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:
-
[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)
- 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. https://doi.org/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. https://doi.org/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 = {Tue Jul 31 00:00:00 EDT 2018},
month = {Tue Jul 31 00:00:00 EDT 2018}
}
Free Publicly Available Full Text
Publisher's Version of Record
Other availability
Search WorldCat to find libraries that may hold this journal
Cited by: 6 works
Citation information provided by
Web of Science
Web of Science
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.
Works referenced in this record:
The portal protein plays essential roles at different steps of the SPP1 DNA packaging process
journal, May 2004
- Isidro, Anabela; Henriques, Adriano O.; Tavares, Paulo
- Virology, Vol. 322, Issue 2
VICTOR: genome-based phylogeny and classification of prokaryotic viruses
journal, July 2017
- Meier-Kolthoff, Jan P.; Göker, Markus
- Bioinformatics, Vol. 33, Issue 21
Ecology of the Oral Microbiome: Beyond Bacteria
journal, May 2017
- Baker, Jonathon L.; Bor, Batbileg; Agnello, Melissa
- Trends in Microbiology, Vol. 25, Issue 5
Roary: rapid large-scale prokaryote pan genome analysis
journal, July 2015
- Page, Andrew J.; Cummins, Carla A.; Hunt, Martin
- Bioinformatics, Vol. 31, Issue 22
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
journal, October 2016
- Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
- Nucleic Acids Research, Vol. 45, Issue D1
Phages in nature
journal, January 2011
- Clokie, Martha R. J.; Millard, Andrew D.; Letarov, Andrey V.
- Bacteriophage, Vol. 1, Issue 1
PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution
journal, February 2008
- Cai, J. J.
- Journal of Heredity, Vol. 99, Issue 4
Global transcription of CRISPR loci in the human oral cavity
journal, May 2015
- Lum, Andrew G.; Ly, Melissa; Santiago-Rodriguez, Tasha M.
- BMC Genomics, Vol. 16, Issue 1
Bacteriophage lysis: mechanism and regulation
journal, September 1992
- Young, R.
- Microbiological Reviews, Vol. 56, Issue 3
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
journal, July 2017
- Paez-Espino, David; Pavlopoulos, Georgios A.; Ivanova, Natalia N.
- Nature Protocols, Vol. 12, Issue 8
MBGD. Microbial Genome Database for Comparative Analysis.
journal, January 2002
- Uchiyama, Ikuo
- Seibutsu Butsuri, Vol. 42, Issue 6
Efficient Inference of Recombination Hot Regions in Bacterial Genomes
journal, February 2014
- Yahara, Koji; Didelot, Xavier; Ansari, M. Azim
- Molecular Biology and Evolution, Vol. 31, Issue 6
Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
journal, September 2017
- Williamson, Kurt E.; Fuhrmann, Jeffry J.; Wommack, K. Eric
- Annual Review of Virology, Vol. 4, Issue 1
Marine viruses — major players in the global ecosystem
journal, October 2007
- Suttle, Curtis A.
- Nature Reviews Microbiology, Vol. 5, Issue 10
Bacteriophage lysis: mechanism and regulation.
journal, January 1992
- Young, R.
- Microbiological Reviews, Vol. 56, Issue 3
Human Case of Atopobium rimae Bacteremia
journal, February 2009
- Angelakis, Emmanouil; Roux, Véronique; Raoult, Didier
- Emerging Infectious Diseases, Vol. 15, Issue 2
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
The Janus-Face of Bacteriophages across Human Body Habitats
journal, June 2016
- Wahida, Adam; Ritter, Klaus; Horz, Hans-Peter
- PLOS Pathogens, Vol. 12, Issue 6
Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013
- Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
- BMC Bioinformatics, Vol. 14, Issue 1
Type II restriction endonucleases—a historical perspective and more
journal, May 2014
- Pingoud, Alfred; Wilson, Geoffrey G.; Wende, Wolfgang
- Nucleic Acids Research, Vol. 42, Issue 12
Commensal Pseudomonas protect Arabidopsis thaliana from a coexisting pathogen via multiple lineage-dependent mechanisms
journal, December 2021
- Shalev, Or; Ashkenazy, Haim; Neumann, Manuela
- The ISME Journal, Vol. 16, Issue 5
DnaSAM: Software to perform neutrality testing for large datasets with complex null models
journal, May 2010
- Eckert, Andrew J.; Liechty, John D.; Tearse, Brandon R.
