Distinctive expansion of gene families associated with plant cell wall degradation, secondary metabolism, and nutrient uptake in the genomes of grapevine trunk pathogens

BackgroundTrunk diseases threaten the longevity and productivity of grapevines in all viticulture production systems. They are caused by distantly-related fungi that form chronic wood infections. Variation in wood-decay abilities and production of phytotoxic compounds are thought to contribute to their unique disease symptoms. We recently released the draft sequences of Eutypa lata, Neofusicoccum parvum and Togninia minima, causal agents of Eutypa dieback, Botryosphaeria dieback and Esca, respectively. In this work, we first expanded genomic resources to three important trunk pathogens, Diaporthe ampelina, Diplodia seriata, and Phaeomoniella chlamydospora, causal agents of Phomopsis dieback, Botryosphaeria dieback, and Esca, respectively. Then we integrated all currently-available information into a genome-wide comparative study to identify gene families potentially associated with host colonization and disease development.ResultsThe integration of RNA-seq, comparative and ab initio approaches improved the protein-coding gene prediction in T. minima, whereas shotgun sequencing yielded nearly complete genome drafts of Dia. ampelina, Dip. seriata, and P. chlamydospora. The predicted proteomes of all sequenced trunk pathogens were annotated with a focus on functions likely associated with pathogenesis and virulence, namely (i) wood degradation, (ii) nutrient uptake, and (iii) toxin production. Specific patterns of gene family expansion were described using Computational Analysis of gene Family Evolution, which revealed lineage-specific evolution of distinct mechanisms of virulence, such as specific cell wall oxidative functions and secondary metabolic pathways in N. parvum, Dia. ampelina, and E. lata. Phylogenetically-informed principal component analysis revealed more similar repertoires of expanded functions among species that cause similar symptoms, which in some cases did not reflect phylogenetic relationships, thereby suggesting patterns of convergent evolution.ConclusionsThis study describes the repertoires of putative virulence functions in the genomes of ubiquitous grapevine trunk pathogens. Gene families with significantly faster rates of gene gain can now provide a basis for further studies of in planta gene expression, diversity by genome re-sequencing, and targeted reverse genetic approaches. The functional validation of potential virulence factors will lead to a more comprehensive understanding of the mechanisms of pathogenesis and virulence, which ultimately will enable the development of accurate diagnostic tools and effective disease management

Facteurs épidémiologiques contribuant à l'adaptation des populations de Leptosphaeria maculans aux résistances spécifiques de Brassica napus : dispersion des pycnidiospores et des ascospores et progression systémique du champignon

