Mondo Stephen J, Grigoriev Igor V
US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
Nat Rev Microbiol. 2025 Jun 30. doi: 10.1038/s41579-025-01195-6.
Originating from aquatic unicellular ancestors, over the course of ~1 billion years, the fungi have evolved to occupy nearly all aerobic environments on the planet, diversified into millions of different 'species' and have developed complex multicellular structures. Their relatively small, simple genomes have facilitated massive-scale sequencing and allowed us to explore genome evolution across an ancient eukaryotic kingdom. With thousands of genomes from diverse lineages now available, this Review will discuss insights into fungal biology and evolution gleaned with genomics and other multi-omics approaches. Using published genomes available through GenBank and the Joint Genome Institute's MycoCosm platform, we generated kingdom-wide phylogenies and used them to highlight how fungal genomes have changed over time. With this phylogeny as a guide, we also discuss major evolutionary transitions that occurred across the fungal kingdom. Although progress has been made, these efforts are hampered by biases in genome representation and limited characterization of gene functions. Here, we discuss these challenges and possible future directions to address them, including initiatives to characterize conserved genes of unknown function and scale up sequencing towards 10,000 annotated fungal genomes.
真菌起源于水生单细胞祖先，在约10亿年的时间里，进化到占据地球上几乎所有的需氧环境，分化成数百万个不同的“物种”，并发展出复杂的多细胞结构。它们相对较小、简单的基因组便于进行大规模测序，使我们能够探索一个古老真核生物界的基因组进化。如今有来自不同谱系的数千个基因组可用，本综述将讨论通过基因组学和其他多组学方法获得的关于真菌生物学和进化的见解。利用通过GenBank和联合基因组研究所（Joint Genome Institute）的MycoCosm平台获得的已发表基因组，我们构建了全界系统发育树，并利用它们来突出真菌基因组随时间的变化。以这个系统发育树为指导，我们还将讨论真菌界发生的主要进化转变。尽管已经取得了进展，但这些努力受到基因组代表性偏差和基因功能表征有限的阻碍。在这里，我们讨论这些挑战以及应对它们的可能未来方向，包括对功能未知的保守基因进行表征以及扩大测序规模以达到10000个注释真菌基因组的计划。