- Molecular Ecology Resources, Vol. 10, Issue 3
MBGD: microbial genome database for comparative analysis
journal, January 2003
- Uchiyama, I.
- Nucleic Acids Research, Vol. 31, Issue 1
Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species
journal, January 2012
- Yahara, Koji; Kawai, Mikihiko; Furuta, Yoshikazu
- Genome Biology and Evolution, Vol. 4, Issue 5
Functional identification of the DNA packaging terminase from Pseudomonas aeruginosa phage PaP3
journal, July 2012
- Shen, Xiaodong; Li, Ming; Zeng, Yijun
- Archives of Virology, Vol. 157, Issue 11
Streptococcus mitis Strains Causing Severe Clinical Disease in Cancer Patients
journal, May 2014
- Shelburne, Samuel A.; Sahasrabhojane, Pranoti; Saldana, Miguel
- Emerging Infectious Diseases, Vol. 20, Issue 5
Complete Genome Sequence of Cellulomonas sp. JZ18, a Root Endophytic Bacterium Isolated from the Perennial Desert Tussock-Grass Panicum turgidum
journal, March 2021
- Eida, Abdul Aziz; Bougouffa, Salim; Alam, Intikhab
- Current Microbiology, Vol. 78, Issue 4
Optimized cultivation of Campylobacter concisus from gut mucosal biopsies in inflammatory bowel disease
journal, June 2016
- Kirk, Karina Frahm; Nielsen, Hans Linde; Thorlacius-Ussing, Ole
- Gut Pathogens, Vol. 8, Issue 1
Uncovering Earth’s virome
journal, August 2016
- Paez-Espino, David; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.
- Nature, Vol. 536, Issue 7617
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
journal, January 2014
- Stamatakis, Alexandros
- Bioinformatics, Vol. 30, Issue 9
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
journal, October 2016
- Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 45, Issue D1
Prokka: rapid prokaryotic genome annotation
journal, March 2014
- Seemann, T.
- Bioinformatics, Vol. 30, Issue 14
Why do RNA viruses recombine?
journal, July 2011
- Simon-Loriere, Etienne; Holmes, Edward C.
- Nature Reviews Microbiology, Vol. 9, Issue 8
A Common Evolutionary Origin for Tailed-Bacteriophage Functional Modules and Bacterial Machineries
journal, September 2011
- Veesler, D.; Cambillau, C.
- Microbiology and Molecular Biology Reviews, Vol. 75, Issue 3
CRISPR–Cas adaptation: insights into the mechanism of action
journal, January 2016
- Amitai, Gil; Sorek, Rotem
- Nature Reviews Microbiology, Vol. 14, Issue 2
Mating pair stabilization mediates bacterial conjugation species specificity
journal, June 2022
- Low, Wen Wen; Wong, Joshua L. C.; Beltran, Leticia C.
- Nature Microbiology, Vol. 7, Issue 7
Evolution of DNA Double-Strand Break Repair by Gene Conversion: Coevolution Between a Phage and a Restriction-Modification System
journal, April 2007
- Yahara, Koji; Horie, Ryota; Kobayashi, Ichizo
- Genetics, Vol. 176, Issue 1
Recombination Promoted by DNA Viruses: Phage λ to Herpes Simplex Virus
journal, September 2014
- Weller, Sandra K.; Sawitzke, James A.
- Annual Review of Microbiology, Vol. 68, Issue 1
Genome-Wide Survey of Mutual Homologous Recombination in a Highly Sexual Bacterial Species
journal, January 2012
- Yahara, Koji; Kawai, Mikihiko; Furuta, Yoshikazu
- Genome Biology and Evolution, Vol. 4, Issue 5
CRISPRDetect: A flexible algorithm to define CRISPR arrays
journal, May 2016
- Biswas, Ambarish; Staals, Raymond H. J.; Morales, Sergio E.
- BMC Genomics, Vol. 17, Issue 1
Evolutionary Ecology of Prokaryotic Immune Mechanisms
journal, July 2016
- van Houte, Stineke; Buckling, Angus; Westra, Edze R.
- Microbiology and Molecular Biology Reviews, Vol. 80, Issue 3
Bacteriophages and their genomes
journal, October 2011
- Hatfull, Graham F.; Hendrix, Roger W.
