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Cited by 7Bacteriophages and microbial interactionsCRISPR and Genetic EngineeringPlant and Fungal Interactions Research

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Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components

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Duan, Changhai, Liu, Yang, Liu, Ying, Liu, Lirui, Cai, Mingwei, Zhang, Rui, Zeng, Qinglu, Koonin, Eugene V, Krupovic, Mart, Li, Meng·2024·ISME Communications
DOI 10.1093/ismeco/ycad011PMC PMC10848311

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Abstract

Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family “Fuxiviridae” harbor an atypical Type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family “Chiyouviridae” encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.

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Research works printed but not linked: 114

  1. Inagaki, 2006, Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean margin, Proc Natl Acad Sci U S A, 103, 2815, 10.1073/pnas.0511033103 · DOI
  2. Kubo, 2012, Archaea of the miscellaneous Crenarchaeotal group are abundant, diverse and widespread in marine sediments, ISME J, 6, 1949, 10.1038/ismej.2012.37 · DOI
  3. Lloyd, 2013, Predominant archaea in marine sediments degrade detrital proteins, Nature, 496, 215, 10.1038/nature12033 · DOI
  4. Lazar, 2015, Environmental controls on intragroup diversity of the uncultured benthic archaea of the miscellaneous Crenarchaeotal group lineage naturally enriched in anoxic sediments of the White Oak River estuary (North Carolina, USA), Environ Microbiol, 17, 2228, 10.1111/1462-2920.12659 · DOI
  5. Zhou, 2018, Bathyarchaeota: globally distributed metabolic generalists in anoxic environments, FEMS Microbiol Rev, 42, 639, 10.1093/femsre/fuy023 · DOI
  6. Fillol, 2016, Insights in the ecology and evolutionary history of the miscellaneous Crenarchaeotic group lineage, ISME J, 10, 665, 10.1038/ismej.2015.143 · DOI
  7. He, 2016, Genomic and enzymatic evidence for acetogenesis among multiple lineages of the archaeal phylum Bathyarchaeota widespread in marine sediments, Nat Microbiol, 1, 16035, 10.1038/nmicrobiol.2016.35 · DOI
  8. Evans, 2015, Methane metabolism in the archaeal phylum Bathyarchaeota revealed by genome-centric metagenomics, Science, 350, 434, 10.1126/science.aac7745 · DOI
  9. Pan, 2020, Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota, Microbiome, 8, 43, 10.1186/s40168-020-00820-1 · DOI
  10. Qi, 2021, Comparative genomics reveals thermal adaptation and a high metabolic diversity in “Candidatus Bathyarchaeia”, mSystems, 6, e00252, 10.1128/mSystems.00252-21 · DOI
  11. Yu, 2018, Growth of sedimentary Bathyarchaeota on lignin as an energy source, Proc Natl Acad Sci U S A, 115, 6022, 10.1073/pnas.1718854115 · DOI
  12. Zhou, 2019, Genomic and transcriptomic insights into the ecology and metabolism of benthic archaeal cosmopolitan, Thermoprofundales (MBG-D archaea), ISME J, 13, 885, 10.1038/s41396-018-0321-8 · DOI
  13. Chevallereau, 2022, Interactions between bacterial and phage communities in natural environments, Nat Rev Microbiol, 20, 49, 10.1038/s41579-021-00602-y · DOI
  14. López-García, 2023, Metagenome-derived virus-microbe ratios across ecosystems, ISME J, 17, 1552, 10.1038/s41396-023-01431-y · DOI
  15. Jiao, 2010, Microbial production of recalcitrant dissolved organic matter: long-term carbon storage in the global ocean, Nat Rev Microbiol, 8, 593, 10.1038/nrmicro2386 · DOI · Paper page
