Spang, A. et al. Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature 521, 173–179 (2015).
Google Scholar
Zaremba-Niedzwiedzka, K. et al. Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature 541, 353–358 (2017).
Google Scholar
Eme, L., Spang, A., Lombard, J., Stairs, C. W. & Ettema, T. J. G. Archaea and the origin of eukaryotes. Nat. Rev. Microbiol. 15, 711–723 (2017).
Google Scholar
Baker, B. J. et al. Diversity, ecology and evolution of Archaea. Nat. Microbiol. 5, 887–900 (2020).
Google Scholar
Imachi, H. et al. Isolation of an archaeon at the prokaryote–eukaryote interface. Nature 577, 519–525 (2020).
Google Scholar
Spang, A. et al. Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism. Nat. Microbiol. 4, 1138–1148 (2019).
Google Scholar
Bell, P. J. L. Evidence supporting a viral origin of the eukaryotic nucleus. Virus Res. 289, 198168 (2020).
Google Scholar
Forterre, P. & Gaïa, M. Giant viruses and the origin of modern eukaryotes. Curr. Opin. Microbiol. 31, 44–49 (2016).
Google Scholar
Chaikeeratisak, V. et al. Assembly of a nucleus-like structure during viral replication in bacteria. Science 355, 194–197 (2017).
Google Scholar
Malone, L. M. et al. 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, 48–55 (2020).
Google Scholar
Iyer, L. M., Aravind, L. & Koonin, E. V. Common origin of four diverse families of large eukaryotic DNA viruses. J. Virol. 75, 11720–11734 (2001).
Google Scholar
Krupovic, M., Dolja, V. V. & Koonin, E. V. The LUCA and its complex virome. Nat. Rev. Microbiol. 18, 661–670 (2020).
Google Scholar
Makarova, K. S. et al. Evolutionary classification of CRISPR-Cas systems: a burst of class 2 and derived variants. Nat. Rev. Microbiol. 18, 67–83 (2020).
Google Scholar
Dombrowski, N., Teske, A. P. & Baker, B. J. Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments. Nat. Commun. 9, 4999 (2018).
Google Scholar
Castelle, C. J. et al. Protein family content uncovers lineage relationships and bacterial pathway maintenance mechanisms in DPANN Archaea. Front. Microbiol. 12, 660052 (2021).
Google Scholar
Langwig, M. V. et al. Large-scale protein level comparison of Deltaproteobacteria reveals cohesive metabolic groups. ISME J. https://doi.org/10.1038/s41396-021-01057-y (2021).
Kieft, K., Zhou, Z. & Anantharaman, K. VIBRANT: automated recovery, annotation and curation of microbial viruses, and evaluation of viral community function from genomic sequences. Microbiome 8, 90 (2020).
Google Scholar
Prangishvili, D. et al. The enigmatic archaeal virosphere. Nat. Rev. Microbiol. 15, 724–739 (2017).
Google Scholar
Nayfach, S. et al. CheckV assesses the quality and completeness of metagenome-assembled viral genomes. Nat. Biotechnol. 39, 578–585 (2021).
Google Scholar
Kazlauskas, D., Krupovic, M. & Venclovas, Č. The logic of DNA replication in double-stranded DNA viruses: insights from global analysis of viral genomes. Nucleic Acids Res. 44, 4551–4564 (2016).
Google Scholar
Pons, J. C. et al. VPF-Class: Taxonomic assignment and host prediction of uncultivated viruses based on viral protein families. Bioinformatics https://doi.org/10.1093/bioinformatics/btab026 (2021).
Krupovic, M., Cvirkaite-Krupovic, V., Iranzo, J., Prangishvili, D. & Koonin, E. V. Viruses of archaea: structural, functional, environmental and evolutionary genomics. Virus Res. 244, 181–193 (2018).
Google Scholar
Yutin, N., Wolf, Y. I., Raoult, D. & Koonin, E. V. Eukaryotic large nucleo-cytoplasmic DNA viruses: clusters of orthologous genes and reconstruction of viral genome evolution. Virol. J. 6, 223 (2009).
Google Scholar
Koonin, E. V. & Dolja, V. V. Virus world as an evolutionary network of viruses and capsidless selfish elements. Microbiol. Mol. Biol. Rev. 78, 278–303 (2014).
Google Scholar
Iranzo, J., Koonin, E. V., Prangishvili, D., Krupovic, M. & Sandri-Goldin, R. M. Bipartite network analysis of the archaeal virosphere: evolutionary connections between viruses and capsidless mobile elements. J. Virol. 90, 11043–11055 (2016).
Google Scholar
Kala, S. et al. HNH proteins are a widespread component of phage DNA packaging machines. Proc. Natl Acad. Sci. USA 111, 6022–6027 (2014).