- Current Opinion in Virology, Vol. 1, Issue 4
Recombination Promoted by DNA Viruses: Phage λ to Herpes Simplex Virus
journal, September 2014
- Weller, Sandra K.; Sawitzke, James A.
- Annual Review of Microbiology, Vol. 68, Issue 1
Coinfection rates in Φ6 bacteriophage are enhanced by virus-induced changes in host cells.
text, January 2009
- Lin, Chao,; L., Burch, Christina; B., Joseph, Sarah
- The University of North Carolina at Chapel Hill University Libraries
CRISPR–Cas adaptation: insights into the mechanism of action
journal, January 2016
- Amitai, Gil; Sorek, Rotem
- Nature Reviews Microbiology, Vol. 14, Issue 2
Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
journal, January 2014
- Meier-Kolthoff, Jan P.; Hahnke, Richard L.; Petersen, Jörn
- Standards in Genomic Sciences, Vol. 9, Issue 1
Efficient Inference of Recombination Hot Regions in Bacterial Genomes
journal, February 2014
- Yahara, Koji; Didelot, Xavier; Ansari, M. Azim
- Molecular Biology and Evolution, Vol. 31, Issue 6
ORIGINAL ARTICLE: Coinfection rates in φ6 bacteriophage are enhanced by virus-induced changes in host cells: Coinfection enhancement in φ6
journal, December 2008
- Joseph, Sarah B.; Hanley, Kathryn A.; Chao, Lin
- Evolutionary Applications, Vol. 2, Issue 1
Endocarditis Due to Actinomyces viscosus
journal, January 2001
- Mardis, Joseph S.; Many, W. J.
- Southern Medical Journal, Vol. 94, Issue 2
Functional identification of the DNA packaging terminase from Pseudomonas aeruginosa phage PaP3
journal, July 2012
- Shen, Xiaodong; Li, Ming; Zeng, Yijun
- Archives of Virology, Vol. 157, Issue 11
TNT, a free program for phylogenetic analysis
journal, October 2008
- Goloboff, Pablo A.; Farris, James S.; Nixon, Kevin C.
- Cladistics, Vol. 24, Issue 5
MUSCLE: multiple sequence alignment with high accuracy and high throughput
journal, March 2004
- Edgar, R. C.
- Nucleic Acids Research, Vol. 32, Issue 5, p. 1792-1797
Endocarditis due to Gemella haemolysans in a newly diagnosed multiple myeloma patient
journal, January 2016
- Liu, Dongyan; Bateman, Thomas; Carr, Elisabeth
- Journal of Community Hospital Internal Medicine Perspectives, Vol. 6, Issue 4
Phages in nature
journal, January 2011
- Clokie, Martha R. J.; Millard, Andrew D.; Letarov, Andrey V.
- Bacteriophage, Vol. 1, Issue 1
Viral capsids: Mechanical characteristics, genome packaging and delivery mechanisms
journal, March 2007
- Roos, W. H.; Ivanovska, I. L.; Evilevitch, A.
- Cellular and Molecular Life Sciences, Vol. 64, Issue 12
IMG/M: integrated genome and metagenome comparative data analysis system
journal, October 2016
- Chen, I-Min A.; Markowitz, Victor M.; Chu, Ken
- Nucleic Acids Research, Vol. 45, Issue D1
Propionibacterium acnes : infection beyond the skin
journal, December 2011
- Perry, Alexandra; Lambert, Peter
- Expert Review of Anti-infective Therapy, Vol. 9, Issue 12
How Many Bootstrap Replicates Are Necessary?
journal, March 2010
- Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
- Journal of Computational Biology, Vol. 17, Issue 3
Marine viruses — major players in the global ecosystem
journal, October 2007
- Suttle, Curtis A.
- Nature Reviews Microbiology, Vol. 5, Issue 10
Bacteriophage genomics
journal, October 2008
- Hatfull, Graham F.
