Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics
Abstract
Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage populations, 17 of which represented by complete or near-complete genomes, in two North American freshwater lakes. Taxonomic analysis suggests that these freshwater virophages represent at least three new candidate genera. Ecologically, virophage populations are repeatedly detected over years and evolutionary stable, yet their distinct abundance profiles and gene content suggest that virophage genera occupy different ecological niches. Co-occurrence analyses reveal 11 virophages strongly associated with uncultivated Mimiviridae, and three associated with eukaryotes among the Dinophyceae, Rhizaria, Alveolata, and Cryptophyceae groups. Together, these findings significantly augment virophage databases, help refine virophage taxonomy, and establish baseline ecological hypotheses and tools to study virophages in nature.
- Authors:
-
- The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology
- USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
- Univ. of Wisconsin, Madison, WI (United States). Dept. of Bacteriology. Dept. of Civil and Environmental Engineering
- The Ohio State Univ., Columbus, OH (United States). Dept. of Microbiology. Dept. of Civil, Environmental and Geodetic Engineering
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC); National Science Foundation (NSF); Gordon and Betty Moore Foundation (United States)
- OSTI Identifier:
- 1459396
- Grant/Contract Number:
- AC02-05CH11231; MCB-0702395; DEB-1344254; DEB-1440297; OCE-1536989; GBMF #3790
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Nature Communications
- Additional Journal Information:
- Journal Volume: 8; Journal ID: ISSN 2041-1723
- Publisher:
- Nature Publishing Group
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; freshwater ecology; metagenomics; microbial ecology; phage biology
Citation Formats
Roux, Simon, Chan, Leong-Keat, Egan, Rob, Malmstrom, Rex R., McMahon, Katherine D., and Sullivan, Matthew B. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. United States: N. p., 2017.
Web. doi:10.1038/s41467-017-01086-2.
Roux, Simon, Chan, Leong-Keat, Egan, Rob, Malmstrom, Rex R., McMahon, Katherine D., & Sullivan, Matthew B. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. United States. https://doi.org/10.1038/s41467-017-01086-2
Roux, Simon, Chan, Leong-Keat, Egan, Rob, Malmstrom, Rex R., McMahon, Katherine D., and Sullivan, Matthew B. Wed .
"Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics". United States. https://doi.org/10.1038/s41467-017-01086-2. https://www.osti.gov/servlets/purl/1459396.
@article{osti_1459396,
title = {Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics},
author = {Roux, Simon and Chan, Leong-Keat and Egan, Rob and Malmstrom, Rex R. and McMahon, Katherine D. and Sullivan, Matthew B.},
abstractNote = {Virophages are small viruses that co-infect eukaryotic cells alongside giant viruses (Mimiviridae) and hijack their machinery to replicate. While two types of virophages have been isolated, their genomic diversity and ecology remain largely unknown. Here we use time series metagenomics to identify and study the dynamics of 25 uncultivated virophage populations, 17 of which represented by complete or near-complete genomes, in two North American freshwater lakes. Taxonomic analysis suggests that these freshwater virophages represent at least three new candidate genera. Ecologically, virophage populations are repeatedly detected over years and evolutionary stable, yet their distinct abundance profiles and gene content suggest that virophage genera occupy different ecological niches. Co-occurrence analyses reveal 11 virophages strongly associated with uncultivated Mimiviridae, and three associated with eukaryotes among the Dinophyceae, Rhizaria, Alveolata, and Cryptophyceae groups. Together, these findings significantly augment virophage databases, help refine virophage taxonomy, and establish baseline ecological hypotheses and tools to study virophages in nature.},
doi = {10.1038/s41467-017-01086-2},
journal = {Nature Communications},
number = ,
volume = 8,
place = {United States},
year = {Wed Oct 11 00:00:00 EDT 2017},
month = {Wed Oct 11 00:00:00 EDT 2017}
}
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Figures / Tables:
Fig. 1: Phylogeny and summarized gene content of virophage genomes. The maximum-likelihood phylogenetic tree was computed from a concatenated alignment of four core genes (major and minor capsid proteins, DNA packaging enzyme, and Cysteine protease). SH-like support are indicated on nodes, and branches with < 50% support are displayed asmore »
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Works referenced in this record:
Analysis of immune, microbiota and metabolome maturation in infants in a clinical trial of Lactobacillus paracasei CBA L74-fermented formula
journal, June 2020
- Roggero, Paola; Liotto, Nadia; Pozzi, Chiara
- Nature Communications, Vol. 11, Issue 1
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
journal, April 2012
- Shapiro, B. Jesse; Friedman, Jonathan; Cordero, Otto X.
- Science, Vol. 336, Issue 6077
Protein homology detection by HMM-HMM comparison
journal, November 2004
- Soding, J.