Management of phoma stem canker of oilseed rape, caused by Leptosphaeria maculans, primarily relies on the cultivation of resistant varieties that lack durable efficiency. Sexual reproduction enhances the evolutionary potential of the fungus submitted to the selection pressure exerted by resistant varieties by allowing acquisition and association of virulence alleles and season-to-season transmission of the disease through ascospore dispersal. We hypothesize that for small, emergent virulent populations, sexual reproduction could be restricted by the reduced mating probability of individuals and that season-to-season transmission of virulent individuals through ascopsore dispersal can be spatially limited. To test these hypotheses, we investigated (i) rain-splash dispersal of pycnidiospores, (ii) systemic growth of the fungus in stem and (iii) the spatial genetic structure of populations to infer ascospore dispersal distances. Pycnidiospores were splash-dispersed over short distances (within 40 cm from the source) from phoma leaf spots, while oilseed rape stubble carrying pycnidia constituted a potential source of primary infections. Stem canker expression via systemic growth increased with the number of infection sites on cotyledon and decreased on polygenic resistant hosts, while density-dependent competition between isolates was shown. In the field at low L. maculans population densities, rain-splash dispersal of pycnidiospores could increase the pathogen population size and enhance sexual reproduction by facilitating the mating of initially spatially distant individuals of opposite mating type, while systemic growth could reduce this mating. From 29 French field populations, most genotypic (minisatellite markers) diversity was found within a single population; the lack of genetic differentiation between populations could not demonstrate restricted gene flow and distances of ascospore dispersal could not be inferred at the spatial scale studied. These results suggest that ascospore dispersal may have a greater range than previously state and/or that effective field population sizes may be very large. These epidemiological findings should be accounted for to improve deploiement of resistant varieties.La lutte contre le Phoma du colza, causé par le champignon Leptosphaeria maculans, repose principalement sur la culture de variétés résistantes dont l'efficacité est peu durable. La reproduction sexuée confère un fort potentiel adaptatif au champignon confronté aux pressions de sélection exercées par les variétés résistantes : elle permet l'acquisition et l'association d'allèles de virulence, alors que les ascospores issues de la reproduction sexuée assurent la transmission de la maladie d'une saison culturale à la suivante. Nous faisons l'hypothèse qu'en début de contournement de résistance, la transmission de la virulence d'une génération à la suivante est limitée d'une part par la faible probabilité de reproduction sexuée entre isolats virulents et d'autre part par une dispersion des ascospores spatialement limitée. Pour tester cette hypothèse nous avons étudié (i) la dispersion des pycnidiospores par la pluie, (ii) la progression systémique du champignon dans la tige de colza et (iii) la structure spatiale des populations de L. maculans pour inférer les distances de dispersion des ascospores. Sous un générateur de gouttes en air calme, les pycnidiospores sont dispersées par les gouttelettes de pluie à moins de 40 cm de la macule source ; des résidus porteurs de pycnides peuvent causer des infections primaires de la maladie. Le succès de la phase systémique détecté par l'expression de nécroses au collet sur des plantules inoculées en conditions contrôlées augmente avec le nombre de points d'infection, mais diminue en présence de la résistance partielle ; la compétition entre individus peut limiter la présence concomitante des types sexuels au collet de la plante. Par conséquent, dans des champs avec des populations de L. maculans à faible densité, la dispersion des pycnidiospores par la pluie peut accroître la taille de la population pathogène et permettre la rencontre d'individus initialement distants, tandis que la progression systémique du champignon peut limiter la rencontre locale d'isolats virulents sexuellement compatibles. Pour 29 populations françaises génotypées à l'aide de marqueurs minisatellites, l'essentiel de la diversité génotypique est détectée à l'échelle d'une population (champ) ; l'absence de différenciation génétique entre populations distantes n'a pas permis de mettre en évidence une limitation des flux de gènes à l'échelle spatiale analysée. Ces résultats suggèrent que la dispersion du Phoma par les ascospores est beaucoup plus élevée que supposée et/ou que les tailles efficaces des populations du champignon dans une parcelle sont très grandes. Ces connaissances épidémiologiques devront être prises en compte pour améliorer les stratégies de déploiement durable des variétés résistantes

Epidemiological factors contributing to the adaptation of Leptosphaeria maculans populations to specific resistance in Brassica napus: pycnidiospore and ascospore dispersal and fungal systemic growth

Management of phoma stem canker of oilseed rape, caused by Leptosphaeria maculans, primarily relies on the cultivation of resistant varieties that lack durable efficiency. Sexual reproduction enhances the evolutionary potential of the fungus submitted to the selection pressure exerted by resistant varieties by allowing acquisition and association of virulence alleles and season-to-season transmission of the disease through ascospore dispersal. We hypothesize that for small, emergent virulent populations, sexual reproduction could be restricted by the reduced mating probability of individuals and that season-to-season transmission of virulent individuals through ascopsore dispersal can be spatially limited. To test these hypotheses, we investigated (i) rain-splash dispersal of pycnidiospores, (ii) systemic growth of the fungus in stem and (iii) the spatial genetic structure of populations to infer ascospore dispersal distances. Pycnidiospores were splash-dispersed over short distances (within 40 cm from the source) from phoma leaf spots, while oilseed rape stubble carrying pycnidia constituted a potential source of primary infections. Stem canker expression via systemic growth increased with the number of infection sites on cotyledon and decreased on polygenic resistant hosts, while density-dependent competition between isolates was shown. In the field at low L. maculans population densities, rain-splash dispersal of pycnidiospores could increase the pathogen population size and enhance sexual reproduction by facilitating the mating of initially spatially distant individuals of opposite mating type, while systemic growth could reduce this mating. From 29 French field populations, most genotypic (minisatellite markers) diversity was found within a single population; the lack of genetic differentiation between populations could not demonstrate restricted gene flow and distances of ascospore dispersal could not be inferred at the spatial scale studied. These results suggest that ascospore dispersal may have a greater range than previously state and/or that effective field population sizes may be very large. These epidemiological findings should be accounted for to improve deploiement of resistant varieties.La lutte contre le Phoma du colza, causé par le champignon Leptosphaeria maculans, repose principalement sur la culture de variétés résistantes dont l'efficacité est peu durable. La reproduction sexuée confère un fort potentiel adaptatif au champignon confronté aux pressions de sélection exercées par les variétés résistantes : elle permet l'acquisition et l'association d'allèles de virulence, alors que les ascospores issues de la reproduction sexuée assurent la transmission de la maladie d'une saison culturale à la suivante. Nous faisons l'hypothèse qu'en début de contournement de résistance, la transmission de la virulence d'une génération à la suivante est limitée d'une part par la faible probabilité de reproduction sexuée entre isolats virulents et d'autre part par une dispersion des ascospores spatialement limitée. Pour tester cette hypothèse nous avons étudié (i) la dispersion des pycnidiospores par la pluie, (ii) la progression systémique du champignon dans la tige de colza et (iii) la structure spatiale des populations de L. maculans pour inférer les distances de dispersion des ascospores. Sous un générateur de gouttes en air calme, les pycnidiospores sont dispersées par les gouttelettes de pluie à moins de 40 cm de la macule source ; des résidus porteurs de pycnides peuvent causer des infections primaires de la maladie. Le succès de la phase systémique détecté par l'expression de nécroses au collet sur des plantules inoculées en conditions contrôlées augmente avec le nombre de points d'infection, mais diminue en présence de la résistance partielle ; la compétition entre individus peut limiter la présence concomitante des types sexuels au collet de la plante. Par conséquent, dans des champs avec des populations de L. maculans à faible densité, la dispersion des pycnidiospores par la pluie peut accroître la taille de la population pathogène et permettre la rencontre d'individus initialement distants, tandis que la progression systémique du champignon peut limiter la rencontre locale d'isolats virulents sexuellement compatibles. Pour 29 populations françaises génotypées à l'aide de marqueurs minisatellites, l'essentiel de la diversité génotypique est détectée à l'échelle d'une population (champ) ; l'absence de différenciation génétique entre populations distantes n'a pas permis de mettre en évidence une limitation des flux de gènes à l'échelle spatiale analysée. Ces résultats suggèrent que la dispersion du Phoma par les ascospores est beaucoup plus élevée que supposée et/ou que les tailles efficaces des populations du champignon dans une parcelle sont très grandes. Ces connaissances épidémiologiques devront être prises en compte pour améliorer les stratégies de déploiement durable des variétés résistantes

