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Nature. 2020 Feb;578(7795):425-431. doi: 10.1038/s41586-020-2007-4. Epub 2020 Feb 12.

Clades of huge phages from across Earth's ecosystems.

Author information

1
Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA.
2
National Food Institute, Technical University of Denmark, Kongens Lyngby, Denmark.
3
Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA.
4
Nuclear Fuel Cycle Engineering Laboratories, Japan Atomic Energy Agency, Tokai-mura, Japan.
5
Department of Microbiology & Immunology, Stanford University, Stanford, CA, USA.
6
Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO, USA.
7
Department of Civil and Mineral Engineering, University of Toronto, Toronto, Ontario, Canada.
8
Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA.
9
DOE Joint Genome Institute, Berkeley, CA, USA.
10
Integrative Biology, University of California Berkeley, Berkeley, CA, USA.
11
School of Life Sciences, Sun Yat-Sen University, Guangzhou, China.
12
Centre for Bioprocess Engineering Research, University of Cape Town, Cape Town, South Africa.
13
Department of Surgery, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA.
14
Laboratoire Microorganismes: Génome et Environnement, Université Clermont Auvergne, CNRS, Clermont-Ferrand, France.
15
Institute of Structural and Molecular Biology, University College London, London, UK.
16
Innovative Genomics Institute, University of California Berkeley, Berkeley, CA, USA. jbanfield@berkeley.edu.
17
Earth and Planetary Science, University of California Berkeley, Berkeley, CA, USA. jbanfield@berkeley.edu.
18
Environmental Science, Policy and Management, University of California Berkeley, Berkeley, CA, USA. jbanfield@berkeley.edu.
19
School of Earth Sciences, University of Melbourne, Melbourne, Victoria, Australia. jbanfield@berkeley.edu.

Abstract

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems.

PMID:
32051592
DOI:
10.1038/s41586-020-2007-4

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