- Bioinformatics, Vol. 21, Issue 7
Recombination and microdiversity in coastal marine cyanophages
journal, November 2009
- Marston, Marcia F.; Amrich, Christopher G.
- Environmental Microbiology, Vol. 11, Issue 11
Genomic insights that advance the species definition for prokaryotes
journal, February 2005
- Konstantinidis, K. T.; Tiedje, J. M.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 7
Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes
journal, February 2008
- Lima-Mendez, G.; Van Helden, J.; Toussaint, A.
- Molecular Biology and Evolution, Vol. 25, Issue 4
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
journal, November 2016
- Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar
- BMC Genomics, Vol. 17, Issue 1
A General Framework for Weighted Gene Co-Expression Network Analysis
journal, January 2005
- Zhang, Bin; Horvath, Steve
- Statistical Applications in Genetics and Molecular Biology, Vol. 4, Issue 1
Temporal variation in freshwater viral and bacterial community composition
journal, June 2008
- Lymer, David; Logue, JÜRg Brendan; Brussaard, Corina P. D.
- Freshwater Biology, Vol. 53, Issue 6
Invasive species triggers a massive loss of ecosystem services through a trophic cascade
journal, March 2016
- Walsh, Jake R.; Carpenter, Stephen R.; Vander Zanden, M. Jake
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 15
WGCNA: an R package for weighted correlation network analysis
journal, December 2008
- Langfelder, Peter; Horvath, Steve
- BMC Bioinformatics, Vol. 9, Issue 1
Identification of ribosomal RNA genes in metagenomic fragments
journal, April 2009
- Huang, Ying; Gilna, Paul; Li, Weizhong
- Bioinformatics, Vol. 25, Issue 10
Horizontal gene transfer enables programmable gene stability in synthetic microbiota
journal, September 2022
- Wang, Teng; Weiss, Andrea; Aqeel, Ammara
- Nature Chemical Biology, Vol. 18, Issue 11
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
journal, February 2016
- Weiss, Sophie; Van Treuren, Will; Lozupone, Catherine
- The ISME Journal, Vol. 10, Issue 7
The virophage as a unique parasite of the giant mimivirus
journal, August 2008
- La Scola, Bernard; Desnues, Christelle; Pagnier, Isabelle
- Nature, Vol. 455, Issue 7209
Isolation and characterization of the novel Pseudomonas stutzeri bacteriophage 8P
journal, January 2021
- Liu, Xinwu; Feng, Zhou; Fan, Xiangyu
- Archives of Virology, Vol. 166, Issue 2
Diversity and dynamics of algal Megaviridae members during a harmful brown tide caused by the pelagophyte, Aureococcus anophagefferens
journal, March 2016
- Moniruzzaman, Mohammad; Gann, Eric R.; LeCleir, Gary R.
- FEMS Microbiology Ecology, Vol. 92, Issue 5
Population Dynamics and Diversity of Viruses, Bacteria and Phytoplankton in a Shallow Eutrophic Lake
journal, October 2007
- Tijdens, Marjolijn; Hoogveld, Hans L.; Kamst-van Agterveld, Miranda P.
- Microbial Ecology, Vol. 56, Issue 1
A Guide to the Natural History of Freshwater Lake Bacteria
journal, March 2011
- Newton, R. J.; Jones, S. E.; Eiler, A.
- Microbiology and Molecular Biology Reviews, Vol. 75, Issue 1
Minimus: a fast, lightweight genome assembler
journal, January 2007
- Sommer, Daniel D.; Delcher, Arthur L.; Salzberg, Steven L.
- BMC Bioinformatics, Vol. 8, Issue 1
Genomic variation landscape of the human gut microbiome
journal, December 2012
- Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi
- Nature, Vol. 493, Issue 7430
Broad Spectrum of Mimiviridae Virophage Allows Its Isolation Using a Mimivirus Reporter
journal, April 2013
- Gaia, Morgan; Pagnier, Isabelle; Campocasso, Angélique
- PLoS ONE, Vol. 8, Issue 4
Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphagamimivirus Strain, and Reannotation of Mimivirus Genes
journal, January 2011
- Colson, Philippe; Yutin, Natalya; Shabalina, Svetlana A.
- Genome Biology and Evolution, Vol. 3
FLASH: fast length adjustment of short reads to improve genome assemblies
journal, September 2011
- Magoc, T.; Salzberg, S. L.
- Bioinformatics, Vol. 27, Issue 21
An Ordination of the Upland Forest Communities of Southern Wisconsin
journal, February 1957
- Bray, J. Roger; Curtis, J. T.
- Ecological Monographs, Vol. 27, Issue 4
UCSF Chimera?A visualization system for exploratory research and analysis
journal, January 2004
- Pettersen, Eric F.; Goddard, Thomas D.; Huang, Conrad C.
