Complete genomes of Asgard archaea reveal diverse integrated and mobile genetic elements DOI Creative Commons
Luis E. Valentin-Alvarado, Ling-Dong Shi, Kathryn E. Appler

et al.

Genome Research, Journal Year: 2024, Volume and Issue: 34(10), P. 1595 - 1609

Published: Oct. 1, 2024

Asgard archaea are of great interest as the progenitors Eukaryotes, but little is known about mobile genetic elements (MGEs) that may shape their ongoing evolution. Here, we describe MGEs replicate in Atabeyarchaeia, a wetland lineage represented by two complete genomes. We used soil depth-resolved population metagenomic data sets to track 18 for which genome structures were defined and precise chromosome integration sites could be identified confident host linkage. Additionally, 20.67 kbp circular plasmid family-level groups viruses linked via CRISPR spacer targeting. Closely related 40 possess hypervariable genomic region encoding combinations specific genes small cysteine-rich proteins structurally similar restriction-homing endonucleases. One 10.9 integrative conjugative element (ICE) integrates genomically into

Language: Английский

Identification of mobile genetic elements with geNomad DOI Creative Commons
Antônio Pedro Camargo, Simon Roux, Frederik Schulz

et al.

Nature Biotechnology, Journal Year: 2023, Volume and Issue: 42(8), P. 1303 - 1312

Published: Sept. 21, 2023

Identifying and characterizing mobile genetic elements in sequencing data is essential for understanding their diversity, ecology, biotechnological applications impact on public health. Here we introduce geNomad, a classification annotation framework that combines information from gene content deep neural network to identify sequences of plasmids viruses. geNomad uses dataset more than 200,000 marker protein profiles provide functional taxonomic assignment viral genomes. Using conditional random field model, also detects proviruses integrated into host genomes with high precision. In benchmarks, achieved performance diverse viruses (Matthews correlation coefficient 77.8% 95.3%, respectively), substantially outperforming other tools. Leveraging geNomad's speed scalability, processed over 2.7 trillion base pairs data, leading the discovery millions are available through IMG/VR IMG/PR databases. at https://portal.nersc.gov/genomad .

Language: Английский

Citations

197
You can move, but you can't hide: identification of mobile genetic elements with geNomad DOI Creative Commons
Antônio Pedro Camargo, Simon Roux, Frederik Schulz

et al.

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2023, Volume and Issue: unknown

Published: March 6, 2023

Identifying and characterizing mobile genetic elements (MGEs) in sequencing data is essential for understanding their diversity, ecology, biotechnological applications, impact on public health. Here, we introduce geNomad, a classification annotation framework that combines information from gene content deep neural network to identify sequences of plasmids viruses. geNomad uses large dataset marker proteins provide functional taxonomic assignment viral genomes. Using conditional random field model, also detects proviruses integrated into host genomes with high precision. In benchmarks included diverse MGE chromosome sequences, significantly outperformed other tools all evaluated clades Leveraging geNomad's speed scalability, were able process metagenomes metatranscriptomes, leading the discovery millions new viruses are available through IMG/VR IMG/PR databases. We anticipate will enable further advancements research, it at https://portal.nersc.gov/genomad.

Language: Английский

Citations

44
Megataxonomy and global ecology of the virosphere DOI Creative Commons
Eugene V. Koonin, Jens H. Kuhn, Valerian V. Dolja

et al.

The ISME Journal, Journal Year: 2024, Volume and Issue: 18(1)

Published: Jan. 1, 2024

Nearly all organisms are hosts to multiple viruses that collectively appear be the most abundant biological entities in biosphere. With recent advances metagenomics and metatranscriptomics, known diversity of substantially expanded. Comparative analysis these using advanced computational methods culminated reconstruction evolution major groups enabled construction a virus megataxonomy, which has been formally adopted by International Committee on Taxonomy Viruses. This comprehensive taxonomy consists six realms, aspired monophyletic assembled based conservation hallmark proteins involved capsid structure formation or genome replication. The different taxa differ host range accordingly ecological niches. In this review article, we outline latest developments megataxonomy discoveries will likely lead reassessment some taxa, particular, split three current realms into two more independent realms. We then discuss correspondence between distribution among niches, as well abundance versus cells habitats. across environments appears primarily determined ranges, i.e. virome is shaped composition biome given habitat, itself affected abiotic factors.

Language: Английский

Citations

25
The virome of the last eukaryotic common ancestor and eukaryogenesis DOI
Mart Krupovìč, Valerian V. Dolja, Eugene V. Koonin

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(6), P. 1008 - 1017

Published: May 1, 2023

Language: Английский

Citations

35
Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome DOI Creative Commons
Rafael Laso-Pérez, Fabai Wu, Antoine Crémière

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(2), P. 231 - 245

Published: Jan. 19, 2023

Abstract ‘ Candidatus Methanophagales’ (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution ANME-1 remain poorly understood. In this study, we use metagenomics on hydrothermal samples to expand diversity uncover the effect virus–host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, Methanospirareceae’, closely related short-chain alkane oxidizers. Global phylogeny near-complete genomes show that hydrogen metabolism within ancient trait was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting archaea, showing unique structural replicative signatures. expansive virome contains metabolic gene repertoire can influence host through virus-mediated displacement. Our results suggest evolutionary continuum between oxidizers underscore effects viruses dynamics methane-driven ecosystems.

Language: Английский

Citations

34
A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment DOI
Sofia Medvedeva, Guillaume Borrel, Mart Krupovìč

et al.

Nature Microbiology, Journal Year: 2023, Volume and Issue: 8(11), P. 2170 - 2182

Published: Sept. 25, 2023

Language: Английский

Citations

27
A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses DOI Creative Commons
Daniel Tamarit, Eva Caceres, Mart Krupovìč

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 948 - 952

Published: June 27, 2022

Asgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology, and particularly their virome, remain enigmatic. We reassembled closed chromosome Candidatus Odinarchaeum yellowstonii LCB_4, through long-range PCR, revealing CRISPR spacers targeting viral contigs. found related viruses in genomes diverse prokaryotes from geothermal environments, including other archaea. These open research avenues into ecology evolution

Language: Английский

Citations

37
Genomes of six viruses that infect Asgard archaea from deep-sea sediments DOI Open Access
Ian M. Rambo, Marguerite V. Langwig, Pedro Leão

et al.

Nature Microbiology, Journal Year: 2022, Volume and Issue: 7(7), P. 953 - 961

Published: June 27, 2022

Language: Английский

Citations

31
Non-negligible roles of archaea in coastal carbon biogeochemical cycling DOI Open Access
Xinxu Zhang, Cui‐Jing Zhang, Yang Liu

et al.

Trends in Microbiology, Journal Year: 2022, Volume and Issue: 31(6), P. 586 - 600

Published: Dec. 23, 2022

Language: Английский

Citations

25
Archaeal virus entry and egress DOI Creative Commons
Bastiaan P. Kuiper, Anna M C Schöntag, Hanna M. Oksanen

et al.

microLife, Journal Year: 2024, Volume and Issue: 5

Published: Jan. 1, 2024

Archaeal viruses display a high degree of structural and genomic diversity. Few details are known about the mechanisms by which these enter exit their host cells. Research on archaeal has lately made significant progress due to advances in genetic tools imaging techniques, such as cryo-electron tomography (cryo-ET). In recent years, steady output newly identified viral receptors egress offered first insight into how interact with cell envelope. As more entry unravelled, patterns starting emerge. This helps better understand interactions between envelope compare infection strategies other domains life. Here, we provide an overview developments field egress, shedding light onto most elusive part virosphere.

Language: Английский

Citations

5