

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