- Journal of Computational Chemistry, Vol. 25, Issue 13
Mimivirus and its Virophage
journal, December 2009
- Claverie, Jean-Michel; Abergel, Chantal
- Annual Review of Genetics, Vol. 43, Issue 1
Large-scale search for genes on which positive selection may operate
journal, May 1996
- Endo, T.; Ikeo, K.; Gojobori, T.
- Molecular Biology and Evolution, Vol. 13, Issue 5
Preterm infants with isolated cerebellar hemorrhage show bilateral cortical alterations at term equivalent age
journal, March 2020
- Dijkshoorn, Aicha B. C.; Turk, Elise; Hortensius, Lisa M.
- Scientific Reports, Vol. 10, Issue 1
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
journal, April 2010
- Legendre, M.; Audic, S.; Poirot, O.
- Genome Research, Vol. 20, Issue 5
Microbial Co-occurrence Relationships in the Human Microbiome
journal, July 2012
- Faust, Karoline; Sathirapongsasuti, J. Fah; Izard, Jacques
- PLoS Computational Biology, Vol. 8, Issue 7
Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists
journal, November 2013
- Chow, Cheryl-Emiliane T.; Kim, Diane Y.; Sachdeva, Rohan
- The ISME Journal, Vol. 8, Issue 4
Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses
journal, January 2014
- Krupovic, Mart; Bamford, Dennis H.; Koonin, Eugene V.
- Biology Direct, Vol. 9, Issue 1
InterProScan 5: genome-scale protein function classification
journal, January 2014
- Jones, P.; Binns, D.; Chang, H. -Y.
- Bioinformatics, Vol. 30, Issue 9
The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection
journal, August 2014
- Taylor, Bradford P.; Cortez, Michael H.; Weitz, Joshua S.
- Journal of Theoretical Biology, Vol. 354
Molecular ecological network analyses
journal, January 2012
- Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng
- BMC Bioinformatics, Vol. 13, Issue 1
Scale-Free Behavior in Protein Domain Networks
journal, September 2001
- Wuchty, Stefan
- Molecular Biology and Evolution, Vol. 18, Issue 9
MEME SUITE: tools for motif discovery and searching
journal, May 2009
- Bailey, T. L.; Boden, M.; Buske, F. A.
- Nucleic Acids Research, Vol. 37, Issue Web Server
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Zamilon, a Novel Virophage with Mimiviridae Host Specificity
journal, April 2014
- Gaia, Morgan; Benamar, Samia; Boughalmi, Mondher
- PLoS ONE, Vol. 9, Issue 4
Alphaherpesvirinae and Gammaherpesvirinae glycoprotein L and CMV UL130 originate from chemokines
journal, January 2013
- Malkowska, Maja; Kokoszynska, Katarzyna; Dymecka, Magdalena
- Virology Journal, Vol. 10, Issue 1
Novel Virophages Discovered in a Freshwater Lake in China
journal, January 2016
- Gong, Chaowen; Zhang, Weijia; Zhou, Xuewen
- Frontiers in Microbiology, Vol. 7
MRBAYES: Bayesian inference of phylogenetic trees
journal, August 2001
- Huelsenbeck, J. P.; Ronquist, F.
- Bioinformatics, Vol. 17, Issue 8
Virophage control of antarctic algal host-virus dynamics
journal, March 2011
- Yau, S.; Lauro, F. M.; DeMaere, M. Z.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 15
A sand fly salivary protein acts as a neutrophil chemoattractant
journal, May 2021
- Guimaraes-Costa, Anderson B.; Shannon, John P.; Waclawiak, Ingrid
- Nature Communications, Vol. 12, Issue 1
A novel group of diverse Polinton-like viruses discovered by metagenome analysis
journal, November 2015
- Yutin, Natalya; Shevchenko, Sofiya; Kapitonov, Vladimir
- BMC Biology, Vol. 13, Issue 1
Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies
journal, January 2013
- Yutin, Natalya; Raoult, Didier; Koonin, Eugene V.
- Virology Journal, Vol. 10, Issue 1
Topological Properties of Co-Occurrence Networks in Published Gene Expression Signatures
journal, January 2008
- Muller, Heiko; Acquati, Francesco
- Bioinformatics and Biology Insights, Vol. 2
Large-scale search for genes on which positive selection may operate
journal, May 1996
- Endo, T.; Ikeo, K.; Gojobori, T.
- Molecular Biology and Evolution, Vol. 13, Issue 5
Host genome integration and giant virus-induced reactivation of the virophage mavirus
journal, December 2016
- Fischer, Matthias G.; Hackl, Thomas
- Nature, Vol. 540, Issue 7632
Structure of Sputnik, a virophage, at 3.5-A resolution
journal, October 2012
- Zhang, X.; Sun, S.; Xiang, Y.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 45
MUSCLE: a multiple sequence alignment method with reduced time and space complexity
journal, August 2004
- Edgar, Robert C.
