Baker Brittany A, McCarthy Charley G P, López-García Purificación, Leroy Romain B, Susko Edward, Roger Andrew J, Eme Laura, Moreira David
Ecologie Société Evolution, Université Paris-Saclay AgroParisTech, CNRS, Gif-sur-Yvette, France.
Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia, Canada.
Nat Microbiol. 2025 Jun 17. doi: 10.1038/s41564-025-02024-5.
The episymbiotic DPANN archaea are thought to be one of the four major archaeal clades. However, the monophyly and placement of DPANN within the archaeal tree remain debated, and their fast-evolving reduced genomes render phylogenetic reconstructions challenging. Here we used 126 highly conserved protein markers, extensive taxon sampling representing the 11 known DPANN phyla and in-depth phylogenomic analyses to reassess DPANN monophyly and their relationships to other archaea. Our analyses robustly support the monophyly and placement within Euryarchaeota, and we identify the probably free-living Altiarchaeota as the earliest diverging DPANN branch. Our phylogenies suggest DPANN probably acquired several hallmark proteins through ancient horizontal gene transfer events from different bacterial donors, notably Patescibacteria and Omnitrophota, two bacterial phyla that also exhibit episymbiotic lifestyles. Overall, the monophyletic DPANN archaea probably evolved from a free-living, euryarchaeal-like ancestor, with proteins of bacterial origin playing a role in the emergence of their episymbiotic lifestyle.
内共生的DPANN古菌被认为是四大古菌分支之一。然而，DPANN在古菌树中的单系性和位置仍存在争议，并且它们快速进化的简化基因组使得系统发育重建具有挑战性。在这里，我们使用了126个高度保守的蛋白质标记，对代表11个已知DPANN门的广泛分类群进行采样，并进行深入的系统发育基因组分析，以重新评估DPANN的单系性及其与其他古菌的关系。我们的分析有力地支持了DPANN在广古菌门中的单系性和位置，并且我们确定可能自由生活的阿尔蒂古菌门是最早分化的DPANN分支。我们的系统发育分析表明，DPANN可能通过来自不同细菌供体的古老水平基因转移事件获得了几种标志性蛋白质，特别是Patescibacteria和Omnitrophota，这两个细菌门也表现出内共生的生活方式。总体而言，单系的DPANN古菌可能从一个自由生活的、类似广古菌的祖先进化而来，来自细菌的蛋白质在它们内共生生活方式的出现中发挥了作用。
