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

Abstract

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.

Authors:
 [1];  [2];  [3]; ORCiD logo [4]; ORCiD logo [5]
  1. Leibniz Institute DSMZ – German Collection of Microorganisms and Cell Cultures, Braunschweig (Germany)
  2. Azabu Univ., Kanagawa (Japan)
  3. Tokyo Medical and Dental Univ., Tokyo (Japan)
  4. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  5. National Inst. of Infectious Diseases, Tokyo (Japan)
Publication Date:
Research Org.:
Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States). National Energy Research Scientific Computing Center (NERSC); Univ. of California, Oakland, CA (United States)
Sponsoring Org.:
USDOE Office of Science (SC)
OSTI Identifier:
1543781
Grant/Contract Number:  
[AC02-05CH11231]
Resource Type:
Accepted Manuscript
Journal Name:
Scientific Reports
Additional Journal Information:
[ Journal Volume: 8; Journal Issue: 1]; Journal ID: ISSN 2045-2322
Publisher:
Nature Publishing Group
Country of Publication:
United States
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; Science & Technology; Other Topics

Citation Formats

Meier-Kolthoff, Jan P., Uchiyama, Jumpei, Yahara, Hiroko, Paez-Espino, David, and Yahara, Koji. Investigation of recombination-intense viral groups and their genes in the Earth’s virome. United States: N. p., 2018. Web. doi:10.1038/s41598-018-29272-2.
Meier-Kolthoff, Jan P., Uchiyama, Jumpei, Yahara, Hiroko, Paez-Espino, David, & Yahara, Koji. Investigation of recombination-intense viral groups and their genes in the Earth’s virome. United States. doi:10.1038/s41598-018-29272-2.
Meier-Kolthoff, Jan P., Uchiyama, Jumpei, Yahara, Hiroko, Paez-Espino, David, and Yahara, Koji. Tue . "Investigation of recombination-intense viral groups and their genes in the Earth’s virome". United States. doi:10.1038/s41598-018-29272-2. https://www.osti.gov/servlets/purl/1543781.
@article{osti_1543781,
title = {Investigation of recombination-intense viral groups and their genes in the Earth’s virome},
author = {Meier-Kolthoff, Jan P. and Uchiyama, Jumpei and Yahara, Hiroko and Paez-Espino, David and Yahara, Koji},
abstractNote = {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.},
doi = {10.1038/s41598-018-29272-2},
journal = {Scientific Reports},
number = [1],
volume = [8],
place = {United States},
year = {2018},
month = {7}
}

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