- Current Opinion in Microbiology, Vol. 11, Issue 5
MBGD. Microbial Genome Database for Comparative Analysis.
journal, January 2002
- Uchiyama, Ikuo
- Seibutsu Butsuri, Vol. 42, Issue 6
Temperate Phages Acquire DNA from Defective Prophages by Relaxed Homologous Recombination: The Role of Rad52-Like Recombinases
journal, March 2014
- De Paepe, Marianne; Hutinet, Geoffrey; Son, Olivier
- PLoS Genetics, Vol. 10, Issue 3
Genomes OnLine Database (GOLD) v.6: data updates and feature enhancements
journal, October 2016
- Mukherjee, Supratim; Stamatis, Dimitri; Bertsch, Jon
- Nucleic Acids Research, Vol. 45, Issue D1
Streptococcus mitis Strains Causing Severe Clinical Disease in Cancer Patients
journal, May 2014
- Shelburne, Samuel A.; Sahasrabhojane, Pranoti; Saldana, Miguel
- Emerging Infectious Diseases, Vol. 20, Issue 5
Optimized cultivation of Campylobacter concisus from gut mucosal biopsies in inflammatory bowel disease
journal, June 2016
- Kirk, Karina Frahm; Nielsen, Hans Linde; Thorlacius-Ussing, Ole
- Gut Pathogens, Vol. 8, Issue 1
Origins of Highly Mosaic Mycobacteriophage Genomes
journal, April 2003
- Pedulla, Marisa L.; Ford, Michael E.; Houtz, Jennifer M.
- Cell, Vol. 113, Issue 2
Roary: rapid large-scale prokaryote pan genome analysis
journal, July 2015
- Page, Andrew J.; Cummins, Carla A.; Hunt, Martin
- Bioinformatics, Vol. 31, Issue 22
Draft Genome Sequence of Comamonas aquatilis Strain LK (= CSUR P6418 = CECT 9772), Isolated from the Planarian Schmidtea mediterranea
journal, February 2021
- Kangale, Luis Johnson; Levasseur, Anthony; Raoult, Didier
- Microbiology Resource Announcements, Vol. 10, Issue 5
Estimating Phylogenetic Trees from Distance Matrices
journal, September 1972
- Farris, James S.
- The American Naturalist, Vol. 106, Issue 951
Understanding the enormous diversity of bacteriophages: The tailed phages that infect the bacterial family Enterobacteriaceae
journal, November 2014
- Grose, Julianne H.; Casjens, Sherwood R.
- Virology, Vol. 468-470
Virus taxonomy in the age of metagenomics
journal, January 2017
- Simmonds, Peter; Adams, Mike J.; Benkő, Mária
- Nature Reviews Microbiology, Vol. 15, Issue 3
An essential role for the baseplate protein Gp45 in phage adsorption to Staphylococcus aureus
journal, May 2016
- Li, Xuehua; Koç, Cengiz; Kühner, Petra
- Scientific Reports, Vol. 6, Issue 1
New Bacterial Species Associated with Chronic Periodontitis
journal, May 2003
- Kumar, P. S.; Griffen, A. L.; Barton, J. A.
- Journal of Dental Research, Vol. 82, Issue 5
Propionibacterium acnes : infection beyond the skin
journal, December 2011
- Perry, Alexandra; Lambert, Peter
- Expert Review of Anti-infective Therapy, Vol. 9, Issue 12
DnaSAM: Software to perform neutrality testing for large datasets with complex null models
journal, May 2010
- Eckert, Andrew J.; Liechty, John D.; Tearse, Brandon R.
- Molecular Ecology Resources, Vol. 10, Issue 3
CRISPR Immunity Drives Rapid Phage Genome Evolution in Streptococcus thermophilus
journal, April 2015
- Paez-Espino, David; Sharon, Itai; Morovic, Wesley
- mBio, Vol. 6, Issue 2
Human Case of Atopobium rimae Bacteremia
journal, February 2009
- Angelakis, Emmanouil; Roux, Véronique; Raoult, Didier
- Emerging Infectious Diseases, Vol. 15, Issue 2
Resolving the paradox of sex and recombination
journal, April 2002
- Otto, Sarah P.; Lenormand, Thomas
- Nature Reviews Genetics, Vol. 3, Issue 4
TNT, a free program for phylogenetic analysis
journal, October 2008
- Goloboff, Pablo A.; Farris, James S.; Nixon, Kevin C.
