Secondary metabolites (SMs) are crucial for fungi and vary in function from beneficial antibiotics to pathogenicity factors. To generate diversified SMs that enable different functions, SM‐coding regions rapidly evolve in fungal genomes. However, the driving force and genetic mechanism of fungal SM diversification in the context of host‐pathogen interactions remain largely unknown. Previously, we grouped field populations of the rice blast fungus Magnaporthe oryzae (syn: Pyricularia oryzae ) into three major globally distributed clades based on population genomic analyses. Here, we characterize a recent duplication of an avirulent gene‐containing SM cluster, ACE1, in a clonal M . oryzae population (Clade 2). We demonstrate that the ACE1 cluster is specifically duplicated in Clade 2, a dominant clade in indica rice‐growing areas. With long‐read sequencing, we obtained chromosome‐level genome sequences of four Clade 2 isolates, which displayed differences in genomic organization of the ACE1 duplication process. Comparative genomic analyses suggested that the original ACE1 cluster experienced frequent rearrangement in Clade 2 isolates and revealed that the new ACE1 cluster is located in a newly formed and transposable element‐rich region. Taken together, these results highlight the frequent mutation and expansion of an avirulent gene‐containing SM cluster through transposable element‐mediated whole‐cluster duplication in the context of host‐pathogen interactions.

中文翻译：

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稻瘟病菌稻瘟病菌克隆种群中杂种PKS-NRPS次生代谢产物簇的出现。

次生代谢产物（SMs）对真菌至关重要，其功能从有益的抗生素到致病性因子不等。为了生成能够实现不同功能的多样化SM，SM编码区在真菌基因组中迅速发展。然而，在宿主-病原体相互作用的背景下，真菌SM多样化的驱动力和遗传机制仍然未知。以前，我们分组稻瘟病菌的田间种群稻瘟病菌：（SYN稻瘟病基于人群基因组分析）分为三个主要分布在全球各地的分支。在这里，我们描述了克隆无性系M中含有无毒基因的SM簇ACE1的最新复制。水稻人口（第2类）。我们证明，ACE1集群进化枝2，处于主导分支专门复制籼水稻种植区。通过长时间测序，我们获得了四个Clade 2分离株的染色体水平基因组序列，这些序列在ACE1复制过程的基因组组织上显示出差异。比较基因组分析表明，最初的ACE1簇在进化枝2分离物中经历了频繁的重排，并揭示了新的ACE1簇位于一个新形成且易位的富含元素的区域。综上所述，这些结果强调了在宿主-病原体相互作用的背景下，通过转座因子介导的全簇复制，一个含无毒基因的SM簇经常发生突变和扩增。