State Key Laboratory of Medicinal Chemical Biology, Key Laboratory of Molecular Microbiology and Technology, and Department of Microbiology, College of Life Science, Nankai University, Tianjin, China.
State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
mBio. 2024 Oct 16;15(10):e0213324. doi: 10.1128/mbio.02133-24. Epub 2024 Aug 29.
Mass extinction has often paved the way for rapid evolutionary radiation, resulting in the emergence of diverse taxa within specific lineages. The emergence and diversification of carnivorous nematode-trapping fungi (NTF) in Ascomycota have been linked to the Permian-Triassic (PT) extinction, but the processes underlying NTF radiation remain unclear. We conducted phylogenomic analyses using 23 genomes that represent three NTF lineages, each employing distinct nematode traps-mechanical traps ( spp.), three-dimensional (3D) adhesive traps ( spp.), and two-dimensional (2D) adhesive traps ( spp.), and the genome of one non-NTF species as the outgroup. These analyses revealed multiple mechanisms that likely contributed to the tempo of the NTF evolution and rapid radiation. The species tree of NTFs based on 2,944 single-copy orthologous genes suggested that emerged earlier than and . Extensive genome-wide phylogenetic discordance was observed, mainly due to incomplete lineage sorting (ILS) between lineages. Two modes of non-vertical evolution (introgression and horizontal gene transfer) also contributed to phylogenetic discordance. The ILS genes that are associated with hyphal growth and trap morphogenesis (e.g., those associated with the cell membrane system and polarized cell division) exhibited signs of positive selection.IMPORTANCEBy conducting a comprehensive phylogenomic analysis of 23 genomes across three NTF lineages, the research reveals how diverse evolutionary mechanisms, including ILS and non-vertical evolution (introgression and horizontal gene transfer), contribute to the swift diversification of NTFs. These findings highlight the complex evolutionary dynamics that drive the rapid radiation of NTFs, providing valuable insights into the processes underlying their diversity and adaptation.
大规模灭绝事件常常为快速进化辐射铺平道路，导致特定谱系内多样化的分类群的出现。肉食性线虫诱捕真菌（NTF）在子囊菌中的出现和多样化与二叠纪-三叠纪（PT）灭绝有关，但 NTF 辐射背后的过程仍不清楚。我们使用代表三个 NTF 谱系的 23 个基因组进行了系统基因组分析，每个谱系采用不同的线虫陷阱-机械陷阱（ spp.）、三维（3D）粘性陷阱（ spp.）和二维（2D）粘性陷阱（ spp.），以及一个非 NTF 物种的基因组作为外群。这些分析揭示了多种可能导致 NTF 进化和快速辐射的机制。基于 2944 个单拷贝直系同源基因的 NTF 种系发生树表明， 比 和 更早出现。观察到广泛的全基因组系统发育分歧，主要是由于谱系之间不完全谱系分选（ILS）。两种非垂直进化模式（基因渗入和水平基因转移）也导致了系统发育分歧。与菌丝生长和诱捕形态发生相关的 ILS 基因（例如，与细胞膜系统和极化细胞分裂相关的基因）表现出正选择的迹象。
重要性
通过对三个 NTF 谱系的 23 个基因组进行全面的系统基因组分析，该研究揭示了多种进化机制（包括 ILS 和非垂直进化（基因渗入和水平基因转移））如何促进 NTF 的快速多样化。这些发现强调了驱动 NTF 快速辐射的复杂进化动态，为它们的多样性和适应性背后的过程提供了有价值的见解。