- Cladistics, Vol. 24, Issue 5
CRISPR-Cas and Restriction-Modification Act Additively against Conjugative Antibiotic Resistance Plasmid Transfer in Enterococcus faecalis
journal, June 2016
- Price, Valerie J.; Huo, Wenwen; Sharifi, Ardalan
- mSphere, Vol. 1, Issue 3
Endocarditis due to Gemella haemolysans in a newly diagnosed multiple myeloma patient
journal, January 2016
- Liu, Dongyan; Bateman, Thomas; Carr, Elisabeth
- Journal of Community Hospital Internal Medicine Perspectives, Vol. 6, Issue 4
Endocarditis Due to Actinomyces viscosus
journal, January 2001
- Mardis, Joseph S.; Many, W. J.
- Southern Medical Journal, Vol. 94, Issue 2
Nontargeted virus sequence discovery pipeline and virus clustering for metagenomic data
journal, July 2017
- Paez-Espino, David; Pavlopoulos, Georgios A.; Ivanova, Natalia N.
- Nature Protocols, Vol. 12, Issue 8
Endocarditis Due to Actinomyces viscosus
journal, January 2001
- Mardis, Joseph S.; Many, W. J.
- Southern Medical Journal, Vol. 94, Issue 2
The Janus-Face of Bacteriophages across Human Body Habitats
text, January 2016
- Wahida, Adam; Ritter, Klaus; Horz, Hans-Peter
- RWTH Aachen University
ORIGINAL ARTICLE: Coinfection rates in φ6 bacteriophage are enhanced by virus-induced changes in host cells: Coinfection enhancement in φ6
journal, December 2008
- Joseph, Sarah B.; Hanley, Kathryn A.; Chao, Lin
- Evolutionary Applications, Vol. 2, Issue 1
Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees
journal, April 2016
- Letunic, Ivica; Bork, Peer
- Nucleic Acids Research, Vol. 44, Issue W1
IMG/VR: a database of cultured and uncultured DNA Viruses and retroviruses
journal, October 2016
- Paez-Espino, David; Chen, I. -Min A.; Palaniappan, Krishna
- Nucleic Acids Research, Vol. 45, Issue D1
Uncovering Earth’s virome
journal, August 2016
- Paez-Espino, David; Eloe-Fadrosh, Emiley A.; Pavlopoulos, Georgios A.
- Nature, Vol. 536, Issue 7617
Why do RNA viruses recombine?
journal, July 2011
- Simon-Loriere, Etienne; Holmes, Edward C.
- Nature Reviews Microbiology, Vol. 9, Issue 8
The Janus-Face of Bacteriophages across Human Body Habitats
text, January 2016
- Wahida, Adam; Ritter, Klaus; Horz, Hans-Peter
- RWTH Aachen University
Bacteriophage genomics
journal, October 2003
- Hendrix, Roger W.
- Current Opinion in Microbiology, Vol. 6, Issue 5
How Many Bootstrap Replicates Are Necessary?
journal, March 2010
- Pattengale, Nicholas D.; Alipour, Masoud; Bininda-Emonds, Olaf R. P.
- Journal of Computational Biology, Vol. 17, Issue 3
Rhizosphere bacteriome structure and functions
journal, February 2022
- Ling, Ning; Wang, Tingting; Kuzyakov, Yakov
- Nature Communications, Vol. 13, Issue 1
The role of bacteriophages in periodontal health and disease
journal, October 2016
- Pinto, Graça; Silva, Maria Daniela; Peddey, Mark
- Future Microbiology, Vol. 11, Issue 10
Bacteriophage genomics
journal, October 2008
- Hatfull, Graham F.
- Current Opinion in Microbiology, Vol. 11, Issue 5
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Characterizing the molecular regulation of inhibitory immune checkpoints with multimodal single-cell screens
journal, March 2021
- Papalexi, Efthymia; Mimitou, Eleni P.; Butler, Andrew W.
- Nature Genetics, Vol. 53, Issue 3
Evolution of DNA Double-Strand Break Repair by Gene Conversion: Coevolution Between a Phage and a Restriction-Modification System
journal, April 2007
- Yahara, Koji; Horie, Ryota; Kobayashi, Ichizo
- Genetics, Vol. 176, Issue 1
Statistical Properties of the Number of Recombination Events in the History of a Sample of dna Sequences
journal, September 1985
- Hudson, Richard R.; Kaplan, Norman L.
