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.

中文翻译：

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广泛宿主范围植物病原真菌核盘菌的基因组中次级代谢物生物合成簇的详细计算机分析。

背景广泛宿主范围的病原体核盘菌感染超过400种植物并导致全世界作物的大量产量损失。已知次级代谢产物在植物病原体的毒力中起重要作用，但对核盘菌的次级代谢产物库知之甚少。在这项研究中，我们预测了核盘菌基因组中的次级代谢物生物合成基因簇，并使用现有的转录组数据集分析了它们在感染欧洲油菜期间的表达。我们还在一组 25 个先前发表的核盘菌分离基因组中调查了它们的序列多样性。结果 我们确定了 80 个推定的次级代谢物簇。超过一半的簇包含至少三个转录协同调节基因。比较基因组学揭示了与密切相关的植物病原体 Botrytis cinerea 中的簇同源的簇，用于生产类胡萝卜素、异羟肟酸铁载体、DHN 黑色素和 botcinic 酸。我们还确定了可能产生聚酮化合物 sclerin 和表聚硫二氧代哌嗪的推定植物毒素簇。次级代谢物簇在亚端粒基因组区域中富集，而那些含有旁系同源物的代谢物簇与重复序列表现出特别强的关联。我们确定的位置偏差通过种内比较得到证实，种内比较显示假定的次级代谢物基因具有更多存在/不存在多态性，并且表现出比其他基因显着更高的序列多样性。结论 这些数据表明 S. 核盘菌在植物感染期间产生大量次级代谢产物，并且它们的基因簇在亚端粒区域经历增强的突变、复制和重组率。导致核盘菌次生代谢产物多样性的微进化机制尚未阐明。本研究中记录的几种潜在植物毒素为未来的功能分析提供了基础。