  16. Brussaard, 2008, Global-scale processes with a nanoscale drive: the role of marine viruses, ISME J, 2, 575, 10.1038/ismej.2008.31 · DOI
  17. Fang, 2019, Transcriptomic responses of the marine cyanobacterium Prochlorococcus to viral lysis products, Environ Microbiol, 21, 2015, 10.1111/1462-2920.14513 · DOI
  18. Xiao, 2021, Viral lysis alters the optical properties and biological availability of dissolved organic matter derived from Prochlorococcus Picocyanobacteria, Appl Environ Microbiol, 87, 10.1128/AEM.02271-20 · DOI
  19. Koonin, 2009, CRISPR-Cas: an adaptive immunity system in prokaryotes, F1000 Biol Rep, 1, 95, 10.3410/B1-95 · DOI
  20. Barrangou, 2007, CRISPR provides acquired resistance against viruses in prokaryotes, Science, 315, 1709, 10.1126/science.1138140 · DOI · Paper page
  21. Dion, 2021, Streamlining CRISPR spacer-based bacterial host predictions to decipher the viral dark matter, Nucleic Acids Res, 49, 3127, 10.1093/nar/gkab133 · DOI
  22. Pawluk, 2018, Anti-CRISPR: discovery, mechanism and function, Nat Rev Microbiol, 16, 12, 10.1038/nrmicro.2017.120 · DOI
  23. Mendoza, 2020, A bacteriophage nucleus-like compartment shields DNA from CRISPR nucleases, Nature, 577, 244, 10.1038/s41586-019-1786-y · DOI
  24. Malone, 2020, A jumbo phage that forms a nucleus-like structure evades CRISPR–Cas DNA targeting but is vulnerable to type III RNA-based immunity, Nat Microbiol, 5, 48, 10.1038/s41564-019-0612-5 · DOI
  25. Borges, 2017, The discovery, mechanisms, and evolutionary impact of anti-CRISPRs, Annu Rev Virol, 4, 37, 10.1146/annurev-virology-101416-041616 · DOI
  26. Marino, 2020, Anti-CRISPR protein applications: natural brakes for CRISPR-Cas technologies, Nat Methods, 17, 471, 10.1038/s41592-020-0771-6 · DOI
  27. Bondy-Denomy, 2015, Multiple mechanisms for CRISPR–Cas inhibition by anti-CRISPR proteins, Nature, 526, 136, 10.1038/nature15254 · DOI
  28. Jia, 2021, Structure-based functional mechanisms and biotechnology applications of anti-CRISPR proteins, Nat Rev Mol Cell Biol, 22, 563, 10.1038/s41580-021-00371-9 · DOI
  29. Athukoralage, 2020, An anti-CRISPR viral ring nuclease subverts type III CRISPR immunity, Nature, 577, 572, 10.1038/s41586-019-1909-5 · DOI
  30. Prangishvili, 2017, The enigmatic archaeal virosphere, Nat Rev Microbiol, 15, 724, 10.1038/nrmicro.2017.125 · DOI
  31. Snyder, 2015, 40 years of archaeal virology: expanding viral diversity, Virology, 479-480, 369, 10.1016/j.virol.2015.03.031 · DOI
  32. Luk, 2014, Viruses of haloarchaea, Life, 4, 681, 10.3390/life4040681 · DOI
  33. Atanasova, 2016, Virus-host interplay in high salt environments, Environ Microbiol Rep, 8, 431, 10.1111/1758-2229.12385 · DOI
  34. Krupovic, 2018, Viruses of archaea: structural, functional, environmental and evolutionary genomics, Virus Res, 244, 181, 10.1016/j.virusres.2017.11.025 · DOI
  35. Medvedeva, 2022, Three families of Asgard archaeal viruses identified in metagenome-assembled genomes, Nat Microbiol, 7, 962, 10.1038/s41564-022-01144-6 · DOI
  36. Rambo, 2022, Genomes of six viruses that infect Asgard archaea from deep-sea sediments, Nat Microbiol, 7, 953, 10.1038/s41564-022-01150-8 · DOI
  37. Tamarit, 2022, A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses, Nat Microbiol, 7, 948, 10.1038/s41564-022-01122-y · DOI
