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Article

Evolutionary Study of the Crassphage Virus at Gene Level

1
Department of Biology, University of Padova, 35131 Padova, Italy
2
Department of Molecular Medicine, University of Padova, 35131 Padova, Italy
3
Department of Biology, University of Copenhagen, 1017 Copenhagen, Denmark
4
CRIBI Biotechnology Center, University of Padua, 35131 Padova, Italy
5
Institute of Biodynamics and Biocomplexity, University of Utrecht, 3508 Utrecht, The Netherlands
*
Author to whom correspondence should be addressed.
Viruses 2020, 12(9), 1035; https://doi.org/10.3390/v12091035
Received: 7 August 2020 / Revised: 3 September 2020 / Accepted: 14 September 2020 / Published: 17 September 2020
crAss-like viruses are a putative family of bacteriophages recently discovered. The eponym of the clade, crAssphage, is an enteric bacteriophage estimated to be present in at least half of the human population and it constitutes up to 90% of the sequences in some human fecal viral metagenomic datasets. We focused on the evolutionary dynamics of the genes encoded on the crAssphage genome. By investigating the conservation of the genes, a consistent variation in the evolutionary rates across the different functional groups was found. Gene duplications in crAss-like genomes were detected. By exploring the differences among the functional categories of the genes, we confirmed that the genes encoding capsid proteins were the most ubiquitous, despite their overall low sequence conservation. It was possible to identify a core of proteins whose evolutionary trees strongly correlate with each other, suggesting their genetic interaction. This group includes the capsid proteins, which are thus established as extremely suitable for rebuilding the phylogenetic tree of this viral clade. A negative correlation between the ubiquity and the conservation of viral protein sequences was shown. Together, this study provides an in-depth picture of the evolution of different genes in crAss-like viruses. View Full-Text
Keywords: metaviromics; gene evolution; crAssphage; mirrortree; human gut metaviromics; gene evolution; crAssphage; mirrortree; human gut
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MDPI and ACS Style

Rossi, A.; Treu, L.; Toppo, S.; Zschach, H.; Campanaro, S.; Dutilh, B.E. Evolutionary Study of the Crassphage Virus at Gene Level. Viruses 2020, 12, 1035. https://doi.org/10.3390/v12091035

AMA Style

Rossi A, Treu L, Toppo S, Zschach H, Campanaro S, Dutilh BE. Evolutionary Study of the Crassphage Virus at Gene Level. Viruses. 2020; 12(9):1035. https://doi.org/10.3390/v12091035

Chicago/Turabian Style

Rossi, Alessandro, Laura Treu, Stefano Toppo, Henrike Zschach, Stefano Campanaro, and Bas E. Dutilh 2020. "Evolutionary Study of the Crassphage Virus at Gene Level" Viruses 12, no. 9: 1035. https://doi.org/10.3390/v12091035

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