The unstable evolutionary position of <i>Korarchaeota</i> and its relationship with other TACK and Asgard archaea

Liu, Yang; Li, Meng

doi:10.1002/mlf2.12020

Cited by 3 publications

(5 citation statements)

References 25 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…This highlights the importance of performing such sophisticated phylogenomic analyses prior to ALE. The different yet more robust and accurate placement of Korarchaeota in our study, compared to F. Vulcano et al (58), J. Pan et al (62) and Y. Liu and M. Li (68) undoubtedly impacts downstream analyses. For example, the previously estimated first divergence time of Korarchaeota (62) – when placed at the base of TACK – will greatly differ.…”

Section: Resultscontrasting

confidence: 55%

See 1 more Smart Citation

Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching

Tahon,

Köstlbacher,

Pelve

et al. 2023

Preprint

View full text Add to dashboard Cite

Our knowledge of archaeal diversity and evolution has expanded rapidly in the past decade. However, hardly any genomes of the phylum Korarchaeota have been obtained due to the difficulty in accessing their natural habitats and – possibly – their limited abundance. As a result, many aspects of Korarchaeota biology, physiology and evolution remain enigmatic. Here, we expand this phylum with five high-quality metagenome-assembled genomes. This improved taxon sampling combined with sophisticated phylogenomic analyses robustly places Korarchaeota at the base of TACK and Asgard clades, revisiting the phylum’s long-assumed position. Furthermore, we observe a clear split between terrestrial and marine thermal clades. Gene tree-aware ancestral reconstructions suggest that the last Korarchaeota common ancestor was a thermophilic autotroph. In contrast, Korarchaeaceae, the lineage where environmental transitions occurred, shifted towards a heterotrophic lifestyle. Terrestrial Korarchaeota gained manycasand CARF genes indicating they may need to manage viral infections. Together, our study provides new insights into these early diverging Archaea and suggests that gradual gene gain and loss shaped their adaptation to different thermal environments.ImportanceKorarchaeota are an ancient group of archaea, but their biology, physiology and evolution have remained obscure. Analysis of five novel Korarchaeota MAGs, and publicly available reference data provides robust phylogenomic evidence that Korarchaeota are placed at the base of Asgard archaea and TACK, revisiting the phylum’s long-assumed position. Gene content reconstruction suggests a versatile thermophilic and autotrophic last Korarchaeota common ancestor. Environmental distribution surveying of public databases places all Korarchaeota in thermophilic environments and indicates that their habitat is limited to hydrothermal vents and hot springs. Our modeling indicates at least two transitions linked to habitat switching between these environments in the evolutionary history of Korarchaeota. Both are linked to a significant alteration of the inferred ancestral gene content, including a shift towards a heterotrophic and potential scavenging lifestyle. Furthermore, hot spring Korarchaeota acquired various genes participating in resistance to viruses, suggesting they may need to manage frequent viral threats.

show abstract

Section: Resultscontrasting

confidence: 55%

“…The above examples show the importance of constructing robust phylogenomic trees including a broad diversity of reference data. Failure to do so (e.g., the work of Y. Liu and M. Li (68)) ultimately leads to incorrect results and conclusions.…”

Section: Resultsmentioning

confidence: 99%

Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching

Tahon,

Köstlbacher,

Pelve

et al. 2023

Preprint

View full text Add to dashboard Cite

show abstract

“…S1a through d ). Furthermore, a recent study showed the unstable evolutionary position of Korarchaeota ( 40 ). All these results suggest that the marker genes should be re-evaluated to allow the construction of a more reliable archaeal tree.…”

