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Cited by 4Bacteriophages and microbial interactionsGenomics and Phylogenetic StudiesChromosomal and Genetic Variations

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Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses

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Rigou, Sofia, Schmitt, Alain, Alempic, Jean-Marie, Lartigue, Audrey, Vendloczki, Peter, Abergel, Chantal, Claverie, Jean-Michel, Legendre, Matthieu·2023·Molecular Biology and Evolution
DOI 10.1093/molbev/msad244PMC PMC10664404

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Abstract

Pithoviridae are amoeba-infecting giant viruses possessing the largest viral particles known so far. Since the discovery of Pithovirus sibericum, recovered from a 30,000-yr-old permafrost sample, other pithoviruses, and related cedratviruses, were isolated from various terrestrial and aquatic samples. Here, we report the isolation and genome sequencing of 2 Pithoviridae from soil samples, in addition to 3 other recent isolates. Using the 12 available genome sequences, we conducted a thorough comparative genomic study of the Pithoviridae family to decipher the organization and evolution of their genomes. Our study reveals a nonuniform genome organization in 2 main regions: 1 concentrating core genes and another gene duplications. We also found that Pithoviridae genomes are more conservative than other families of giant viruses, with a low and stable proportion (5% to 7%) of genes originating from horizontal transfers. Genome size variation within the family is mainly due to variations in gene duplication rates (from 14% to 28%) and massive invasion by inverted repeats. While these repeated elements are absent from cedratviruses, repeat-rich regions cover as much as a quarter of the pithoviruses genomes. These regions, identified using a dedicated pipeline, are hotspots of mutations, gene capture events, and genomic rearrangements that contribute to their evolution.

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Metadata

Authors
Rigou, S., Schmitt, A., Alempic, J.-M., Lartigue, A., Vendloczki, P., Abergel, C., Claverie, J.-M., & Legendre, M.
Affiliations
Centre National de la Recherche Scientifique (FR)
Corresponding author
Legendre, Matthieu
ORCID
Venue
Molecular Biology and Evolution
Publisher
Oxford University Press (OUP)
Published
2023-11
Volume
40
Issue
11
ISSN
  • 0737-4038 (ISSN-L)
  • 1537-1719
DOI
10.1093/molbev/msad244
PMC
PMC10664404
OpenAlex
W4388586220
Cited by
4
References
2
Citations by year
2026: 1 · 2025: 2 · 2024: 1
FWCI
0.65
Type
journal article
Language
en
Open access
Licence
Locations
  • Molecular Biology and Evolution (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • HAL (submittedVersion, cc-by-nc-nd)
Funders
  • Agence Nationale de la Recherche (ANR-22-CE12-0041, ANR-10-INBS-09-08)
  • CNRS Projet de Recherche Conjoint (PRC1484-2018, GENCI-IDRIS, 2022-AD011013526)
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Chromosomal and Genetic Variations
Keywords
giant viruses, inverted repeats, genome evolution, gene duplication, horizontal gene transfer, gene capture, genome rearrangement, soil viruses, viral genome structure
MeSH terms
Giant Viruses, Phylogeny, Virion, Genome, Viral, Evolution, Molecular, Genomics

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