BackgroundThe broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.ResultsWe identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.ConclusionsThese data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

Sclerotiniaceae) is a broad host range pathogen that infects over 400 plant species and causes substantial yield losses in crops worldwide. Crops affected are mainly dicotyledonous plants including oilseed rape and other brassicas, sunflower, chickpea, soybean, peanut and lentils, as well as some monocotyledonous plants such as onion and tulip [1]. Like other members of the Sclerotiniaceae, S.sclerotiorum spends approximately 90% of its life cycle as sclerotia: melanised hyphal aggregates that can remain viable for up to eight years in the soil and that play a major role in the disease cycle [2,3]. Infection proceeds when sclerotia germinate either myceliogenically to directly infect a plant, or carpogenically to form an apothecium and disseminate ascospores [2]. After penetrating the plant cuticle S. sclerotiorum proliferates inside the host in a brief biotrophic phase (approximately 24 hours in Brassica napus (oilseed rape)) before commencing a necrotrophic phase in which it kills plant cells, then feeds off the dead tissue [4].The large host range of S. sclerotiorum, its ability to spread via wind dispersal and its persistence in the soil make this fungus a difficult pathogen to control. As a result, there is a need to better understand the molecular basis of S. sclerotiorum disease. One aspect of infection that has been little investigated in S. sclerotiorum is production of secondary metabolites: small, structurally diverse organic molecules that contribute to fungal growth and survival in diverse environments [5]. Secondary metabolites are synthesised by pathogenic fungi for defence, signalling, nutrient uptake and interfering with host cell structure and function [6]. Secondary metabolites that have been shown to contribute to the virulence of plant pathogenic fungi include siderophores, pigments and phytotoxins [7,8]. Although it may be argued that some pigments and siderophores are primary metabolites as they are essential for survival, we refer to them as secondary metabolites in this study as a disambiguation as they are produced by genes in families frequently involved in production of secondary metabolites sensu stricto.Siderophores are small, iron-chelating compounds used by fungi both to scavenge iron from the environment and to bind intracellular iron. Fungi require iron for many essential biochemical processes including respiration, the tricarboxylic acid cycle and the synthesis of deoxyribonucleotides,

Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum . In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.

Background The broad host range pathogen Sclerotinia sclerotiorum infects over 400 plant species and causes substantial yield losses in crops worldwide. Secondary metabolites are known to play important roles in the virulence of plant pathogens, but little is known about the secondary metabolite repertoire of S. sclerotiorum. In this study, we predicted secondary metabolite biosynthetic gene clusters in the genome of S. sclerotiorum and analysed their expression during infection of Brassica napus using an existing transcriptome data set. We also investigated their sequence diversity among a panel of 25 previously published S. sclerotiorum isolate genomes.Results We identified 80 putative secondary metabolite clusters. Over half of the clusters contained at least three transcriptionally coregulated genes. Comparative genomics revealed clusters homologous to clusters in the closely related plant pathogen Botrytis cinerea for production of carotenoids, hydroxamate siderophores, DHN melanin and botcinic acid. We also identified putative phytotoxin clusters that can potentially produce the polyketide sclerin and an epipolythiodioxopiperazine. Secondary metabolite clusters were enriched in subtelomeric genomic regions, and those containing paralogues showed a particularly strong association with repeats. The positional bias we identified was borne out by intraspecific comparisons that revealed putative secondary metabolite genes suffered more presence / absence polymorphisms and exhibited a significantly higher sequence diversity than other genes.Conclusions These data suggest that S. sclerotiorum produces numerous secondary metabolites during plant infection and that their gene clusters undergo enhanced rates of mutation, duplication and recombination in subtelomeric regions. The microevolutionary regimes leading to S. sclerotiorum secondary metabolite diversity have yet to be elucidated. Several potential phytotoxins documented in this study provide the basis for future functional analyses.