Cladosporium fulvum is a fungal pathogen that causes leaf mould of tomato. The reference genome of this pathogen was released in 2012 but its high repetitive DNA content prevented a contiguous assembly and further prohibited the analysis of its genome architecture. In this study, we combined third generation sequencing technology with the Hi-C chromatin conformation capture technique, to produce a high-quality and near complete genome assembly and gene annotation of a Race 5 isolate of C. fulvum. The resulting genome assembly contained 67.17 Mb organized into 14 chromosomes (Chr1-to-Chr14), all of which were assembled telomere-to-telomere. The smallest of the chromosomes, Chr14, is only 460 kb in size and contains 25 genes that all encode hypothetical proteins. Notably, PCR assays revealed that Chr14 was absent in 19 out of 24 isolates of a world-wide collection of C. fulvum, indicating that Chr14 is dispensable. Thus, C. fulvum is currently the second species of Capnodiales shown to harbour dispensable chromosomes. The genome of C. fulvum Race 5 is 49.7 % repetitive and contains 14 690 predicted genes with an estimated completeness of 98.9%, currently one of the highest among the Capnodiales. Genome structure analysis revealed a compartmentalized architecture composed of gene-dense and repeat-poor regions interspersed with gene-sparse and repeat-rich regions. Nearly 39.2 % of the C. fulvum Race 5 genome is affected by Repeat-Induced Point (RIP) mutations and evidence of RIP leakage toward non-repetitive regions was observed in all chromosomes, indicating the RIP plays an important role in the evolution of this pathogen. Finally, 345 genes encoding candidate effectors were identified in C. fulvum Race 5, with a significant enrichment of their location in gene-sparse regions, in accordance with the ‘two-speed genome’ model of evolution. Overall, the new reference genome of C. fulvum presents several notable features and is a valuable resource for studies in plant pathogens.

Berries of 13 Greek grape wine cultivars were evaluated for resistance to Botrytis bunch rot. Artificial inoculations on detached berries revealed that the Greek cultivars tested varied regarding their susceptibility to Botrytis cinerea. Cultivar (cv.) “Limnio” was found to be highly resistant, while higher susceptibility was observed on berries of cv. “Roditis”. To determine the molecular basis of the observed resistance or susceptibility of cv. “Limnio” and “Roditis”, an expression analysis of 12 defence-related genes, was carried out on artificially inoculated berries of the two cultivars at different time points after inoculation. Gene expression measurements in the resistant cv. “Limnio” showed that the artificial inoculation with the pathogen triggered the induction of genes encoding pathogenesis-related (PR) proteins such as chitinases (CHIT), polygalacturonase-inhibiting protein (PGIP), serine proteinase inhibitor (PIN) and enzymes involved in phytoalexin synthesis such as phenylalanine ammonia-lyase (PAL) and stilbene synthase (STS). In contrast, on the susceptible cv. “Roditis”, most of the same genes were down-regulated. Metabolomic analysis revealed significant differences in the initial metabolic profiles of “Limnio” and “Roditis” berries. Furthermore, in response to inoculation, the abundance of several metabolites increased in the resistant cultivar indicating intensification of metabolic processes. Proline and mannitol accumulation, as well as the modification of metabolites related to phenylpropanoid and lignin biosynthesis, are among the major players in defence responses of the “Limnio” cultivar. The above findings enhance our understanding of the resistance of Greek grape wine cultivars to B. cinerea and, at the same time, lay the foundation for breeding wine grape cultivars in the future.