Centre for Crop Health, Institute for Life Sciences and the Environment, Research and Innovation Division, University of Southern Queensland, Toowoomba, QLD, Australia.
Graham Centre for Agricultural Innovation, (Charles Sturt University and NSW Department of Primary Industries), School of Agricultural and Wine Sciences, Charles Sturt University, Wagga Wagga, NSW, Australia.
PLoS One. 2020 May 29;15(5):e0227396. doi: 10.1371/journal.pone.0227396. eCollection 2020.
Elsinoë fawcettii, a necrotrophic fungal pathogen, causes citrus scab on numerous citrus varieties around the world. Known pathotypes of E. fawcettii are based on host range; additionally, cryptic pathotypes have been reported and more novel pathotypes are thought to exist. E. fawcettii produces elsinochrome, a non-host selective toxin which contributes to virulence. However, the mechanisms involved in potential pathogen-host interactions occurring prior to the production of elsinochrome are unknown, yet the host-specificity observed among pathotypes suggests a reliance upon such mechanisms. In this study we have generated a whole genome sequencing project for E. fawcettii, producing an annotated draft assembly 26.01 Mb in size, with 10,080 predicted gene models and low (0.37%) coverage of transposable elements. A small proportion of the assembly showed evidence of AT-rich regions, potentially indicating genomic regions with increased plasticity. Using a variety of computational tools, we mined the E. fawcettii genome for potential virulence genes as candidates for future investigation. A total of 1,280 secreted proteins and 276 candidate effectors were predicted and compared to those of other necrotrophic (Botrytis cinerea, Parastagonospora nodorum, Pyrenophora tritici-repentis, Sclerotinia sclerotiorum and Zymoseptoria tritici), hemibiotrophic (Leptosphaeria maculans, Magnaporthe oryzae, Rhynchosporium commune and Verticillium dahliae) and biotrophic (Ustilago maydis) plant pathogens. Genomic and proteomic features of known fungal effectors were analysed and used to guide the prioritisation of 120 candidate effectors of E. fawcettii. Additionally, 378 carbohydrate-active enzymes were predicted and analysed for likely secretion and sequence similarity with known virulence genes. Furthermore, secondary metabolite prediction indicated nine additional genes potentially involved in the elsinochrome biosynthesis gene cluster than previously described. A further 21 secondary metabolite clusters were predicted, some with similarity to known toxin producing gene clusters. The candidate virulence genes predicted in this study provide a comprehensive resource for future experimental investigation into the pathogenesis of E. fawcettii.
Elsinoë fawcettii，一种坏死型真菌病原体，可导致世界上众多柑橘品种感染疮痂病。已知的 E. fawcettii 致病型是基于宿主范围的；此外，还报道了隐生致病型，并且认为存在更多新型致病型。E. fawcettii 产生非寄主选择性毒素 elsinochrome，该毒素有助于其毒性。然而，在产生 elsinochrome 之前发生的潜在病原体-宿主相互作用的机制尚不清楚，但观察到的致病型之间的宿主特异性表明依赖于此类机制。在这项研究中，我们为 E. fawcettii 生成了一个全基因组测序项目，产生了一个大小为 26.01 Mb 的注释草案组装，其中包含 10080 个预测的基因模型和低（0.37%）转座元件覆盖率。组装的一小部分显示出富含 AT 的区域的证据，可能表明基因组中具有更高的可塑性。我们使用各种计算工具从 E. fawcettii 基因组中挖掘潜在的毒力基因，作为未来研究的候选基因。共预测了 1280 种分泌蛋白和 276 种候选效应子，并与其他坏死型（Botrytis cinerea、Parastagonospora nodorum、Pyrenophora tritici-repentis、Sclerotinia sclerotiorum 和 Zymoseptoria tritici）、半活体型（Leptosphaeria maculans、Magnaporthe oryzae、Rhynchosporium commune 和 Verticillium dahliae）和活体型（Ustilago maydis）植物病原体进行了比较。分析了已知真菌效应子的基因组和蛋白质组特征，并用于指导 E. fawcettii 120 种候选效应子的优先级排序。此外，预测了 378 种碳水化合物活性酶，并分析了它们的可能分泌和与已知毒力基因的序列相似性。此外，次生代谢产物预测表明，与先前描述的 elsinochrome 生物合成基因簇相比，该基因簇中可能还有另外 9 个基因参与。还预测了另外 21 个次生代谢物簇，其中一些与已知产毒基因簇相似。本研究预测的候选毒力基因为未来深入研究 E. fawcettii 的发病机制提供了全面的资源。