- BMC Bioinformatics, Vol. 5, Issue 1, p. 113
Network biology: understanding the cell's functional organization
journal, February 2004
- Barabási, Albert-László; Oltvai, Zoltán N.
- Nature Reviews Genetics, Vol. 5, Issue 2
Diversity and dynamics of algal Megaviridae members during a harmful brown tide caused by the pelagophyte, Aureococcus anophagefferens
journal, March 2016
- Moniruzzaman, Mohammad; Gann, Eric R.; LeCleir, Gary R.
- FEMS Microbiology Ecology, Vol. 92, Issue 5
The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
preprint, March 2016
- Rodriguez-R, Luis M.; Konstantinidis, Konstantinos T.
- PeerJ Preprints 4:e1900v1
Population Dynamics and Diversity of Viruses, Bacteria and Phytoplankton in a Shallow Eutrophic Lake
journal, October 2007
- Tijdens, Marjolijn; Hoogveld, Hans L.; Kamst-van Agterveld, Miranda P.
- Microbial Ecology, Vol. 56, Issue 1
A classification system for virophages and satellite viruses
journal, October 2015
- Krupovic, Mart; Kuhn, Jens H.; Fischer, Matthias G.
- Archives of Virology, Vol. 161, Issue 1
Dynamic Viral Populations in Hypersaline Systems as Revealed by Metagenomic Assembly
journal, July 2012
- Emerson, Joanne B.; Thomas, Brian C.; Andrade, Karen
- Applied and Environmental Microbiology, Vol. 78, Issue 17
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
journal, November 2012
- Xia, Li C.; Ai, Dongmei; Cram, Jacob
- Bioinformatics, Vol. 29, Issue 2
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
A new family of hybrid virophages from an animal gut metagenome
journal, April 2015
- Yutin, Natalya; Kapitonov, Vladimir V.; Koonin, Eugene V.
- Biology Direct, Vol. 10, Issue 1
Plankton networks driving carbon export in the oligotrophic ocean
journal, February 2016
- Guidi, Lionel; Chaffron, Samuel; Bittner, Lucie
- Nature, Vol. 532, Issue 7600
Related Giant Viruses in Distant Locations and Different Habitats: Acanthamoeba polyphaga moumouvirus Represents a Third Lineage of the Mimiviridae That Is Close to the Megavirus Lineage
journal, December 2012
- Yoosuf, Niyaz; Yutin, Natalya; Colson, Philippe
- Genome Biology and Evolution, Vol. 4, Issue 12
Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics: Comparative freshwater metagenomics
journal, November 2013
- Eiler, Alexander; Zaremba-Niedzwiedzka, Katarzyna; Martínez-García, Manuel
- Environmental Microbiology, Vol. 16, Issue 9
Broad Spectrum of Mimiviridae Virophage Allows Its Isolation Using a Mimivirus Reporter
journal, April 2013
- Gaia, Morgan; Pagnier, Isabelle; Campocasso, Angélique
- PLoS ONE, Vol. 8, Issue 4
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
journal, January 2016
- Bendall, Matthew L.; Stevens, Sarah LR; Chan, Leong-Keat
- The ISME Journal, Vol. 10, Issue 7
Population Genomics of Early Events in the Ecological Differentiation of Bacteria
journal, April 2012
- Shapiro, B. Jesse; Friedman, Jonathan; Cordero, Otto X.
- Science, Vol. 336, Issue 6077
Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses
journal, January 2014
- Krupovic, Mart; Bamford, Dennis H.; Koonin, Eugene V.
- Biology Direct, Vol. 9, Issue 1
Recombination and microdiversity in coastal marine cyanophages
journal, November 2009
- Marston, Marcia F.; Amrich, Christopher G.
- Environmental Microbiology, Vol. 11, Issue 11
Invasive species triggers a massive loss of ecosystem services through a trophic cascade
journal, March 2016
- Walsh, Jake R.; Carpenter, Stephen R.; Vander Zanden, M. Jake
- Proceedings of the National Academy of Sciences, Vol. 113, Issue 15
Viruses with More Than 1,000 Genes: Mamavirus, a New Acanthamoeba polyphagamimivirus Strain, and Reannotation of Mimivirus Genes
journal, January 2011
- Colson, Philippe; Yutin, Natalya; Shabalina, Svetlana A.
- Genome Biology and Evolution, Vol. 3
Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer
journal, November 2016
- Gregory, Ann C.; Solonenko, Sergei A.; Ignacio-Espinoza, J. Cesar
- BMC Genomics, Vol. 17, Issue 1
An Ordination of the Upland Forest Communities of Southern Wisconsin
journal, February 1957
- Bray, J. Roger; Curtis, J. T.
