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. 2024 Apr 2;16(4):evae053.
doi: 10.1093/gbe/evae053.

Microbial Diversity and Open Questions about the Deep Tree of Life

Laura Eme  1 , Daniel Tamarit  2
Affiliations

Microbial Diversity and Open Questions about the Deep Tree of Life

Laura Eme et al. Genome Biol Evol. .

Abstract

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.

Keywords: Tree of Life; artificial intelligence; metagenomics; microbial diversity; microbial genomics; phylogenomics; single-cell omics.

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Figures

Fig. 1.
Fig. 1.
Schematic depiction of the uncertainty related to some key branches of the ToL discussed in this work.
Fig. 2.
Fig. 2.
Axes of improvement for the accurate reconstruction of the ToL.
See this image and copyright information in PMC

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