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Peer-reviewedCC BY-NC-NDNature Microbiology

Genomic catalogue of giant viruses reveals expanded diversity and functional potential

  • Yumary M. Vasquez1
  • Tiago Nardi2,3
  • Gbocho Masato Terasaki4,3
  • Petra K Byl5,3
  • Tomáš Brůna3
  • Juan C. Villada3
  • Miguel F. Romero6,3
  • Thomas Möck7
  • Timothy Yong James8
  • Katherine D. McMahon9
  • Rick Cavicchioli10
  • Steven Hallam11
18 more authors
  • Barbara Campbell12
  • Byron C. Crump13
  • Dana E. Hunt14
  • Karthik Anantharaman15
  • Holly M. Simon16
  • R. Michael McKay17
  • David A. Walsh18
  • Joan L. Slonczewski19
  • Konstantinos T. Konstantinidis20
  • David L. Valentine21
  • Neslihan Taş22
  • Pia H. Moisander23
  • Roland Hatzenpichler24
  • Matthew B. Sullivan25
  • Sean Crowe26,11
  • Nathan A. Ahlgren27
  • Tanja Woyke28,3
  • Frederik Schulz29
29 affiliations
  1. 1United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [email protected]
  2. 2Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
  3. 3United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  4. 4Department of Applied Mathematics, University of California, Merced, Merced, CA, USA
  5. 5School of Ocean and Earth Science and Technology, University of Hawai'i Mānoa, Honolulu, HI, USA
  6. 6Instituto de Biología, Universidad Nacional Autónoma de México, Mexico City, Mexico
  7. 7School of Environmental Sciences, University of East Anglia, Norwich, UK
  8. 8Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
  9. 9Departments of Civil and Environmental Engineering and Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
  10. 10School of Biotechnology and Biomolecular Sciences, UNSW Sydney, Sydney, New South Wales, Australia
  11. 11Department of Microbiology and Immunology, University of British Columbia, Vancouver, British Columbia, Canada
  12. 12Department of Biological Sciences, College of Science, Clemson University, Clemson, SC, USA
  13. 13College of Earth, Ocean, and Atmospheric Sciences, Oregon State University, Corvallis, OR, USA
  14. 14Microbial Ecology, Duke University, Durham, NC, USA
  15. 15Department of Bacteriology, University of Wisconsin-Madison, Madison, WI, USA
  16. 16Division of Environmental and Biomolecular Systems, Institute of Environmental Health, Oregon Health and Science University, Portland, OR, USA
  17. 17Great Lakes Institute for Environmental Research, University of Windsor, Windsor, Ontario, Canada
  18. 18Biology Department, Concordia University, Montreal, Quebec, Canada
  19. 19Department of Biology, Kenyon College, Gambier, OH, USA
  20. 20School of Civil and Environmental Engineering, Georgia Tech, Atlanta, GA, USA
  21. 21Department of Earth Science and Marine Science Institute, UC Santa Barbara, Santa Barbara, CA, USA
  22. 22Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
  23. 23Department of Biology and Department of Estuarine and Ocean Sciences, University of Massachusetts Dartmouth, Dartmouth, MA, USA
  24. 24Department of Chemistry and Biochemistry, Thermal Biology Institute, Montana State University, Bozeman, MT, USA
  25. 25College of Arts and Sciences and College of Engineering, Ohio State University, Columbus, OH, USA
  26. 26Department of Earth, Ocean and Atmospheric Sciences, University of British Columbia, Vancouver, British Columbia, Canada
  27. 27Lasry Center for Bioscience, Clark University, Worcester, MA, USA
  28. 28Life and Environmental Sciences, University of California, Merced, Merced, CA, USA
  29. 29United States Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA. [email protected]
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Abstract

Nucleocytoplasmic large DNA viruses (NCLDV) of the phyla Nucleocytoviricota and viruses of the newly proposed Duplodnaviria phylum, Mirusviricota , exhibit taxonomic richness which continues to expand due to metagenomic sequencing of Earth’s biomes. Giant viruses contain complex genomes encoding genes of both viral and cellular origin, representing a reservoir of unexplored biological functions with potential implications for ecology, evolution, and biotechnology. Here, we present the largest curated database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level clusters inferred from 18,727 genomes, originating from marine, freshwater, anthropogenic and terrestrial environments, a six-fold increase from the previous giant virus phylogenetic frameworks. Phylogenomics and relative evolutionary distance analysis revealed 712 novel genera, 13 previously unknown viral families and a new proposed order, tentatively named Mycodnavirales. We improved gene calling of 12% of giant virus genomes by accounting for alternative and custom genetic codes, enabling more accurate identification of protein-coding genes. Database mining uncovered endogenous viral elements in a broad spectrum of eukaryotes, spanning algae, fungi, and parasitic protists highlighting that giant virus integration is both widespread and evolutionarily persistent. Orthologous clustering of 2.5 million proteins identified 135,998 orthogroups representing comprehensive metabolic capabilities, such as enrichment of genes involved in aromatic compound degradation (commonly associated with bioremediation) in Algavirales genomes. Furthermore, we detected widespread biosynthetic gene clusters underpinning antimicrobial activity and antibiotic resistance, suggesting roles of giant viruses in host defense and in the dissemination of antibiotic resistance genes. Conversely, 67% of orthogroups have unknown functions, underscoring a substantial unexplored potential. This comprehensive publicly available database provides a critical resource for the giant virus research community and a foundation for uncovering virus-host interactions, exploring viral evolution, and identifying reservoirs for novel enzymes with the potential to advance biotechnological applications.

