Genomic and transcriptomic analysis of the interaction of roses with the black spot fungus Diplocarpon rosae

authored by
Enzo Neu
supervised by
Thomas Debener

Due to the high economical importance of roses and the severe damage caused on them by the hemibiotrophic fungus Diplocarpon rosae, the causing agent of the black spot disease, their interaction is one best studied on cultivated roses. However, both interaction partners are lacking a public available genome sequence and very little is known about the molecular mechanisms of their interaction. Due to this fact, in this study next generation sequencing was applied to assemble a draft genome sequence of the D. rosae isolate DortE4 as well as of the resistant rose genotype 88/124-46, and larger sets of transcriptome data and other external sources were used for evidence supported genome annotation with the MAKER pipeline. Bioinformatic and experimental analyses of genes, normally occurring as single copy genes in all eukaryotic genomes, indicate that a large portion of the D. rosae genome is duplicated, which might indicate a whole genome duplication. Different bioinformatic approaches were combined to predict the secretome of the fungus and to identify potential effector genes in it. As expected, a significant proportion of the predicted secretome comprises enzymes for the degradation of cell wall components. 52 of 251 effector candidates matched several bioinformatic criteria and contained a Y/F/WxC motif, which is of particular interest because so far this motif was only found in effector genes of obligate biotrophic fungi. Transcriptomic data show that the majority of the predicted effector candidates are expressed during the early stages of infection and some belong to the genes with the highest expression value, making these candidates a promising starting point for various analyses. Additionally, the transcriptomic response of the susceptible rose variety ‘Pariser Charme’ after inoculation with the powdery mildew fungus Podosphaera pannosa and D. rosae was investigated by applying the MACE approach. The comparison of the two interaction systems revealed that besides a similar response to both pathogens, pathogen-specific reactions occur. Genes related to photosynthesis and cell wall modification are down-regulated in response to P. pannosa, whereas genes from the phenylpropanoid and flavonoid pathways as well as of salicylic acid-signalling pathway are specifically up-regulated in response to D. rosae.

Section Molecular Plant Breeding
Doctoral thesis
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Electronic version(s) (Access: Open)