- Ecological Monographs, Vol. 27, Issue 4
Related Giant Viruses in Distant Locations and Different Habitats: Acanthamoeba polyphaga moumouvirus Represents a Third Lineage of the Mimiviridae That Is Close to the Megavirus Lineage
journal, December 2012
- Yoosuf, Niyaz; Yutin, Natalya; Colson, Philippe
- Genome Biology and Evolution, Vol. 4, Issue 12
Genomic variation landscape of the human gut microbiome
journal, December 2012
- Schloissnig, Siegfried; Arumugam, Manimozhiyan; Sunagawa, Shinichi
- Nature, Vol. 493, Issue 7430
An efficient algorithm for large-scale detection of protein families
journal, April 2002
- Enright, A. J.
- Nucleic Acids Research, Vol. 30, Issue 7
Anaerobic hydrocarbon degradation in candidate phylum ‘Atribacteria’ (JS1) inferred from genomics
journal, June 2019
- Liu, Yi-Fan; Qi, Zhen-Zhen; Shou, Li-Bin
- The ISME Journal, Vol. 13, Issue 9
Ray Meta: scalable de novo metagenome assembly and profiling
journal, January 2012
- Boisvert, Sébastien; Raymond, Frédéric; Godzaridis, Élénie
- Genome Biology, Vol. 13, Issue 12
The virophage as a unique parasite of the giant mimivirus
journal, August 2008
- La Scola, Bernard; Desnues, Christelle; Pagnier, Isabelle
- Nature, Vol. 455, Issue 7209
Diversity of Virophages in Metagenomic Data Sets
journal, February 2013
- Zhou, J.; Zhang, W.; Yan, S.
- Journal of Virology, Vol. 87, Issue 8
WGCNA: an R package for weighted correlation network analysis
journal, December 2008
- Langfelder, Peter; Horvath, Steve
- BMC Bioinformatics, Vol. 9, Issue 1
Minimus: a fast, lightweight genome assembler
journal, January 2007
- Sommer, Daniel D.; Delcher, Arthur L.; Salzberg, Steven L.
- BMC Bioinformatics, Vol. 8, Issue 1
Easyfig: a genome comparison visualizer
journal, January 2011
- Sullivan, M. J.; Petty, N. K.; Beatson, S. A.
- Bioinformatics, Vol. 27, Issue 7
Species identification, phylogenetic analysis and detection of herbicide-resistant biotypes of Amaranthus based on ALS and ITS
journal, July 2020
- Xu, Han; Pan, Xubin; Wang, Cong
- Scientific Reports, Vol. 10, Issue 1
Reticulate Representation of Evolutionary and Functional Relationships between Phage Genomes
journal, February 2008
- Lima-Mendez, G.; Van Helden, J.; Toussaint, A.
- Molecular Biology and Evolution, Vol. 25, Issue 4
Three Novel Virophage Genomes Discovered from Yellowstone Lake Metagenomes
journal, November 2014
- Zhou, Jinglie; Sun, Dawei; Childers, Alyson
- Journal of Virology, Vol. 89, Issue 2
The Neutral Theory of Molecular Evolution in the Genomic Era
journal, September 2010
- Nei, Masatoshi; Suzuki, Yoshiyuki; Nozawa, Masafumi
- Annual Review of Genomics and Human Genetics, Vol. 11, Issue 1
Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China
journal, January 2016
- Ma, Bin; Wang, Haizhen; Dsouza, Melissa
- The ISME Journal, Vol. 10, Issue 8
Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes
journal, June 2013
- Santini, S.; Jeudy, S.; Bartoli, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 26
Efficient statistical significance approximation for local similarity analysis of high-throughput time series data
journal, November 2012
- Xia, Li C.; Ai, Dongmei; Cram, Jacob
- Bioinformatics, Vol. 29, Issue 2
Temporal variation in freshwater viral and bacterial community composition
journal, June 2008
- Lymer, David; Logue, JÜRg Brendan; Brussaard, Corina P. D.
- Freshwater Biology, Vol. 53, Issue 6
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
The virus of my virus is my friend: Ecological effects of virophage with alternative modes of coinfection
journal, August 2014
- Taylor, Bradford P.; Cortez, Michael H.; Weitz, Joshua S.
- Journal of Theoretical Biology, Vol. 354
The SILVA ribosomal RNA gene database project: improved data processing and web-based tools
journal, November 2012
- Quast, Christian; Pruesse, Elmar; Yilmaz, Pelin
- Nucleic Acids Research, Vol. 41, Issue D1
Structure of Sputnik, a virophage, at 3.5-A resolution
journal, October 2012
- Zhang, X.; Sun, S.; Xiang, Y.
- Proceedings of the National Academy of Sciences, Vol. 109, Issue 45
Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution
journal, December 2014
- Krupovic, Mart; Koonin, Eugene V.
