Sauters Thomas J C, Rokas Antonis
Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
Department of Biological Sciences and Evolutionary Studies Initiative, Vanderbilt University, Nashville, TN, USA.
Curr Biol. 2025 Jun 9;35(11):R527-R544. doi: 10.1016/j.cub.2025.04.003.
The fungal kingdom is a diverse eukaryotic clade largely composed of microbial organisms. Comprised of indispensable plant symbionts, major environmental decomposers, and important plant and animal pathogens, fungi directly shape the biological world. Advancements in genomics have increased our understanding of fungal genomic variation, the mechanisms that generate it, and the association of genomic plasticity with fungal ecological lifestyles and adaptation. In this review, we discuss the patterns and mechanisms underlying fungal genomic plasticity, juxtaposing them, where known, with patterns and mechanisms observed in plants and animals. We begin by describing the plasticity of fungal genomes, which ranges from large-scale variation in size and ploidy to the physical or temporal compartmentalization of evolutionary rates. We summarize notable patterns of genomic plasticity that have evolved independently across the fungal kingdom, including but not limited to accessory chromosomes, two-speed genomes, and hypermutation; some of these patterns are unique to fungi and largely absent from animals or plants. Strikingly, certain patterns are associated with specific ecological lifestyles, raising the hypothesis that the plasticity of fungal genomes facilitates these lifestyles. We then describe the wide variety of mechanisms that contribute to fungal genome plasticity, including sexual reproduction, transposable-element mobilization, and aneuploidy. Some mechanisms appear to be lineage-specific (for example, Starship transposable elements and repeat-induced point mutations), whereas others are more broadly distributed (parasexual and sexual reproduction). We conclude by discussing how a more balanced sampling of fungal genomes, including population genomic data, will lead to greater insights into fungal genome plasticity and its origins.
真菌界是一个多样化的真核生物分支，主要由微生物组成。真菌包括不可或缺的植物共生体、主要的环境分解者以及重要的动植物病原体，直接塑造了生物世界。基因组学的进展加深了我们对真菌基因组变异、产生变异的机制以及基因组可塑性与真菌生态生活方式和适应性之间关联的理解。在这篇综述中，我们讨论真菌基因组可塑性的模式和机制，并在已知的情况下，将它们与在植物和动物中观察到的模式和机制进行对比。我们首先描述真菌基因组的可塑性，其范围从大小和倍性的大规模变异到进化速率的物理或时间上的区室化。我们总结了在整个真菌界独立进化的显著基因组可塑性模式，包括但不限于附属染色体、双速基因组和超突变；其中一些模式是真菌特有的，在动物或植物中基本不存在。引人注目的是，某些模式与特定的生态生活方式相关，这引发了一种假设，即真菌基因组的可塑性促进了这些生活方式。然后，我们描述了导致真菌基因组可塑性的多种机制，包括有性生殖、转座元件移动和非整倍体。一些机制似乎是谱系特异性的（例如，星际转座元件和重复诱导的点突变），而其他机制分布更广泛（准性生殖和有性生殖）。我们最后讨论了更均衡地采样真菌基因组，包括群体基因组数据，将如何带来对真菌基因组可塑性及其起源的更深入见解。