  38. Medvedeva, 2023, A compendium of viruses from methanogenic archaea reveals their diversity and adaptations to the gut environment, Nat Microbiol, 8, 2170, 10.1038/s41564-023-01485-w · DOI
  39. Laso-Pérez, 2023, Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome, Nat Microbiol, 8, 231, 10.1038/s41564-022-01297-4 · DOI · Paper page
  40. Zhou, 2023, Diverse viruses of marine archaea discovered using metagenomics, Environ Microbiol, 25, 367, 10.1111/1462-2920.16287 · DOI
  41. López-Pérez, 2019, Novel Caudovirales associated with marine group I Thaumarchaeota assembled from metagenomes, Environ Microbiol, 21, 1980, 10.1111/1462-2920.14462 · DOI
  42. Kim, 2019, Spindle-shaped viruses infect marine ammonia-oxidizing thaumarchaea, Proc Natl Acad Sci U S A, 116, 15645, 10.1073/pnas.1905682116 · DOI
  43. Ahlgren, 2019, Discovery of several novel, widespread, and ecologically distinct marine Thaumarchaeota viruses that encode amoC nitrification genes, ISME J, 13, 618, 10.1038/s41396-018-0289-4 · DOI
  44. Philosof, 2017, Novel abundant oceanic viruses of uncultured marine group II Euryarchaeota, Curr Biol, 27, 1362, 10.1016/j.cub.2017.03.052 · DOI
  45. Nigro, 2017, Viruses in the oceanic basement, mBio, 8, 10.1128/mBio.02129-16 · DOI
  46. Yi, 2023, A systematic analysis of marine lysogens and proviruses, Nat Commun, 14, 6013, 10.1038/s41467-023-41699-4 · DOI
  47. Krupovic, 2020, The LUCA and its complex virome, Nat. Rev. Microbiol., 18, 661, 10.1038/s41579-020-0408-x · DOI
  48. Li, 2021, Deep sea sediments associated with cold seeps are a subsurface reservoir of viral diversity, ISME J, 15, 2366, 10.1038/s41396-021-00932-y · DOI
  49. Yin, 2021, Subgroup level differences of physiological activities in marine Lokiarchaeota, ISME J, 15, 848, 10.1038/s41396-020-00818-5 · DOI
  50. Hou, 2023, Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early earth surface environment, Sci Adv, 9, eadf5069, 10.1126/sciadv.adf5069 · DOI
  51. Roux, 2021, IMG/VR v3: an integrated ecological and evolutionary framework for interrogating genomes of uncultivated viruses, Nucleic Acids Res, 49, D764, 10.1093/nar/gkaa946 · DOI
  52. Koonin, 2021, Viruses defined by the position of the virosphere within the replicator space, Microbiol Mol Biol Rev, 85, e0019320, 10.1128/MMBR.00193-20 · DOI
  53. Bin Jang, 2019, Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks, Nat Biotechnol, 37, 632, 10.1038/s41587-019-0100-8 · DOI
  54. Krupovic, 2021, Adnaviria: a new realm for archaeal filamentous viruses with linear A-form double-stranded DNA genomes, J Virol, 95, e0067321, 10.1128/JVI.00673-21 · DOI
  55. Liu, 2021, Diversity, taxonomy, and evolution of archaeal viruses of the class Caudoviricetes, PLoS Biol, 19, e3001442, 10.1371/journal.pbio.3001442 · DOI · Paper page
  56. Sheppard, 2017, Structure and mechanisms of viral transcription factors in archaea, Extremophiles, 21, 829, 10.1007/s00792-017-0951-1 · DOI
  57. Kazlauskas, 2016, The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes, Nucleic Acids Res, 44, 4551, 10.1093/nar/gkw322 · DOI
  58. Brosius, 1978, Primary structure of protein L19 from the large subunit of Escherichia coli ribosomes, Biochemistry, 17, 508, 10.1021/bi00596a021 · DOI
  59. Mizuno, 2019, Numerous cultivated and uncultivated viruses encode ribosomal proteins, Nat Commun, 10, 752, 10.1038/s41467-019-08672-6 · DOI
  60. Wang, 2022, Spindle-shaped archaeal viruses evolved from rod-shaped ancestors to package a larger genome, Cell, 185, 1297, 10.1016/j.cell.2022.02.019 · DOI