Section: Resultsmentioning

confidence: 99%

Wood–Ljungdahl pathway found in novel marine Korarchaeota groups illuminates their evolutionary history

et al. 2023

Self Cite

View full text Add to dashboard Cite

Korarchaeota, due to its rarity in common environments, is one of the archaeal phyla that has received the least attention from researchers. It was previously thought to consist solely of strict thermophiles. However, our study provides genetic evidence for the presence of korarchaeal members in temperate subsurface seawater. Furthermore, a systematic reclassification of the Korarchaeota based on 16S rRNA genes and genomes has revealed three novel marine groups (Kor-6 to Kor-8) at the root of the Korarchaeota branch. Kor-6 contains microbes that are present in moderate temperatures. All three novel marine phyla possess genes for the Wood–Ljungdahl pathway, and Kor-7 and Kor-8 possess fewer genes encoding oxygen resistance traits than other korarchaeal groups, suggesting a distinct lifestyle for these novel phyla. Our results, together with estimations of Korarchaeota divergence times, suggest that oxygen availability may be one of the important factors that have influenced the evolution of Korarchaeota. IMPORTANCE Korarchaeota were previously thought to inhabit exclusively high-temperature environments. However, our study provides genetic evidence for their unexpected presence in temperate marine waters. Through analysis of publicly available korarchaeal reference data, we have systematically reclassified Korarchaeota and identified the existence of three previously unknown marine groups (Kor-6, Kor-7, and Kor-8) at the root of the Korarchaeota branch. Comparative analysis of their gene content revealed that these novel groups exhibit a lifestyle distinct from other Korarchaeota. Specifically, they have the ability to fix carbon exclusively via the Wood–Ljungdahl (WL) pathway, and the genomes within Kor-7 and Kor-8 contain few genes encoding antioxidant enzymes, indicating their strictly anaerobic lifestyle. Further studies suggest that the genes related to methane metabolism and the WL pathway may have been inherited from a common ancestor of the Korarchaeota and that oxygen availability may be one of the important evolutionary factors that shaped the diversification of this archaeal phylum.

show abstract

“…Inclusion of conserved core genes with few or no signal of duplications and horizontal gene transfers (HGTs) either within or among genomes/lineages would be a possible solution. It is also suggested to use a set of custom‐ranked markers that are suitable to solve the depth of phylogeny 54 . Meanwhile, improved/balanced sampling of taxa for better representation of tree topology and lineage placement is required 53 .…”

Section: Future Directionsmentioning

confidence: 99%

“…Later on, many Asgard lineages were discovered in the recent 5 years from groups around the world 47 , 48 , 50 , 55 . In 2021, Wukongarchaeota —the Asgard archaea named after Sun Wukong (The Monkey King), a figure in Chinese mythology—was discovered and currently believed to be the closest relative 45 , 48 , 54 . Based on different ways to reconstruct the phylogeny of eukaryotes and archaea, there is still some support for placing eukaryotes basal within archaea other than within the “expanded Heimdallarchaeota – Wukongarchaeota ” branch 45 .…”

Section: Future Directionsmentioning

confidence: 99%

The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis

Zhou

Liu

Anantharaman

et al. 2022

mLife

Self Cite

View full text Add to dashboard Cite

The division of organisms on the Tree of Life into either a three-domain (3D) tree or a two-domain (2D) tree has been disputed for a long time. Ever since the discovery of Archaea by Carl Woese in 1977 using 16S ribosomal RNA sequence as the evolutionary marker, there has been a great advance in our knowledge of not only the growing diversity of Archaea but also the evolutionary relationships between different lineages of living organisms. Here, we present this perspective to summarize the progress of archaeal diversity and changing notion of the Tree of Life. Meanwhile, we provide the latest progress in genomics/physiology-based discovery of Asgard archaeal lineages as the closest relative of Eukaryotes. Furthermore, we propose three major directions for future research on exploring the "next one" closest Eukaryote relative, deciphering the function of archaeal eukaryotic signature proteins and eukaryogenesis from both genomic and physiological aspects, and understanding the roles of horizontal gene transfer, viruses, and mobile elements in eukaryogenesis.

show abstract

The unstable evolutionary position of Korarchaeota and its relationship with other TACK and Asgard archaea

Cited by 3 publications

References 25 publications

Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching

Phylogenomics and ancestral reconstruction of Korarchaeota reveals genomic adaptation to habitat switching

Wood–Ljungdahl pathway found in novel marine Korarchaeota groups illuminates their evolutionary history

The expanding Asgard archaea invoke novel insights into Tree of Life and eukaryogenesis

Contact Info

Product

Resources

About