Medical Research Council Centre for Medical Mycology at the University of Exeter, Exeter EX4 4QD, United Kingdom.
Medical Research Council (MRC) Centre for Global Infectious Disease Analysis, Imperial College London, London W12 0BZ, United Kingdom.
Proc Natl Acad Sci U S A. 2023 Jan 10;120(2):e2212633120. doi: 10.1073/pnas.2212633120. Epub 2023 Jan 3.
The origins and evolution of virulence in amphibian-infecting chytrids () and ( are largely unknown. Here, we use deep nanopore sequencing of and comparative genomics against 21 high-quality genome assemblies that span the fungal Chytridiomycota. We discover that has the most repeat-rich genome of the Chytridiomycota, comprising 40.9% repetitive elements; this genome has expanded to more than 3× the length of its conspecific , with autonomous and fully functional LTR/Gypsy elements contributing significantly to the expansion. The M36 metalloprotease virulence factors are highly expanded ( = 177) in , most of which (53%) are flanked by transposable elements, suggesting they have a repeat-associated expansion. We find enrichment upstream of M36 metalloprotease genes of three novel repeat families belonging to the repeat superfamily of LINEs that are implicated with gene copy number variations. Additionally, has a highly compartmentalized genome architecture, with virulence factors enriched in gene-sparse/repeat-rich compartments, while core conserved genes are enriched in gene-rich/repeat-poor compartments. Genes upregulated during infection are primarily found in the gene-sparse/repeat-rich compartment in both and . Furthermore, genes with signatures of positive selection in are enriched in repeat-rich regions, suggesting these regions are a cradle for the evolution of chytrid pathogenicity. These are the hallmarks of two-speed genome evolution, and this study provides evidence of two-speed genomes in an animal pathogen, shedding light on the evolution of fungal pathogens of vertebrates driving global declines and extinctions.
两栖动物感染的壶菌（）和（）的毒力起源和进化在很大程度上是未知的。在这里，我们使用深度纳米孔测序和比较基因组学，针对跨越真菌壶菌门的 21 个高质量基因组组装进行研究。我们发现，具有壶菌门中最富含重复序列的基因组，包含 40.9%的重复元件；这个基因组的长度扩展到了其同物种的 3 倍以上，自主和功能齐全的 LTR/Gypsy 元件对此扩展做出了重大贡献。M36 金属蛋白酶毒力因子在中高度扩张（=177），其中大多数（53%）侧翼有转座元件，表明它们具有重复相关的扩张。我们发现，在 M36 金属蛋白酶基因的上游，三个新的属于 LINE 重复超家族的重复家族富集，这些家族与基因拷贝数变异有关。此外，具有高度分隔的基因组结构，毒力因子富集在基因稀疏/重复丰富的隔室中，而核心保守基因富集在基因丰富/重复贫乏的隔室中。在感染过程中上调的基因主要存在于和中的基因稀疏/重复丰富隔室中。此外，在中具有正选择特征的基因在富含重复的区域富集，表明这些区域是壶菌致病进化的摇篮。这些是双速基因组进化的特征，本研究为动物病原体中的双速基因组提供了证据，揭示了驱动全球减少和灭绝的脊椎动物真菌病原体的进化。