- Nature Reviews Microbiology, Vol. 13, Issue 2
Origin and Evolution of Eukaryotic Large Nucleo-Cytoplasmic DNA Viruses
journal, January 2010
- Koonin, Eugene V.; Yutin, Natalya
- Intervirology, Vol. 53, Issue 5
Zamilon, a Novel Virophage with Mimiviridae Host Specificity
journal, April 2014
- Gaia, Morgan; Benamar, Samia; Boughalmi, Mondher
- PLoS ONE, Vol. 9, Issue 4
Molecular ecological network analyses
journal, January 2012
- Deng, Ye; Jiang, Yi-Huei; Yang, Yunfeng
- BMC Bioinformatics, Vol. 13, Issue 1
Microcystin mcyA and mcyE Gene Abundances Are Not Appropriate Indicators of Microcystin Concentrations in Lakes
journal, May 2015
- Beversdorf, Lucas J.; Chaston, Sheena D.; Miller, Todd R.
- PLOS ONE, Vol. 10, Issue 5
Rhizosphere bacteriome structure and functions
journal, February 2022
- Ling, Ning; Wang, Tingting; Kuzyakov, Yakov
- Nature Communications, Vol. 13, Issue 1
MRBAYES: Bayesian inference of phylogenetic trees
journal, August 2001
- Huelsenbeck, J. P.; Ronquist, F.
- Bioinformatics, Vol. 17, Issue 8
Plankton networks driving carbon export in the oligotrophic ocean
journal, February 2016
- Guidi, Lionel; Chaffron, Samuel; Bittner, Lucie
- Nature, Vol. 532, Issue 7600
The Neutral Theory of Molecular Evolution in the Genomic Era
journal, September 2010
- Nei, Masatoshi; Suzuki, Yoshiyuki; Nozawa, Masafumi
- Annual Review of Genomics and Human Genetics, Vol. 11, Issue 1
Temporal Dynamics and Decay of Putatively Allochthonous and Autochthonous Viral Genotypes in Contrasting Freshwater Lakes
journal, July 2012
- Hewson, Ian; Barbosa, Jorge G.; Brown, Julia M.
- Applied and Environmental Microbiology, Vol. 78, Issue 18
Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists
journal, November 2013
- Chow, Cheryl-Emiliane T.; Kim, Diane Y.; Sachdeva, Rohan
- The ISME Journal, Vol. 8, Issue 4
Fast gapped-read alignment with Bowtie 2
journal, March 2012
- Langmead, Ben; Salzberg, Steven L.
- Nature Methods, Vol. 9, Issue 4
Productivity and salinity structuring of the microplankton revealed by comparative freshwater metagenomics: Comparative freshwater metagenomics
journal, November 2013
- Eiler, Alexander; Zaremba-Niedzwiedzka, Katarzyna; Martínez-García, Manuel
- Environmental Microbiology, Vol. 16, Issue 9
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
Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
journal, January 2016
- Bendall, Matthew L.; Stevens, Sarah LR; Chan, Leong-Keat
- The ISME Journal, Vol. 10, Issue 7
Effects of Plants on Metacommunities and Correlation Networks of Soil Microbial Groups in an Ecologically Restored Wetland
journal, October 2020
- Jeong, So-Yeon; Kim, Tae Gwan
- Microbial Ecology, Vol. 81, Issue 3
Mimivirus and its Virophage
journal, December 2009
- Claverie, Jean-Michel; Abergel, Chantal
- Annual Review of Genetics, Vol. 43, Issue 1
Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes
journal, April 2013
- Hingamp, Pascal; Grimsley, Nigel; Acinas, Silvia G.
- The ISME Journal, Vol. 7, Issue 9
Voluntary exposure to a toxin: the genetic influence on ethanol consumption
journal, December 2017
- Hoffman, Paula L.; Saba, Laura M.; Vanderlinden, Lauren A.
- Mammalian Genome, Vol. 29, Issue 1-2
Correlation detection strategies in microbial data sets vary widely in sensitivity and precision
journal, February 2016
- Weiss, Sophie; Van Treuren, Will; Lozupone, Catherine
- The ISME Journal, Vol. 10, Issue 7
mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus
journal, April 2010
- Legendre, M.; Audic, S.; Poirot, O.
- Genome Research, Vol. 20, Issue 5
Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes
journal, June 2013
- Santini, S.; Jeudy, S.; Bartoli, J.
- Proceedings of the National Academy of Sciences, Vol. 110, Issue 26
The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes
preprint, March 2016
- Rodriguez-R., Luis M.; Konstantinidis, Konstantinos T.
A classification system for virophages and satellite viruses
journal, October 2015
- Krupovic, Mart; Kuhn, Jens H.; Fischer, Matthias G.
- Archives of Virology, Vol. 161, Issue 1
Genomic insights that advance the species definition for prokaryotes
journal, February 2005
- Konstantinidis, K. T.; Tiedje, J. M.
