BACKGROUND The gene content of a species largely governs its ecological interactions and adaptive potential. A species is therefore defined by both core genes shared between all individuals and accessory genes segregating presence-absence variation. There is growing evidence that eukaryotes, similar to bacteria, show intra-specific variability in gene content. However, it remains largely unknown how functionally relevant such a pangenome structure is for eukaryotes and what mechanisms underlie the emergence of highly polymorphic genome structures. RESULTS Here, we establish a reference-quality pangenome of a fungal pathogen of wheat based on 19 complete genomes from isolates sampled across six continents. Zymoseptoria tritici causes substantial worldwide losses to wheat production due to rapidly evolved tolerance to fungicides and evasion of host resistance. We performed transcriptome-assisted annotations of each genome to construct a global pangenome. Major chromosomal rearrangements are segregating within the species and underlie extensive gene presence-absence variation. Conserved orthogroups account for only ~ 60% of the species pangenome. Investigating gene functions, we find that the accessory genome is enriched for pathogenesis-related functions and encodes genes involved in metabolite production, host tissue degradation and manipulation of the immune system. De novo transposon annotation of the 19 complete genomes shows that the highly diverse chromosomal structure is tightly associated with transposable element content. Furthermore, transposable element expansions likely underlie recent genome expansions within the species. CONCLUSIONS Taken together, our work establishes a highly complex eukaryotic pangenome providing an unprecedented toolbox to study how pangenome structure impacts crop-pathogen interactions.

中文翻译：

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小麦真菌 Zymoseptoria tritici 的 19 个分离株参考质量全球全基因组。


背景技术物种的基因内容在很大程度上决定其生态相互作用和适应潜力。因此，一个物种是由所有个体共享的核心基因和隔离存在与不存在变异的辅助基因来定义的。越来越多的证据表明，真核生物与细菌类似，在基因内容上表现出种内变异。然而，这种全基因组结构对于真核生物的功能相关性如何以及高度多态性基因组结构的出现背后的机制仍然很大程度上未知。结果在这里，我们基于来自六大洲采样的分离株的 19 个完整基因组，建立了小麦真菌病原体的参考质量全基因组。由于快速进化出对杀菌剂的耐受性和逃避宿主抗性，小麦发酵斑孢菌在全球范围内造成了小麦生产的重大损失。我们对每个基因组进行转录组辅助注释，以构建全局泛基因组。主要的染色体重排在物种内发生分离，并成为广泛的基因存在与缺失变异的基础。保守的直系群仅占物种全基因组的 60%。通过研究基因功能，我们发现辅助基因组富含与发病机制相关的功能，并编码参与代谢物产生、宿主组织降解和免疫系统操纵的基因。 19个完整基因组的从头转座子注释表明，高度多样化的染色体结构与转座元件含量紧密相关。此外，转座元件的扩展可能是该物种内最近基因组扩展的基础。 结论 综上所述，我们的工作建立了一个高度复杂的真核全基因组，为研究全基因组结构如何影响作物-病原体相互作用提供了前所未有的工具箱。