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Nat Commun. 2018 Jun 11;9(1):2285. doi: 10.1038/s41467-018-04698-4.

Diversity and evolution of the emerging Pandoraviridae family.

Author information

1
Aix Marseille Univ, CNRS, Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479), 163 Avenue de Luminy, Case 934, 13288, Marseille cedex 9, France. legendre@igs.cnrs-mrs.fr.
2
Aix Marseille Univ, CNRS, Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479), 163 Avenue de Luminy, Case 934, 13288, Marseille cedex 9, France.
3
Univ. Grenoble Alpes, CEA, Inserm, BIG-BGE, 38000, Grenoble, France.
4
CEA-Institut de Génomique, GENOSCOPE, Centre National de Séquençage, 2 rue Gaston Crémieux, CP5706, 91057, Evry Cedex, France.
5
Aix Marseille Univ, CNRS, Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479), 163 Avenue de Luminy, Case 934, 13288, Marseille cedex 9, France. Chantal.Abergel@igs.cnrs-mrs.fr.
6
Aix Marseille Univ, CNRS, Structural and Genomic Information Laboratory, UMR 7256 (IMM FR 3479), 163 Avenue de Luminy, Case 934, 13288, Marseille cedex 9, France. Jean-Michel.Claverie@univ-amu.fr.

Abstract

With DNA genomes reaching 2.5 Mb packed in particles of bacterium-like shape and dimension, the first two Acanthamoeba-infecting pandoraviruses remained up to now the most complex viruses since their discovery in 2013. Our isolation of three new strains from distant locations and environments is now used to perform the first comparative genomics analysis of the emerging worldwide-distributed Pandoraviridae family. Thorough annotation of the genomes combining transcriptomic, proteomic, and bioinformatic analyses reveals many non-coding transcripts and significantly reduces the former set of predicted protein-coding genes. Here we show that the pandoraviruses exhibit an open pan-genome, the enormous size of which is not adequately explained by gene duplications or horizontal transfers. As most of the strain-specific genes have no extant homolog and exhibit statistical features comparable to intergenic regions, we suggest that de novo gene creation could contribute to the evolution of the giant pandoravirus genomes.

PMID:
29891839
PMCID:
PMC5995976
DOI:
10.1038/s41467-018-04698-4
[Indexed for MEDLINE]
Free PMC Article

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