Transcriptome analysis of Xanthomonas fragariae in strawberry leaves 15 days after inoculation
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ABSTRACT:
PROVIDER: PRJEB33676 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3452530_1.fastq.gz | Fastqsanger.gz | |||
| ERR3452530_2.fastq.gz | Fastqsanger.gz | |||
| ERR3452540_1.fastq.gz | Fastqsanger.gz | |||
| ERR3452540_2.fastq.gz | Fastqsanger.gz | |||
| ERR3452531_1.fastq.gz | Fastqsanger.gz |
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Project description:The aim of our study was to determine the changes in gene expression of an X. fragariae during infection and disease development of strawberry at the transcriptome level. For this purpose, we applied an RNA-seq technique to see the global changes in gene expression of X. fragariae.
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Project description:Strawberry is economically important and widely grown but susceptible to a large variety of phytopathogenic organisms. Among them, Xanthomonas fragariae is a quarantine bacterial pathogen threatening strawberry productions by causing angular leaf spots. Using whole transcriptome sequencing, gene expression of both plant and bacteria in planta was analyzed at two time points, 12- and 29-days post inoculation, in order to compare pathogen and host response between the stages of early visible and of well-developed symptoms. Among 28’588 known genes in strawberry and 4’046 known genes in X. fragariae expressed at both time points, a total of 361 plant and 144 bacterial genes were significantly differentially expressed, respectively. The identified higher expressed genes in the plants were pathogen-associated molecular pattern receptors and pathogenesis related thaumatin encoding genes, whereas the more expressed early genes were related to chloroplast metabolism as well as photosynthesis related coding genes. Most of X. fragariae genes involved in host interactions, recognitions and pathogenesis, were lower expressed at late-phase infection. This study gives a first insight on the interaction of X. fragariae with its host. The strawberry plant changed its metabolism consistently with the progression of infection.
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Project description:Xanthomonas fragariae is a quarantine bacterial pathogen that causes angular leaf spot on strawberry. The aim of our study was to analyse the mechanism of interaction of this bacterium with its host plant at the transcriptome level. For this purpose, mRNAs of X. fragariae growing in Wilbrink's medium and from infected strawberry cv. Elsanta plants were isolated and sequenced using the Illumina MiSeq platform. The expression profiles of the bacteria in Wilbrink's medium and in planta were very diverse. Of the 3939 CDSs recorded, 1995 had significantly different expression in planta (966 and 1029 genes were down- and upregulated, respectively). Among the genes showing increased expression in planta, those with eggNOG/COG (evolutionary genealogy of genes: Non-supervised Orthologous Groups/Cluster of Orthologous Groups) categories associated with bacterial cell motility, signal transduction, transport and metabolism of inorganic ions and carbohydrates and transcription were overrepresented. Among the genes with the most increased expression in planta, genes primarily associated with flagella synthesis and chemotaxis were found. It is also interesting to note that out of the 31 genes localized on a plasmid, 16 were expressed differently in planta, which may indicate their potential role in plant-pathogen interactions. Many genes with differentiated expression that were localized on chromosome and plasmid encode proteins of unknown function.
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