Facteurs épidémiologiques contribuant à l adaptation des populations de Leptosphaeria maculans aux résistances spécifiques de Brassica napus : dispersion des pycnidiospores et des ascospores et progression systémique du dispersion des pycnidiospores et des ascospores et progresssion systémique du champignon

La lutte contre le Phoma du colza, causé par le champignon Leptosphaeria maculans, repose principalement sur la culture de variétés résistantes dont l efficacité est peu durable. La reproduction sexuée confère un fort potentiel adaptatif au champignon confronté aux pressions de sélection exercées par les variétés résistantes : elle permet l acquisition et l association d allèle de virulence, alors que les ascospores issues de la reproduction sexuée assurent la transmission de la maladie d une saison culturale à la suivante. Nous faison l hypothèse qu en début de contournement de résistance, la transmission dela virulence d une génération à la suivante est limitée d une part par la faible probabilité de reproduction sexuée entre isolats virulents et d autre part par une dispersion des ascospores spatialement limitée. Pour tester cette hypothèse nous avons étudié (i) la dispersion des pycnidiospores. Sous un générateur de gouttes en air calme, les pycnidiospores sont dispersées par les gouttelettes de pluie à moins de 40 cm de la macule source ; des résidus porteurs de pycnides peuvent causer des infections primaires de la maladie. Le succès de la phase systémique détecté par l expression de nécroses au collet sur des plantules inoculées en conditions contrôlées augmente avec le nombre de points d infection, mais diminue en présence de la résistance partielle ; la compétition entre individus peut limiter la présence concoittante des types sexuels au collet de la plante. Par conséquent dans des champs avec des populations de L. Maculans à faible densité, la dispersion des pycnidiospores par la pluie peut accroître la taille de la populatino pathogène et permettre la rencontre d individus initialement distants, tandis que la progression systémique du champignon peut limiter la rencontre locale d isolats virulents sexuellement compatibles.Management of homa stem canker of oilseed rape,caused by Leptosphaeria maculans, primarily relies on the cultivation of resistant varieties that lack durable efficiency. Sexual reproduction enhances the evolutionary potential of the fungus submitted to the selection pressure exerted by resistant varieties by allowing acquisition and association of virulence alleles and season-to-season transmission of the disease through ascospore dispersal. We hypothesize that for small, emergent virulent populations, sexual reproduction could be restricted by the reduced mating probability of individuals and that season-to-season transmission of virulent individuals through ascopsore dispersal can be spatially limited. To test these hypotheses, we investigated (i) rain-splash dispersal of pycnidiospores, (ii) systemic growth of the fungus in stem and (iii) the spatial genetic structure of populations to infer ascospore dispersal distances. Pycnidiospores were splash-dispersed over short distances (within 40 cm from the source) from phoma leaf sports, while oilseed rape stubble carrying pycnidia constituted a potential source of primary infections.RENNES-Agrocampus-CRD (352382323) / SudocSudocFranceF

Whole genome sequencing and analysis of multiple isolates of Ceratocystis destructans, the causal agent of Ceratocystis canker of almond in California.

