Conservative taxonomy and quality assessment of giant virus genomes with GVClass DOI Creative Commons
Thomas M. Pitot, Tomáš Brůna, Frederik Schulz

et al.

npj Viruses, Journal Year: 2024, Volume and Issue: 2(1)

Published: Nov. 25, 2024

Large double-stranded DNA viruses of the phylum Nucleocytoviricota (Giant Viruses; GVs) are largest known viruses, infecting various eukaryotic hosts, particularly protists and algae. These impact biogeochemical cycles host genome evolution but challenging to identify classify due their complex genomes. We present GVClass, a tool for identifying giant in sequence data, providing taxonomic assignments, estimating completeness contamination. GVClass employs optimized gene calling conservative approach using consensus single-protein phylogenies robust classification, relying on highly conserved orthologous groups. Benchmarking demonstrates over 90% accuracy at genus-level >99% higher ranks. addresses classification challenges is available as standalone integrated into Integrated Microbial Genomes/Virus database (IMG/VR).

Language: Английский

20 years of research on giant viruses DOI Creative Commons

Tressy Bosmon,

Chantal Abergel, Jean‐Michel Claverie

et al.

npj Viruses, Journal Year: 2025, Volume and Issue: 3(1)

Published: Feb. 11, 2025

Abstract Some twenty years ago, the discovery of first giant virus, Acanthamoeba polyphaga mimivirus (now bradfordmassiliense species), paved way for more than 10 new families protist-infecting DNA viruses with unexpected diversity in virion shape and size, gene content, genome topology mode replication. Following their brief description, we examine how historical concepts virology have held up light this knowledge. Although initial emphasis was on gigantism newly described infecting amoebae, subsequent intermediate sizes gradually re-established a continuum between smallest largest within phylum Nucleocytoviricota .

Language: Английский

Citations

0
Cryptic infection of a giant virus in a unicellular green alga DOI
Maria P. Erazo-Garcia, Uri Sheyn, Zachary K. Barth

et al.

Science, Journal Year: 2025, Volume and Issue: unknown

Published: April 10, 2025

Latency is a common strategy in wide range of viral lineages, but its prevalence giant viruses remains unknown. Here we describe 617 kbp integrated element the model green alga Chlamydomonas reinhardtii . We resolve genome using long-read sequencing, identify putative polinton-like integrase, and show that particles accumulate primarily during stationary growth phase. A diverse array viral-encoded selfish genetic elements expressed activity, including several Fanzor nuclease-encoding transposable elements. In addition, field isolates sp. harbor signatures endogenous related to C. virus exhibit similar infection dynamics, suggesting latency prevalent natural host communities. Our work describes an unusually large temperate unicellular eukaryote, substantially expanding scope cryptic infections virosphere.

Language: Английский

Citations

0
Adaptation strategies of giant viruses to low-temperature marine ecosystems DOI Creative Commons

Marianne Buscaglia,

José Luis Iriarte, Frederik Schulz

et al.

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

Published: Jan. 1, 2024

Abstract Microbes in marine ecosystems have evolved their gene content to thrive successfully the cold. Although this process has been reasonably well studied bacteria and selected eukaryotes, less is known about impact of cold environments on genomes viruses that infect eukaryotes. Here, we analyzed adaptations giant (Nucleocytoviricota Mirusviricota) from austral compared them with Arctic temperate counterparts. We recovered virus metagenome-assembled (98 Nucleocytoviricota 12 Mirusviricota MAGs) 61 newly sequenced metagenomes metaviromes sub-Antarctic Patagonian fjords Antarctic seawater samples. When analyzing our data set alongside MAGs already deposited Global Ocean Eukaryotic Viral database, found predominantly inhabit sub-10°C environments, featuring a high proportion unique phylotypes each ecosystem. In contrast, were subject broader temperature ranges showed lower degree endemicity. However, despite differences distribution, inhabiting low-temperature genomic cold-adaptation strategies led changes genetic functions amino acid frequencies ultimately affect both protein structure. Such seem be absent mesophilic The uniqueness these cold-adapted may now threatened by climate change, leading potential reduction biodiversity.

Language: Английский

Citations

2
Spatiotemporal dynamics of giant viruses within a deep freshwater lake reveal a distinct dark-water community DOI Creative Commons
Liwen Zhang, Lingjie Meng,

Yue Fang

et al.

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

Published: Jan. 1, 2024

Language: Английский

Citations

2
Conservative taxonomy and quality assessment of giant virus genomes with GVClass DOI Creative Commons
Thomas M. Pitot, Tomáš Brůna, Frederik Schulz

et al.

npj Viruses, Journal Year: 2024, Volume and Issue: 2(1)

Published: Nov. 25, 2024

Large double-stranded DNA viruses of the phylum Nucleocytoviricota (Giant Viruses; GVs) are largest known viruses, infecting various eukaryotic hosts, particularly protists and algae. These impact biogeochemical cycles host genome evolution but challenging to identify classify due their complex genomes. We present GVClass, a tool for identifying giant in sequence data, providing taxonomic assignments, estimating completeness contamination. GVClass employs optimized gene calling conservative approach using consensus single-protein phylogenies robust classification, relying on highly conserved orthologous groups. Benchmarking demonstrates over 90% accuracy at genus-level >99% higher ranks. addresses classification challenges is available as standalone integrated into Integrated Microbial Genomes/Virus database (IMG/VR).

Language: Английский

Citations

2