Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics View Full Text


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Article Info

DATE

2017-10-11

AUTHORS

Simon Roux, Leong-Keat Chan, Rob Egan, Rex R. Malmstrom, Katherine D. McMahon, Matthew B. Sullivan

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.Virophages are recently-identified small viruses that infect larger viruses, yet their diversity and ecological roles are poorly understood. Here, Roux and colleagues present time series metagenomics data revealing new virophage genera and their putative ecological interactions in two freshwater lakes. More... »

PAGES

858

References to SciGraph publications

  • 2004-02. Network biology: understanding the cell's functional organization in NATURE REVIEWS GENETICS
  • 2013-04-11. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2016-02-23. Correlation detection strategies in microbial data sets vary widely in sensitivity and precision in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2013-05-23. Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies in VIROLOGY JOURNAL
  • 2015-10-07. A classification system for virophages and satellite viruses in ARCHIVES OF VIROLOGY
  • 2013-11-07. Top-down controls on bacterial community structure: microbial network analysis of bacteria, T4-like viruses and protists in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2015-11-11. A novel group of diverse Polinton-like viruses discovered by metagenome analysis in BMC BIOLOGY
  • 2007-02-26. Minimus: a fast, lightweight genome assembler in BMC BIOINFORMATICS
  • 2008-08-06. The virophage as a unique parasite of the giant mimivirus in NATURE
  • 2016-01-15. Geographic patterns of co-occurrence network topological features for soil microbiota at continental scale in eastern China in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2012-03-04. Fast gapped-read alignment with Bowtie 2 in NATURE METHODS
  • 2008-12-29. WGCNA: an R package for weighted correlation network analysis in BMC BIOINFORMATICS
  • 2016-11-16. Genomic differentiation among wild cyanophages despite widespread horizontal gene transfer in BMC GENOMICS
  • 2016-02-10. Plankton networks driving carbon export in the oligotrophic ocean in NATURE
  • 2011-12-14. Extended local similarity analysis (eLSA) of microbial community and other time series data with replicates in BMC SYSTEMS BIOLOGY
  • 2015-06-02. Tritagonist as a new term for uncharacterised microorganisms in environmental systems in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2004-08-19. MUSCLE: a multiple sequence alignment method with reduced time and space complexity in BMC BIOINFORMATICS
  • 2015-04-25. A new family of hybrid virophages from an animal gut metagenome in BIOLOGY DIRECT
  • 2013-01-02. Alphaherpesvirinae and Gammaherpesvirinae glycoprotein L and CMV UL130 originate from chemokines in VIROLOGY JOURNAL
  • 2012-12-05. Genomic variation landscape of the human gut microbiome in NATURE
  • 2007-10-10. Population Dynamics and Diversity of Viruses, Bacteria and Phytoplankton in a Shallow Eutrophic Lake in MICROBIAL ECOLOGY
  • 2016-01-08. Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations in THE ISME JOURNAL: MULTIDISCIPLINARY JOURNAL OF MICROBIAL ECOLOGY
  • 2014-12-22. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution in NATURE REVIEWS MICROBIOLOGY
  • 2016-12-07. Host genome integration and giant virus-induced reactivation of the virophage mavirus in NATURE
  • 2012-01-03. GuiTope: an application for mapping random-sequence peptides to protein sequences in BMC BIOINFORMATICS
  • 2012-05-30. Molecular ecological network analyses in BMC BIOINFORMATICS
  • 2014-04-29. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses in BIOLOGY DIRECT
  • 2013-04-04. Mimiviridae: clusters of orthologous genes, reconstruction of gene repertoire evolution and proposed expansion of the giant virus family in VIROLOGY JOURNAL
  • 2012-12-22. Ray Meta: scalable de novo metagenome assembly and profiling in GENOME BIOLOGY
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    http://scigraph.springernature.com/pub.10.1038/s41467-017-01086-2

    DOI

    http://dx.doi.org/10.1038/s41467-017-01086-2

    DIMENSIONS

    https://app.dimensions.ai/details/publication/pub.1092102050

    PUBMED

    https://www.ncbi.nlm.nih.gov/pubmed/29021524


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