  61. Quemin Emmanuelle, 2015, Sulfolobus spindle-shaped virus 1 contains glycosylated capsid proteins, a cellular chromatin protein, and host-derived lipids, J Virol, 89, 11681, 10.1128/JVI.02270-15 · DOI
  62. Zhan, 2015, Site-specific recombination by SSV2 integrase: substrate requirement and domain functions, J Virol, 89, 10934, 10.1128/JVI.01637-15 · DOI
  63. Khomyakova, 2023, Phenotypic and genomic characterization of Bathyarchaeum tardum gen. nov., sp. nov., a cultivated representative of the archaeal class Bathyarchaeia, Front Microbiol, 14, 10.3389/fmicb.2023.1214631 · DOI
  64. Baquero, 2020, New virus isolates from Italian hydrothermal environments underscore the biogeographic pattern in archaeal virus communities, ISME J, 14, 1821, 10.1038/s41396-020-0653-z · DOI
  65. Wang, 2020, Structures of filamentous viruses infecting hyperthermophilic archaea explain DNA stabilization in extreme environments, Proc Natl Acad Sci U S A, 117, 19643, 10.1073/pnas.2011125117 · DOI
  66. Quemin, 2013, First insights into the entry process of hyperthermophilic archaeal viruses, J Virol, 87, 13379, 10.1128/JVI.02742-13 · DOI
  67. Prangishvili, 2013, Genomics and biology of Rudiviruses, a model for the study of virus-host interactions in archaea, Biochem Soc Trans, 41, 443, 10.1042/BST20120313 · DOI
  68. Baquero, 2020, Structure and assembly of archaeal viruses, Adv Virus Res, 108, 127, 10.1016/bs.aivir.2020.09.004 · DOI
  69. Pinilla-Redondo, 2020, Type IV CRISPR–Cas systems are highly diverse and involved in competition between plasmids, Nucleic Acids Res, 48, 2000, 10.1093/nar/gkz1197 · DOI
  70. Faure, 2019, CRISPR–Cas in mobile genetic elements: counter-defence and beyond, Nat Rev Microbiol, 17, 513, 10.1038/s41579-019-0204-7 · DOI
  71. Moya-Beltrán, 2021, Evolution of type IV CRISPR-Cas systems: insights from CRISPR loci in integrative conjugative elements of Acidithiobacillia, Crispr J, 4, 656, 10.1089/crispr.2021.0051 · DOI
  72. Al-Shayeb, 2022, Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors, Cell, 185, 4574, 10.1016/j.cell.2022.10.020 · DOI
  73. Zhou, 2021, Structure of a type IV CRISPR-Cas ribonucleoprotein complex, iScience, 24, 102201, 10.1016/j.isci.2021.102201 · DOI
  74. Medvedeva, 2019, Virus-borne mini-CRISPR arrays are involved in interviral conflicts, Nat Commun, 10, 5204, 10.1038/s41467-019-13205-2 · DOI
  75. Shiimori, 2018, Cas4 nucleases define the PAM, length, and orientation of DNA fragments integrated at CRISPR loci, Mol Cell, 70, 814, 10.1016/j.molcel.2018.05.002 · DOI
  76. Hudaiberdiev, 2017, Phylogenomics of Cas4 family nucleases, BMC Evol Biol, 17, 232, 10.1186/s12862-017-1081-1 · DOI
  77. Zhang, 2019, Cas4 nucleases can effect specific integration of CRISPR spacers, J Bacteriol, 201, 10.1128/JB.00747-18 · DOI
  78. Guo, 2015, Functional characterization of a conserved archaeal viral operon revealing single-stranded DNA binding, annealing and nuclease activities, J Mol Biol, 427, 2179, 10.1016/j.jmb.2015.03.013 · DOI
  79. Wandera, 2022, Anti-CRISPR prediction using deep learning reveals an inhibitor of Cas13b nucleases, Mol Cell, 82, 2714, 10.1016/j.molcel.2022.05.003 · DOI
  80. Yang, 2022, Insights into the inhibition of type I-F CRISPR-Cas system by a multifunctional anti-CRISPR protein AcrIF24, Nat Commun, 13, 1931, 10.1038/s41467-022-29581-1 · DOI
  81. Parks, 2022, GTDB: an ongoing census of bacterial and archaeal diversity through a phylogenetically consistent, rank normalized and complete genome-based taxonomy, Nucleic Acids Res, 50, D785, 10.1093/nar/gkab776 · DOI · Paper page