- Proceedings of the National Academy of Sciences, Vol. 102, Issue 7
EMBOSS: The European Molecular Biology Open Software Suite
journal, June 2000
- Rice, Peter; Longden, Ian; Bleasby, Alan
- Trends in Genetics, Vol. 16, Issue 6
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
A Virophage at the Origin of Large DNA Transposons
journal, March 2011
- Fischer, M. G.; Suttle, C. A.
- Science, Vol. 332, Issue 6026
The virus of my virus is my friend: ecological effects of virophage with alternative modes of coinfection
preprint, January 2013
- Taylor, Bradford P.; Cortez, Michael H.; Weitz, Joshua S.
- arXiv
The Sequence Alignment/Map format and SAMtools
journal, June 2009
- Li, H.; Handsaker, B.; Wysoker, A.
- Bioinformatics, Vol. 25, Issue 16
Virophage control of antarctic algal host-virus dynamics
journal, March 2011
- Yau, S.; Lauro, F. M.; DeMaere, M. Z.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 15
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Metagenomics Reveals a Novel Virophage Population in a Tibetan Mountain Lake
journal, January 2016
- Oh, Seungdae; Yoo, Dongwan; Liu, Wen-Tso
- Microbes and environments, Vol. 31, Issue 2
MetaBAT, an efficient tool for accurately reconstructing single genomes from complex microbial communities
journal, January 2015
- Kang, Dongwan D.; Froula, Jeff; Egan, Rob
- PeerJ, Vol. 3
Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates
journal, January 2011
- Xia, Li C.; Steele, Joshua A.; Cram, Jacob A.
- BMC Systems Biology, Vol. 5, Issue Suppl 2
SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler
journal, December 2012
- Luo, Ruibang; Liu, Binghang; Xie, Yinlong
- GigaScience, Vol. 1, Issue 1
FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments
journal, March 2010
- Price, Morgan N.; Dehal, Paramvir S.; Arkin, Adam P.
- PLoS ONE, Vol. 5, Issue 3
Works referencing / citing this record:
Viva lavidaviruses! Five features of virophages that parasitize giant DNA viruses
journal, March 2019
- Duponchel, Sarah; Fischer, Matthias G.
- PLOS Pathogens, Vol. 15, Issue 3
Virophages of Giant Viruses: An Update at Eleven
journal, August 2019
- Mougari, Said; Sahmi-Bounsiar, Dehia; Levasseur, Anthony
- Viruses, Vol. 11, Issue 8
Metagenomics detection and characterisation of viruses in faecal samples from Australian wild birds
journal, June 2018
- Vibin, Jessy; Chamings, Anthony; Collier, Fiona
- Scientific Reports, Vol. 8, Issue 1
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
text, January 2019
- Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh
- BioMed Central
Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks
journal, May 2019
- Bin Jang, Ho; Bolduc, Benjamin; Zablocki, Olivier
- Nature Biotechnology, Vol. 37, Issue 6
Charting the diversity of uncultured viruses of Archaea and Bacteria
journal, December 2019
- Coutinho, F. H.; Edwards, R. A.; Rodríguez-Valera, F.
- BMC Biology, Vol. 17, Issue 1
Metagenomic Analysis of Virus Diversity and Relative Abundance in a Eutrophic Freshwater Harbour
journal, August 2019
- Palermo, Christine N.; Fulthorpe, Roberta R.; Saati, Rosemary
- Viruses, Vol. 11, Issue 9
Charting the diversity of uncultured viruses of Archaea and Bacteria
journal, December 2019
- Coutinho, F. H.; Edwards, R. A.; Rodríguez-Valera, F.
- BMC Biology, Vol. 17, Issue 1
Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome
journal, April 2018
- Andreani, Julien; Verneau, Jonathan; Raoult, Didier
- Virology Journal, Vol. 15, Issue 1
Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
journal, January 2018
- Linz, Alexandra M.; He, Shaomei; Stevens, Sarah L. R.
- PeerJ, Vol. 6
Archaeal Viruses from High-Temperature Environments
journal, February 2018
- Munson-McGee, Jacob; Snyder, Jamie; Young, Mark
- Genes, Vol. 9, Issue 3
Mimiviridae: An Expanding Family of Highly Diverse Large dsDNA Viruses Infecting a Wide Phylogenetic Range of Aquatic Eukaryotes
journal, September 2018
- Claverie, Jean-Michel; Abergel, Chantal
- Viruses, Vol. 10, Issue 9
Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome
journal, April 2018
- Andreani, Julien; Verneau, Jonathan; Raoult, Didier
- Virology Journal, Vol. 15, Issue 1
Genome-Resolved Metagenomics Extends the Environmental Distribution of the Verrucomicrobia Phylum to the Deep Terrestrial Subsurface
journal, December 2019
- Nixon, Sophie L.; Daly, Rebecca A.; Borton, Mikayla A.
