Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses
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 aquat...
Published in: | Molecular Biology and Evolution |
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Oxford University Press (OUP)
2023
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Online Access: | http://dx.doi.org/10.1093/molbev/msad244 https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msad244/53253432/msad244.pdf https://academic.oup.com/mbe/article-pdf/40/11/msad244/53676949/msad244.pdf |
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croxfordunivpr:10.1093/molbev/msad244 2024-06-23T07:56:08+00:00 Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses Rigou, Sofia Schmitt, Alain Alempic, Jean-Marie Lartigue, Audrey Vendloczki, Peter Abergel, Chantal Claverie, Jean-Michel Legendre, Matthieu Hepp, Crystal Agence Nationale de la Recherche CNRS Projet de Recherche Conjoint 2023 http://dx.doi.org/10.1093/molbev/msad244 https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msad244/53253432/msad244.pdf https://academic.oup.com/mbe/article-pdf/40/11/msad244/53676949/msad244.pdf en eng Oxford University Press (OUP) https://creativecommons.org/licenses/by/4.0/ Molecular Biology and Evolution volume 40, issue 11 ISSN 0737-4038 1537-1719 journal-article 2023 croxfordunivpr https://doi.org/10.1093/molbev/msad244 2024-06-04T06:08:51Z 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. Article in Journal/Newspaper permafrost Oxford University Press Molecular Biology and Evolution 40 11 |
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Open Polar |
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Oxford University Press |
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croxfordunivpr |
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English |
description |
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. |
author2 |
Hepp, Crystal Agence Nationale de la Recherche CNRS Projet de Recherche Conjoint |
format |
Article in Journal/Newspaper |
author |
Rigou, Sofia Schmitt, Alain Alempic, Jean-Marie Lartigue, Audrey Vendloczki, Peter Abergel, Chantal Claverie, Jean-Michel Legendre, Matthieu |
spellingShingle |
Rigou, Sofia Schmitt, Alain Alempic, Jean-Marie Lartigue, Audrey Vendloczki, Peter Abergel, Chantal Claverie, Jean-Michel Legendre, Matthieu Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses |
author_facet |
Rigou, Sofia Schmitt, Alain Alempic, Jean-Marie Lartigue, Audrey Vendloczki, Peter Abergel, Chantal Claverie, Jean-Michel Legendre, Matthieu |
author_sort |
Rigou, Sofia |
title |
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses |
title_short |
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses |
title_full |
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses |
title_fullStr |
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses |
title_full_unstemmed |
Pithoviruses Are Invaded by Repeats That Contribute to Their Evolution and Divergence from Cedratviruses |
title_sort |
pithoviruses are invaded by repeats that contribute to their evolution and divergence from cedratviruses |
publisher |
Oxford University Press (OUP) |
publishDate |
2023 |
url |
http://dx.doi.org/10.1093/molbev/msad244 https://academic.oup.com/mbe/advance-article-pdf/doi/10.1093/molbev/msad244/53253432/msad244.pdf https://academic.oup.com/mbe/article-pdf/40/11/msad244/53676949/msad244.pdf |
genre |
permafrost |
genre_facet |
permafrost |
op_source |
Molecular Biology and Evolution volume 40, issue 11 ISSN 0737-4038 1537-1719 |
op_rights |
https://creativecommons.org/licenses/by/4.0/ |
op_doi |
https://doi.org/10.1093/molbev/msad244 |
container_title |
Molecular Biology and Evolution |
container_volume |
40 |
container_issue |
11 |
_version_ |
1802649028942364672 |