Apple Glomerella leaf spot (GLS) is an emerging fungal disease caused by Colletotrichum fructicola and other Colletotrichum species. These species are polyphyletic and it is currently unknown how these pathogens convergently evolved to infect apple. We generated chromosome‐level genome assemblies of a GLS‐adapted isolate and a non‐adapted isolate in C. fructicola using long‐read sequencing. Additionally, we resequenced 17 C. fructicola and C. aenigma isolates varying in GLS pathogenicity using short‐read sequencing. Genome comparisons revealed a conserved bipartite genome architecture involving minichromosomes (accessory chromosomes) shared by C. fructicola and other closely related species within the C. gloeosporioides species complex. Moreover, two repeat‐rich genomic regions (1.61 Mb in total) were specifically conserved among GLS‐pathogenic isolates in C. fructicola and C. aenigma. Single‐gene deletion of 10 accessory genes within the GLS‐specific regions of C. fructicola identified three that were essential for GLS pathogenicity. These genes encoded a putative non‐ribosomal peptide synthetase, a flavin‐binding monooxygenase and a small protein with unknown function. These results highlight the crucial role accessory genes play in the evolution of Colletotrichum pathogenicity and imply the significance of an unidentified secondary metabolite in GLS pathogenesis.

中文翻译：

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基因组比较揭示了对炭疽菌中苹果球小球菌叶斑病致病性进化至关重要的辅助基因

苹果球粒菌叶斑病 (GLS) 是一种新出现的真菌病害，由以下原因引起：果炭疽菌和别的炭疽菌属物种。这些物种是多系的，目前尚不清楚这些病原体如何聚合进化来感染苹果。我们生成了 GLS 适应分离株和非适应分离株的染色体水平基因组组装果果红藻使用长读长测序。此外，我们对 17 个果果红藻和恩尼格玛使用短读长测序分离出不同 GLS 致病性的菌株。基因组比较揭示了一种保守的二分基因组结构，涉及由果果红藻以及该区域内其他密切相关的物种炭疽杆菌物种复杂。此外，两个重复丰富的基因组区域（总共 1.61 Mb）在 GLS 致病分离株中特别保守。果果红藻和恩尼格玛。 GLS特异性区域内10个辅助基因的单基因缺失果果红藻确定了三个对于 GLS 致病性至关重要的因素。这些基因编码一种假定的非核糖体肽合成酶、一种黄素结合单加氧酶和一种功能未知的小蛋白质。这些结果强调了辅助基因在进化中发挥的关键作用炭疽菌属致病性并暗示未鉴定的次级代谢产物在 GLS 发病机制中的重要性。