- mSphere, Vol. 4, Issue 6
Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
journal, October 2019
- Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh
- Microbiome, Vol. 7, Issue 1
Viva lavidaviruses! Five features of virophages that parasitize giant DNA viruses
journal, March 2019
- Duponchel, Sarah; Fischer, Matthias G.
- PLOS Pathogens, Vol. 15, Issue 3
Diversity, evolution, and classification of virophages uncovered through global metagenomics
journal, December 2019
- Paez-Espino, David; Zhou, Jinglie; Roux, Simon
- Microbiome, Vol. 7, Issue 1
Capsid protein structure, self-assembly, and processing reveal morphogenesis of the marine virophage mavirus
journal, June 2018
- Born, Diana; Reuter, Lukas; Mersdorf, Ulrike
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 28
Defective viral genomes are key drivers of the virus–host interaction
journal, June 2019
- Vignuzzi, Marco; López, Carolina B.
- Nature Microbiology, Vol. 4, Issue 7
Genome‐resolved viral and cellular metagenomes revealed potential key virus‐host interactions in a deep freshwater lake
journal, September 2019
- Okazaki, Yusuke; Nishimura, Yosuke; Yoshida, Takashi
- Environmental Microbiology, Vol. 21, Issue 12
Hidden diversity of soil giant viruses
journal, November 2018
- Schulz, Frederik; Alteio, Lauren; Goudeau, Danielle
- Nature Communications, Vol. 9, Issue 1
Metagenomic Analysis of the Diversity of DNA Viruses in the Surface and Deep Sea of the South China Sea
journal, August 2019
- Liang, Yantao; Wang, Long; Wang, Zengmeng
- Frontiers in Microbiology, Vol. 10
Viruses of Eukaryotic Algae: Diversity, Methods for Detection, and Future Directions
journal, September 2018
- Coy, Samantha; Gann, Eric; Pound, Helena
- Viruses, Vol. 10, Issue 9
Diversity, evolution, and classification of virophages uncovered through global metagenomics
journal, December 2019
- Paez-Espino, David; Zhou, Jinglie; Roux, Simon
- Microbiome, Vol. 7, Issue 1
Capsid protein structure, self-assembly, and processing reveal morphogenesis of the marine virophage mavirus
journal, June 2018
- Born, Diana; Reuter, Lukas; Mersdorf, Ulrike
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 28
Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales
journal, June 2018
- Borton, Mikayla A.; Hoyt, David W.; Roux, Simon
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 28
Freshwater carbon and nutrient cycles revealed through reconstructed population genomes
journal, January 2018
- Linz, Alexandra M.; He, Shaomei; Stevens, Sarah L. R.
- PeerJ, Vol. 6
Defective viral genomes are key drivers of the virus–host interaction
journal, June 2019
- Vignuzzi, Marco; López, Carolina B.
- Nature Microbiology, Vol. 4, Issue 7
Hidden diversity of soil giant viruses
journal, November 2018
- Schulz, Frederik; Alteio, Lauren; Goudeau, Danielle
- Nature Communications, Vol. 9, Issue 1
Assessing the viral content of uncultured picoeukaryotes in the global‐ocean by single cell genomics
journal, September 2019
- Castillo, Yaiza M.; Mangot, Jean‐François; Benites, Luiz Felipe
- Molecular Ecology, Vol. 28, Issue 18
Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales
journal, June 2018
- Borton, Mikayla A.; Hoyt, David W.; Roux, Simon
- Proceedings of the National Academy of Sciences, Vol. 115, Issue 28
Phage-specific metabolic reprogramming of virocells
journal, January 2020
- Howard-Varona, Cristina; Lindback, Morgan M.; Bastien, G. Eric
- The ISME Journal, Vol. 14, Issue 4
CAMISIM: simulating metagenomes and microbial communities
journal, February 2019
- Fritz, Adrian; Hofmann, Peter; Majda, Stephan
- Microbiome, Vol. 7, Issue 1
Correction to: Phage-centric ecological interactions in aquatic ecosystems revealed through ultra-deep metagenomics
journal, March 2020
- Kavagutti, Vinicius S.; Andrei, Adrian-Ştefan; Mehrshad, Maliheh
- Microbiome, Vol. 8, Issue 1
Virophages of Giant Viruses: An Update at Eleven
journal, August 2019
- Mougari, Said; Sahmi-Bounsiar, Dehia; Levasseur, Anthony
- Viruses, Vol. 11, Issue 8
Phage-specific metabolic reprogramming of virocells
journal, January 2020
- Howard-Varona, Cristina; Lindback, Morgan M.; Bastien, G. Eric
- The ISME Journal, Vol. 14, Issue 4
Prokaryotic and viral community structure in the singular chaotropic salt lake Salar de Uyuni
journal, February 2019
- Ramos‐Barbero, María Dolores; Martínez, José M.; Almansa, Cristina
- Environmental Microbiology, Vol. 21, Issue 6
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