Ceratocystis canker caused by Ceratocystis destructans is a severe disease of almond, reducing the longevity and productivity of infected trees. Once the disease has established in an individual tree, there is no cure, and management efforts are often limited to removing the infected area of cankers. In this study, we present the genome assemblies of five C. destructans isolates isolated from symptomatic almond trees. The genomes were assembled into a genome size of 27.2 ± 0.9 Mbp with an average of 6924 ± 135 protein-coding genes and an average GC content of 48.8 ± 0.02%. We concentrated our efforts on identifying putative virulence factors of canker pathogens. Analysis of the secreted carbohydrate-active enzymes showed that the genomes harbored 83.4 ± 1.8 secreted CAZymes. The secreted CAZymes covered all the known categories of CAZymes. AntiSMASH revealed that the genomes had at least 7 biosynthetic gene clusters, with one of the non-ribosomal peptide synthases encoding dimethylcoprogen, a conserved virulence determinant of plant pathogenic ascomycetes. From the predicted proteome, we also annotated cytochrome P450 monooxygenases, and transporters, these are well-established virulence determinants of canker pathogens. Moreover, we managed to identify 57.4 ± 2.1 putative effector proteins. Gene Ontology (GO) annotation was applied to compare gene content with two closely related species C. fimbriata, and C. albifundus. This study provides the first genome assemblies for C. destructans, expanding genomic resources for an important almond canker pathogen. The acquired knowledge provides a foundation for further advanced studies, such as molecular interactions with the host, which is critical for breeding for resistance

Whole genome sequencing and analysis of multiple isolates of Ceratocystis destructans, the causal agent of Ceratocystis canker of almond in California

Abstract Ceratocystis canker caused by Ceratocystis destructans is a severe disease of almond, reducing the longevity and productivity of infected trees. Once the disease has established in an individual tree, there is no cure, and management efforts are often limited to removing the infected area of cankers. In this study, we present the genome assemblies of five C. destructans isolates isolated from symptomatic almond trees. The genomes were assembled into a genome size of 27.2 ± 0.9 Mbp with an average of 6924 ± 135 protein-coding genes and an average GC content of 48.8 ± 0.02%. We concentrated our efforts on identifying putative virulence factors of canker pathogens. Analysis of the secreted carbohydrate-active enzymes showed that the genomes harbored 83.4 ± 1.8 secreted CAZymes. The secreted CAZymes covered all the known categories of CAZymes. AntiSMASH revealed that the genomes had at least 7 biosynthetic gene clusters, with one of the non-ribosomal peptide synthases encoding dimethylcoprogen, a conserved virulence determinant of plant pathogenic ascomycetes. From the predicted proteome, we also annotated cytochrome P450 monooxygenases, and transporters, these are well-established virulence determinants of canker pathogens. Moreover, we managed to identify 57.4 ± 2.1 putative effector proteins. Gene Ontology (GO) annotation was applied to compare gene content with two closely related species C. fimbriata, and C. albifundus. This study provides the first genome assemblies for C. destructans, expanding genomic resources for an important almond canker pathogen. The acquired knowledge provides a foundation for further advanced studies, such as molecular interactions with the host, which is critical for breeding for resistance

Conduite, taille de la vigne et esca : les premieres conditionnent l'autre

National audienc

Conduite, taille de la vigne et esca : les premieres conditionnent l'autre

National audienc

Identifying Economic Hurdles to Early Adoption of Preventative Practices: The Case of Trunk Diseases in California Winegrape Vineyards

Despite the high likelihood of infection and substantial yield losses from trunk diseases, many California practitioners wait to adopt field-tested, preventative practices (delayed pruning, double pruning, and application of pruning-wound protectants) until after disease symptoms appear in the vineyard at around 10 years old. We evaluate net benefits from adoption of these practices before symptoms appear in young Cabernet Sauvignon vineyards and after they become apparent in mature vineyards to identify economic hurdles to early adoption. We simulate production in five regions of California and find widespread benefits from early adoption, increasing vineyard profitable lifespans, in some cases, by more than 50%. However, hurdles to adopt may result from uncertainty about the cost and returns from adoption, labor constraints, long time lags in benefits from early adoption, growers’ perceived probabilities of infection, and their discount rate. The development of extension resources to communicate these benefits and potential hurdles to growers are likely to reduce uncertainty, leading to increased early adoption