First in planta transcriptome of the strawberry bacterial pathogen Xanthomonas fragariae
Picture: A strawberry leaf showing angular leaf spot symptoms caused by the bacterial phytopathogen Xanthomonas fragariae. These typical water-soaked leaf lesions could be observed 15 days after inoculation by spraying of ab- and adaxial surface of leaves under greenhouse controlled conditions. Bacterial RNA isolated from this type of symptoms were subjected to whole transcriptome sequencing (RNA-seq).
The first in planta transcriptome of the strawberry bacterial pathogen Xanthomonas fragariae (Xf) has been completed by the DROPSA consortium.
It was first necessary to optimize strawberry inoculation techniques under greenhouse controlled conditions and to develop an efficient method for isolation of high quality bacterial RNA from inoculated plant leaves.
Whole transcriptome sequencing, also called RNA-seq, was used to identify differentially expressed genes (DEGs) involved in the succession of events required for successful strawberry plant colonization by this bacterium. These DEGs should provide information on virulence factors, fitness determinants and environmental modulators.
To investigate this, the in planta transcriptome was compared to the transcriptome of the bacterium grown under pure culture conditions in rich medium. This has highlighted up- and down-regulation of different gene categories during growth under in planta conditions. These are currently being analysed in greater details and will be validated using reverse transcription-quantitative PCR (RT-qPCR).
Our RNA-seq analyses were aided by the availability of the complete genome of this plant pathogen. The RNA-seq data could in turn help identify new genes and improve the annotation of the pathogen genome. As the presence of a plasmid was revealed during genome sequence determination, it has also helped specify the location of the DEGs and determine the role the plasmid plays during the infection process.
Altogether the results obtained within the DROPSA project constitute crucial information to identify the ‘Achilles’ heel’ targets in the bacterium that could be used to design custom antibacterial compounds.
Joël F. Pothier
Zurich University of Applied Sciences (ZHAW)