Vitis vinifera berries are sensitive towards infection by the necrotrophic pathogen Botrytis cinerea, leading to important economic losses worldwide. The combined analysis of the transcriptome and metabolome associated with fungal infection has not been performed previously in grapes or in another fleshy fruit. In an attempt to identify the molecular and metabolic mechanisms associated with the infection, peppercorn-sized fruits were infected in the field. Green and veraison berries were collected following infection for microarray analysis complemented with metabolic profiling of primary and other soluble metabolites and of volatile emissions. The results provided evidence of a reprogramming of carbohydrate and lipid metabolisms towards increased synthesis of secondary metabolites involved in plant defence, such as trans-resveratrol and gallic acid. This response was already activated in infected green berries with the putative involvement of jasmonic acid, ethylene, polyamines, and auxins, whereas salicylic acid did not seem to be involved. Genes encoding WRKY transcription factors, pathogenesis-related proteins, glutathione S-transferase, stilbene synthase, and phenylalanine ammonia-lyase were upregulated in infected berries. However, salicylic acid signalling was activated in healthy ripening berries along with the expression of proteins of the NBS-LRR superfamily and protein kinases, suggesting that the pathogen is able to shut down defences existing in healthy ripening berries. Furthermore, this study provided metabolic biomarkers of infection such as azelaic acid, a substance known to prime plant defence responses, arabitol, ribitol, 4-amino butanoic acid, 1-O-methyl- glucopyranoside, and several fatty acids that alone or in combination can be used to monitor Botrytis infection early in the vineyard.

Ilyonectria radicicola and its Cylindrocarpon-like anamorph represent a species complex that is commonly associated with root rot disease symptoms on a range of hosts. During the course of this study, several species could be distinguished from I. radicicola sensu stricto based on morphological and culture characteristics. DNA sequence analysis of the partial β-tubulin, histone H3, translation elongation factor 1-α and nuclear ribosomal RNA-Internal Transcribed Spacer (nrRNA-ITS) genes were employed to provide further support for the morphological species resolved among 68 isolates associated with root rot disease symptoms. Of the various loci screened, nrRNA-ITS sequences were the least informative, while histone H3 sequences were the most informative, resolving the same number of species as the combined dataset across the four genes. Within the Ilyonectria radicicola species complex, 12 new taxa are delineated occurring on a diverse range of hosts, the most common being Cyclamen, Lilium, Panax, Pseudotsuga, Quercus and Vitis.

Black foot disease is a serious disease of grapevine crops in most areas where vines are grown. Mainly two species of Cylindrocarpon, C. destructans and C. macrodidymum, are associated with this disease. Recent studies have revealed a tremendous molecular variation within the former but only slight molecular variation within the latter, indicating that C. destructans presents a complex of several species The present study elucidates the taxonomic status of C. destructans-like isolates associated with black foot disease of grapevines. Grapevine isolates were studied morphologically, subjected to DNA analyses of their ITS and partial beta-tubulin genes, and were mated in all combinations in vitro. Cylindrocarpon destructans strains isolated from grapevines in Europe and South Africa appeared morphologically and genetically identical, and had identical ITS and partial beta-tubulin gene sequences. Phylogenetic analyses placed these strains in a clade closely related but clearly distinct from other clades with C. destructans-like anamorphs obtained from various herbaceous or woody hosts. Only the ex-type strain of Cylindrocarpon liriodendri had identical sequences to strains isolated from grapevines, and could also not be distinguished by morphological characters. The grapevine isolates are therefore reidentified here as Cylindrocarpon liriodendri. Cylindrocarpn liriodendri formed perithecia in heterothallic conditions and the holomorph of this species is described as Neonectria liriodendri sp. nov. Neonectria liriodendri is genetically distinct from the ex-type strain of Neonectria radicicola, which originated from Cyclamen in Sweden. Both ex-type strains also differ from at least two other clades comprising additional C. destructans-like strains. Many of these strains originated from Panax sp., which is the host of the type of C. destructans. Our phylogenetic analyses indicate that C. destructans is not the anamorph of N. radicicola and that N. liriodendri, N. radicicola and several C. destructans-like taxa may have evolved independently within the same phylogenetic species complex.

Botryosphaeria dieback is a grapevine trunk disease with a worldwide distribution associated with Diplodia seriata and Neofusicoccum parvum, among several other Botryosphaeriaceae species. The aforementioned xylem-inhabiting fungi cause wood lesions and leaf and berry symptoms, and eventually lead to the death of the plant. The aim of this work was to develop a simple model system to reproduce the foliar symptoms caused by D. seriata and N. parvum to better characterize fungal pathogenicity and determine the mechanisms involved in symptom development. Green stems of grafted ‘Aragonez’ grapevine cuttings were inoculated with three isolates of N. parvum and two isolates of D. seriata with different degrees of virulence and the experiment was repeated four times from 2011 to 2014. Three months after inoculation, the lesions associated with N. parvum were larger than those associated with D. seriata. Similarly, 8 months after inoculation, the percentage of plants showing foliar symptoms was greater in the N. parvum treatments than in the D. seriata treatments. During the emergence of foliar symptoms, plant stress-related responses were modulated in green stems and leaves, especially a downregulation of superoxide dismutase (SOD) and fasciclin-like arabinogalactan protein (fascAGP) and an upregulation of stilbene synthase (STS) genes with an accumulation of phenolics. In conclusion, the simple model system developed allowed a good characterization of isolate pathogenicity and correlation with foliar symptoms of Botryosphaeria dieback, namely spots on leaf margin and blade.