Ecologie Systématique Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Gif sur-Yvette, France.
Theoretical Biology and Bioinformatics, Utrecht University, Utrecht 3584CH, The Netherlands.
Genome Biol Evol. 2024 Apr 2;16(4). doi: 10.1093/gbe/evae053.
In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring debates surrounding various aspects of the microbial Tree of Life, focusing on recent advances in some of its deepest nodes, such as the roots of bacteria, archaea, and eukaryotes. We also bring forth current limitations in genome recovery and phylogenomic methodology, as well as new avenues of research to uncover additional key microbial lineages and resolve the shape of the Tree of Life.
在这个视角下，我们探讨了宏基因组学和单细胞基因组学对我们理解微生物多样性及其与生命之树整合的变革性影响和固有局限性。我们深入研究了通过先进的系统发生基因组学方法将新的微生物谱系纳入生命之树所面临的关键挑战。此外，我们还探讨了围绕微生物生命之树各个方面的持久争论，重点关注细菌、古菌和真核生物等最深节点的最新进展。我们还提出了当前在基因组恢复和系统发生方法学方面的局限性，以及新的研究途径，以揭示其他关键的微生物谱系并解决生命之树的形状问题。