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Cite

BibTeXRIS
BibTeX
@article{vasquez2026genomic,
  title = {{Genomic catalogue of giant viruses reveals expanded diversity and functional potential}},
  author = {Yumary M. Vasquez and Tiago Nardi and Gbocho Masato Terasaki and Petra K Byl and Tomáš Brůna and Juan C. Villada and Miguel F. Romero and Thomas Möck and Timothy Yong James and Katherine D. McMahon and Rick Cavicchioli and Steven Hallam and Barbara Campbell and Byron C. Crump and Dana E. Hunt and Karthik Anantharaman and Holly M. Simon and R. Michael McKay and David A. Walsh and Joan L. Slonczewski and Konstantinos T. Konstantinidis and David L. Valentine and Neslihan Taş and Pia H. Moisander and Roland Hatzenpichler and Matthew B. Sullivan and Sean Crowe and Nathan A. Ahlgren and Tanja Woyke and Frederik Schulz},
  journal = {Nature Microbiology},
  year = {2026},
  month = aug,
  doi = {10.1038/s41564-026-02435-y},
  url = {https://doi.org/10.1038/s41564-026-02435-y},
  note = {CC BY-NC-ND},
}
RIS
TY  - JOUR
TI  - Genomic catalogue of giant viruses reveals expanded diversity and functional potential
AU  - Yumary M. Vasquez
AU  - Tiago Nardi
AU  - Gbocho Masato Terasaki
AU  - Petra K Byl
AU  - Tomáš Brůna
AU  - Juan C. Villada
AU  - Miguel F. Romero
AU  - Thomas Möck
AU  - Timothy Yong James
AU  - Katherine D. McMahon
AU  - Rick Cavicchioli
AU  - Steven Hallam
AU  - Barbara Campbell
AU  - Byron C. Crump
AU  - Dana E. Hunt
AU  - Karthik Anantharaman
AU  - Holly M. Simon
AU  - R. Michael McKay
AU  - David A. Walsh
AU  - Joan L. Slonczewski
AU  - Konstantinos T. Konstantinidis
AU  - David L. Valentine
AU  - Neslihan Taş
AU  - Pia H. Moisander
AU  - Roland Hatzenpichler
AU  - Matthew B. Sullivan
AU  - Sean Crowe
AU  - Nathan A. Ahlgren
AU  - Tanja Woyke
AU  - Frederik Schulz
PY  - 2026
DA  - 2026/08/13
JO  - Nature Microbiology
DO  - 10.1038/s41564-026-02435-y
UR  - https://doi.org/10.1038/s41564-026-02435-y
AB  - Nucleocytoplasmic large DNA viruses (NCLDV) of the phyla Nucleocytoviricota and viruses of the newly proposed Duplodnaviria phylum, Mirusviricota , exhibit taxonomic richness which continues to expand due to metagenomic sequencing of Earth’s biomes. Giant viruses contain complex genomes encoding genes of both viral and cellular origin, representing a reservoir of unexplored biological functions with potential implications for ecology, evolution, and biotechnology. Here, we present the largest curated database of giant virus metagenome-assembled genomes (GVMAGs V2), comprising 8,508 species-level clusters inferred from 18,727 genomes, originating from marine, freshwater, anthropogenic and terrestrial environments, a six-fold increase from the previous giant virus phylogenetic frameworks. Phylogenomics and relative evolutionary distance analysis revealed 712 novel genera, 13 previously unknown viral families and a new proposed order, tentatively named Mycodnavirales. We improved gene calling of 12% of giant virus genomes by accounting for alternative and custom genetic codes, enabling more accurate identification of protein-coding genes. Database mining uncovered endogenous viral elements in a broad spectrum of eukaryotes, spanning algae, fungi, and parasitic protists highlighting that giant virus integration is both widespread and evolutionarily persistent. Orthologous clustering of 2.5 million proteins identified 135,998 orthogroups representing comprehensive metabolic capabilities, such as enrichment of genes involved in aromatic compound degradation (commonly associated with bioremediation) in Algavirales genomes. Furthermore, we detected widespread biosynthetic gene clusters underpinning antimicrobial activity and antibiotic resistance, suggesting roles of giant viruses in host defense and in the dissemination of antibiotic resistance genes. Conversely, 67% of orthogroups have unknown functions, underscoring a substantial unexplored potential. This comprehensive publicly available database provides a critical resource for the giant virus research community and a foundation for uncovering virus-host interactions, exploring viral evolution, and identifying reservoirs for novel enzymes with the potential to advance biotechnological applications.
SN  - 2058-5276
ER  -