Investigation of recombination-intense viral groups and their genes in the Earth’s virome

Meier-Kolthoff, Jan P.; Uchiyama, Jumpei; Yahara, Hiroko; Paez-Espino, David; Yahara, Koji

doi:10.1038/s41598-018-29272-2

Investigation of recombination-intense viral groups and their genes in the Earth’s virome

Journal Article · Tue Jul 31 00:00:00 EDT 2018 · Scientific Reports

DOI:https://doi.org/10.1038/s41598-018-29272-2· OSTI ID:1543781

Meier-Kolthoff, Jan P. ^[1]; Uchiyama, Jumpei ^[2]; Yahara, Hiroko ^[3]; ^[4]; ^[5]

Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
Azabu Univ., Kanagawa (Japan)
Tokyo Medical and Dental Univ., Tokyo (Japan)
USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
National Inst. of Infectious Diseases, Tokyo (Japan)

Bacteriophages (phages), or bacterial viruses, are the most abundant and diverse biological entities that impact the global ecosystem. Recent advances in metagenomics have revealed their rampant abundance in the biosphere. A fundamental aspect of bacteriophages that remains unexplored in metagenomic data is the process of recombination as a driving force in evolution that occurs among different viruses within the same bacterial host. Here, we systematically examined signatures of recombination in every gene from 211 species-level viral groups in a recently obtained dataset of the Earth’s virome that contain corresponding information on the host bacterial species. Our study revealed that signatures of recombination are widespread (84%) among the diverse viral groups. We identified 25 recombination-intense viral groups, widely distributed across the viral taxonomy, and present in bacterial species living in the human oral cavity. We also revealed a significant inverse association between the recombination-intense viral groups and Type II restriction endonucleases, that could be effective in reducing recombination among phages in a cell. Furthermore, we identified recombination-intense genes that are significantly enriched for encoding phage morphogenesis proteins. Changes in the viral genomic sequence by recombination may be important to escape cleavage by the host bacterial immune systems.

View Accepted Manuscript (DOE)

Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 1543781

Journal Information:: Scientific Reports, Journal Name: Scientific Reports Journal Issue: 1 Vol. 8; ISSN 2045-2322

Publisher:: Nature Publishing GroupCopyright Statement

Country of Publication:: United States

Language:: English

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