  82. Chaumeil, 2022, GTDB-Tk v2: memory friendly classification with the genome taxonomy database, Bioinformatics, 38, 5315, 10.1093/bioinformatics/btac672 · DOI
  83. Rozewicki, 2019, MAFFT-DASH: integrated protein sequence and structural alignment, Nucleic Acids Res, 47, W5
  84. Capella-Gutierrez, 2009, trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses, Bioinformatics, 25, 1972, 10.1093/bioinformatics/btp348 · DOI
  85. Minh, 2020, IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era, Mol Biol Evol, 37, 1530, 10.1093/molbev/msaa015 · DOI · Paper page
  86. Parks, 2015, CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes, Genome Res, 25, 1043, 10.1101/gr.186072.114 · DOI · Paper page
  87. Chan, 2019, tRNAscan-SE: searching for tRNA genes in genomic sequences, Methods Mol Biol, 1962, 1, 10.1007/978-1-4939-9173-0_1 · DOI
  88. Parks, 2018, A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life, Nat Biotechnol, 36, 996, 10.1038/nbt.4229 · DOI · Paper page
  89. Payne, 2021, Identification and classification of antiviral defence systems in bacteria and archaea with PADLOC reveals new system types, Nucleic Acids Res, 49, 10868, 10.1093/nar/gkab883 · DOI
  90. Tesson, 2022, Systematic and quantitative view of the antiviral arsenal of prokaryotes, Nat Commun, 13, 2561, 10.1038/s41467-022-30269-9 · DOI
  91. Russel, 2020, CRISPRCasTyper: automated identification, annotation, and classification of CRISPR-Cas loci, CRISPR J, 3, 462, 10.1089/crispr.2020.0059 · DOI
  92. Bland, 2007, CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics, 8, 209, 10.1186/1471-2105-8-209 · DOI
  93. Buchfink, 2015, Fast and sensitive protein alignment using DIAMOND, Nat Methods, 12, 59, 10.1038/nmeth.3176 · DOI · Paper page
  94. Camacho, 2009, BLAST+: architecture and applications, BMC Bioinformatics, 10, 421, 10.1186/1471-2105-10-421 · DOI · Paper page
  95. Guo, 2021, VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses, Microbiome, 9, 37, 10.1186/s40168-020-00990-y · DOI
  96. Nayfach, 2021, CheckV assesses the quality and completeness of metagenome-assembled viral genomes, Nat Biotechnol, 39, 578, 10.1038/s41587-020-00774-7 · DOI
  97. Seemann, 2014, Prokka: rapid prokaryotic genome annotation, Bioinformatics, 30, 2068, 10.1093/bioinformatics/btu153 · DOI
  98. Shaffer, 2020, DRAM for distilling microbial metabolism to automate the curation of microbiome function, Nucleic Acids Res, 48, 8883, 10.1093/nar/gkaa621 · DOI
  99. Steinegger, 2019, HH-suite3 for fast remote homology detection and deep protein annotation, BMC Bioinformatics, 20, 473, 10.1186/s12859-019-3019-7 · DOI · Paper page
  100. Grant, 2023, Proksee: in-depth characterization and visualization of bacterial genomes, Nucleic Acids Res, 51, W484, 10.1093/nar/gkad326 · DOI
  101. Shannon, 2003, Cytoscape: a software environment for integrated models of biomolecular interaction networks, Genome Res, 13, 2498, 10.1101/gr.1239303 · DOI · Paper page
  102. Nishimura, 2017, ViPTree: the viral proteomic tree server, Bioinformatics, 33, 2379, 10.1093/bioinformatics/btx157 · DOI
  103. Meier-Kolthoff, 2017, VICTOR: genome-based phylogeny and classification of prokaryotic viruses, Bioinformatics, 33, 3396, 10.1093/bioinformatics/btx440 · DOI
  104. Mirdita, 2022, ColabFold: making protein folding accessible to all, Nat Methods, 19, 679, 10.1038/s41592-022-01488-1 · DOI · Paper page