- Genetics, Vol. 111, Issue 1
Viruses in Soil Ecosystems: An Unknown Quantity Within an Unexplored Territory
journal, September 2017
- Williamson, Kurt E.; Fuhrmann, Jeffry J.; Wommack, K. Eric
- Annual Review of Virology, Vol. 4, Issue 1
Complete genome sequence of DSM 30083T, the type strain (U5/41T) of Escherichia coli, and a proposal for delineating subspecies in microbial taxonomy
journal, January 2014
- Meier-Kolthoff, Jan P.; Hahnke, Richard L.; Petersen, Jörn
- Standards in Genomic Sciences, Vol. 9, Issue 1
Lysogeny in nature: mechanisms, impact and ecology of temperate phages
journal, March 2017
- Howard-Varona, Cristina; Hargreaves, Katherine R.; Abedon, Stephen T.
- The ISME Journal, Vol. 11, Issue 7
MVP: a microbe–phage interaction database
journal, November 2017
- Gao, Na L.; Zhang, Chengwei; Zhang, Zhanbing
- Nucleic Acids Research, Vol. 46, Issue D1
HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment
journal, December 2011
- Remmert, Michael; Biegert, Andreas; Hauser, Andreas
- Nature Methods, Vol. 9, Issue 2
Bacteremia Caused by Capnocytophaga Species in Patients with Neutropenia and Cancer: Results of a Multicenter Study
journal, August 2001
- Martino, Rodrigo; Rámila, Elena; Capdevila, Josep A.
- Clinical Infectious Diseases, Vol. 33, Issue 4
New Bacterial Species Associated with Chronic Periodontitis
journal, May 2003
- Kumar, P. S.; Griffen, A. L.; Barton, J. A.
- Journal of Dental Research, Vol. 82, Issue 5
The Human Gut Phage Community and Its Implications for Health and Disease
journal, June 2017
- Manrique, Pilar; Dills, Michael; Young, Mark
- Viruses, Vol. 9, Issue 6
Resolving the paradox of sex and recombination
journal, April 2002
- Otto, Sarah P.; Lenormand, Thomas
- Nature Reviews Genetics, Vol. 3, Issue 4
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
text, January 2014
- Stamatakis, A.
- Karlsruhe
Type II restriction endonucleases — a historical perspective and more
journal, June 2016
- Pingoud, Alfred; Wilson, Geoffrey G.; Wende, Wolfgang
- Nucleic Acids Research, Vol. 44, Issue 16
CRISPRDetect: A flexible algorithm to define CRISPR arrays
journal, May 2016
- Biswas, Ambarish; Staals, Raymond H. J.; Morales, Sergio E.
- BMC Genomics, Vol. 17, Issue 1
Global transcription of CRISPR loci in the human oral cavity
journal, May 2015
- Lum, Andrew G.; Ly, Melissa; Santiago-Rodriguez, Tasha M.
- BMC Genomics, Vol. 16, Issue 1
Genome sequence-based species delimitation with confidence intervals and improved distance functions
journal, January 2013
- Meier-Kolthoff, Jan P.; Auch, Alexander F.; Klenk, Hans-Peter
- BMC Bioinformatics, Vol. 14, Issue 1
Bacteriophages and their genomes
journal, October 2011
- Hatfull, Graham F.; Hendrix, Roger W.
- Current Opinion in Virology, Vol. 1, Issue 4
Bacteriophage lysis: mechanism and regulation
journal, September 1992
- Young, R.
- Microbiological Reviews, Vol. 56, Issue 3
Statistical Properties of the Number of Recombination Events in the History of a Sample of dna Sequences
journal, September 1985
- Hudson, Richard R.; Kaplan, Norman L.
- Genetics, Vol. 111, Issue 1
Works referencing / citing this record:
Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species
journal, August 2019
- Yahara, Koji; Lehours, Philippe; Vale, Filipa F.
- Microbial Genomics, Vol. 5, Issue 8
Ecological and Evolutionary Processes Shaping Viral Genetic Diversity
text, January 2019
- Retel, Cas; Märkle, Hanna; Becks, Lutz
- Molecular Diversity Preservation International MDPI
Analysis of genetic recombination and the pan-genome of a highly recombinogenic bacteriophage species
journal, August 2019
- Yahara, Koji; Lehours, Philippe; Vale, Filipa F.
- Microbial Genomics, Vol. 5, Issue 8
IMG/VR v.2.0: an integrated data management and analysis system for cultivated and environmental viral genomes
journal, November 2018
- Paez-Espino, David; Roux, Simon; Chen, I-Min A.
- Nucleic Acids Research, Vol. 47, Issue D1