ID | 63878 |
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Uchiyama, Jumpei
Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University
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Takemura-Uchiyama, Iyo
Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University
Gotoh, Kazuyoshi
Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University
Kato, Shin-ichiro
Research Institute of Molecular Genetics, Kochi University
Sakaguchi, Yoshihiko
Department of Microbiology, Kitasato University School of Medicine
Murakami, Hironobu
School of Veterinary Medicine, Azabu University
Fukuyama, Tomoki
School of Veterinary Medicine, Azabu University
Kaneki, Mao
School of Veterinary Medicine, Azabu University
Matsushita, Osamu
Department of Bacteriology, Graduate School of Medicine Dentistry and Pharmaceutical Sciences, Okayama University
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Matsuzaki, Shigenobu
Department of Medical Laboratory Science, Faculty of Health Sciences, Kochi Gakuen University
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Abstract | Bacteriophages (phages) are the most diverse and abundant life-form on Earth. Jumbophages are phages with double-stranded DNA genomes longer than 200 kbp. Among these, some jumbophages with uracil in place of thymine as a nucleic acid base, which we have tentatively termed "dU jumbophages" in this study, have been reported. Because the dU jumbophages are considered to be a living fossil from the RNA world, the evolutionary traits of dU jumbophages are of interest. In this study, we examined the phylogeny of dU jumbophages. First, tBLASTx analysis of newly sequenced dU jumbophages such as Bacillus phage PBS1 and previously isolated Staphylococcus phage S6 showed similarity to the other dU jumbophages. Second, we detected the two partial genome sequences of uncultured phages possibly relevant to dU jumbophages, scaffold_002 and scaffold_007, from wastewater metagenomics. Third, according to the gene-sharing network analysis, the dU jumbophages, including phages PBS1 and S6, and uncultured phage scaffold_002 formed a cluster, which suggested a new viral subfamily/family. Finally, analyses of the phylogenetic relationship with other phages showed that the dU jumbophage cluster, which had two clades of phages infecting Gram-negative and Gram-positive bacteria, diverged from the single ancestral phage. These findings together with previous reports may imply that dU jumbophages evolved from the same origin before divergence of Gram-negative and Gram-positive bacteria.
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Keywords | Environmental virus
Jumbophage
Metagenomics
Evolution
Uncultured phage
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Note | © 2022 Elsevier B.V. This manuscript version is made available under the CC-BY-NC-ND 4.0 License. http://creativecommons.org/licenses/by-nc-nd/4.0/.
This is the accepted manuscript version. The formal published version is available at [https://doi.org/10.1016/j.virusres.2022.198881] .
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Published Date | 2022-10-02
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Publication Title |
Virus Research
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Volume | volume319
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Publisher | Elsevier BV
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Start Page | 198881
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ISSN | 0168-1702
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Content Type |
Journal Article
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language |
English
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OAI-PMH Set |
岡山大学
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Copyright Holders | © 2022 Elsevier B.V.
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File Version | author
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Related Url | isVersionOf https://doi.org/10.1016/j.virusres.2022.198881
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License | http://creativecommons.org/licenses/by-nc-nd/4.0/.
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Funder Name |
Ministry of Education, Culture, Sports, Science and Technology
The Japan Science Society
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助成番号 | 15K19095
28-604
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