  105. Hatcher, 2017, Virus variation resource - improved response to emergent viral outbreaks, Nucleic Acids Res, 45, D482, 10.1093/nar/gkw1065 · DOI
  106. Edgar, 2004, MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Res, 32, 1792, 10.1093/nar/gkh340 · DOI · Paper page
  107. Kalyaanamoorthy, 2017, ModelFinder: fast model selection for accurate phylogenetic estimates, Nat Methods, 14, 587, 10.1038/nmeth.4285 · DOI · Paper page
  108. Xie, 2023, Tree visualization by one table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees, Nucleic Acids Res, 51, W587, 10.1093/nar/gkad359 · DOI
  109. Schmartz, 2022, PLSDB: advancing a comprehensive database of bacterial plasmids, Nucleic Acids Res, 50, D273, 10.1093/nar/gkab1111 · DOI
  110. Pourcel, 2020, CRISPRCasdb a successor of CRISPRdb containing CRISPR arrays and cas genes from complete genome sequences, and tools to download and query lists of repeats and spacers, Nucleic Acids Res, 48, D535
  111. Bondy-Denomy, 2018, A unified resource for tracking anti-CRISPR names, Crispr J, 1, 304, 10.1089/crispr.2018.0043 · DOI
  112. Zhang, 2005, TM-align: a protein structure alignment algorithm based on the TM-score, Nucleic Acids Res, 33, 2302, 10.1093/nar/gki524 · DOI · Paper page
  113. Ren, 2019, Phylogenomics suggests oxygen availability as a driving force in Thaumarchaeota evolution, ISME J, 13, 2150, 10.1038/s41396-019-0418-8 · DOI
  114. Dobson, 2015, CCTOP: a consensus constrained TOPology prediction web server, Nucleic Acids Res, 43, W408, 10.1093/nar/gkv451 · DOI

Metadata

Authors
Duan, C., Liu, Y., Liu, Y., Liu, L., Cai, M., Zhang, R., Zeng, Q., Koonin, E. V., Krupovic, M., & Li, M.
Affiliations
  • Shenzhen University (CN)
  • Institut Pasteur (FR)
  • Hong Kong University of Science and Technology (HK)
  • National Institutes of Health (US)
  • Institut Pasteur, Université Paris Cité , Archaeal Virology Unit, Paris 75015 , France
Corresponding author
Li, Meng
ORCID
Venue
ISME Communications
Publisher
Oxford University Press (OUP)
Published
2024-01-01
Volume
4
Issue
1
Pages
ycad011-ycad011
ISSN
2730-6151 (ISSN-L)
DOI
10.1093/ismeco/ycad011
PMC
PMC10848311
OpenAlex
W4390740627
Cited by
7
References
4
Citations by year
2026: 1 · 2025: 3 · 2024: 3
FWCI
1.91
Type
journal article
Language
en
Open access
Licence
Locations
  • ISME Communications (publishedVersion, cc-by)
  • bioRxiv (Cold Spring Harbor Laboratory) (acceptedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • PubMed Central (submittedVersion, cc-by-nc-nd)
  • Rare & Special e-Zone (The Hong Kong University of Science and Technology) (submittedVersion)
Funders
  • National Key Research and Development Program of China (2022YFA0912200)
  • National Natural Science Foundation of China (32225003, 92251306, 31970105)
  • Innovation Team Project of Universities in Guangdong Province (2020KCXTD023)
  • Shenzhen Science and Technology Program (JCYJ20200109105010363)
  • Shenzhen University 2035 Program for Excellent Research (2022B002)
  • Intramural Research Program of the National Insitutes of Health of the USA
Topics
  • Life Sciences › Immunology and Microbiology › Virology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Immunology and Microbiology › Virology › Plant and Fungal Interactions Research
Keywords
archaea, metagenome-assembled genomes, virus families, CRISPR-Cas, host defense evasion, virome

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