Google Scholar
Guilliam, T. A., Keen, B. A., Brissett, N. C. & Doherty, A. J. Primase-polymerases are a functionally diverse superfamily of replication and repair enzymes. Nucleic Acids Res. 43, 6651–6664 (2015).
Google Scholar
Gupta, A., Lad, S. B., Ghodke, P. P., Pradeepkumar, P. I. & Kondabagil, K. Mimivirus encodes a multifunctional primase with DNA/RNA polymerase, terminal transferase and translesion synthesis activities. Nucleic Acids Res. 47, 6932–6945 (2019).
Google Scholar
MacNeill, S. A. PCNA-binding proteins in the archaea: novel functionality beyond the conserved core. Curr. Genet. 62, 527–532 (2016).
Google Scholar
Mazzon, C. et al. Cytosolic and mitochondrial deoxyribonucleotidases: activity with substrate analogs, inhibitors and implications for therapy. Biochem. Pharmacol. 66, 471–479 (2003).
Google Scholar
Colson, P., La Scola, B., Levasseur, A., Caetano-Anollés, G. & Raoult, D. Mimivirus: leading the way in the discovery of giant viruses of amoebae. Nat. Rev. Microbiol. 15, 243–254 (2017).
Google Scholar
Doherty, A. J., Serpell, L. C. & Ponting, C. P. The helix-hairpin-helix DNA-binding motif: a structural basis for non-sequence-specific recognition of DNA. Nucleic Acids Res. 24, 2488–2497 (1996).
Google Scholar
Iyer, L. M., Balaji, S., Koonin, E. V. & Aravind, L. Evolutionary genomics of nucleo-cytoplasmic large DNA viruses. Virus Res. 117, 156–184 (2006).
Google Scholar
Sim, S., Hughes, K., Chen, X. & Wolin, S. L. The bacterial Ro60 protein and its noncoding Y RNA regulators. Annu. Rev. Microbiol. 74, 387–407 (2020).
Google Scholar
Ho, C. K., Wang, L. K., Lima, C. D. & Shuman, S. Structure and mechanism of RNA ligase. Structure 12, 327–339 (2004).
Google Scholar
Tang, Q., Wu, P., Chen, H. & Li, G. Pleiotropic roles of the ubiquitin-proteasome system during viral propagation. Life Sci. 207, 350–354 (2018).
Google Scholar
Murphy, J., Mahony, J., Ainsworth, S., Nauta, A. & van Sinderen, D. Bacteriophage orphan DNA methyltransferases: insights from their bacterial origin, function, and occurrence. Appl. Environ. Microbiol. 79, 7547–7555 (2013).
Google Scholar
Jeudy, S. et al. Exploration of the propagation of transpovirons within Mimiviridae reveals a unique example of commensalism in the viral world. ISME J. 14, 727–739 (2020).
Google Scholar
Agarkova, I. V., Dunigan, D. D. & Van Etten, J. L. Virion-associated restriction endonucleases of chloroviruses. J. Virol. 80, 8114–8123 (2006).
Google Scholar
Markine-Goriaynoff, N. et al. Glycosyltransferases encoded by viruses. J. Gen. Virol. 85, 2741–2754 (2004).
Google Scholar
Piacente, F., Gaglianone, M., Laugieri, M. E. & Tonetti, M. G. The autonomous glycosylation of large DNA viruses. Int. J. Mol. Sci. 16, 29315–29328 (2015).
Google Scholar
Hagelueken, G. et al. A coiled-coil domain acts as a molecular ruler to regulate O-antigen chain length in lipopolysaccharide. Nat. Struct. Mol. Biol. 22, 50–56 (2014).
Google Scholar
Tamarit, D. et al. A closed Candidatus Odinarchaeum chromosome exposes Asgard archaeal viruses. Nat. Microbiol. https://doi.org/10.1038/s41564-022-01122-y (2022).
Google Scholar
Medvedeva, S. et al. Three families of Asgard archaeal viruses identified in metagenome-assembled genomes. Nat. Microbiol. https://doi.org/10.1038/s41564-022-01144-6 (2022).
Google Scholar
Joshi, N.A. & Fass, J.N. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) [Software] (2011). https://github.com/najoshi/sickle
Peng, Y., Leung, H. C. M., Yiu, S. M. & Chin, F. Y. L. IDBA-UD: a de novo assembler for single-cell and metagenomic sequencing data with highly uneven depth. Bioinformatics 28, 1420–1428 (2012).
Google Scholar
Parks, D. H., Imelfort, M., Skennerton, C. T., Hugenholtz, P. & Tyson, G. W. CheckM: assessing the quality of microbial genomes recovered from isolates, single cells, and metagenomes. Genome Res. 25, 1043–1055 (2015).
Google Scholar
Alneberg, J. et al. Binning metagenomic contigs by coverage and composition. Nat. Methods 11, 1144–1146 (2014).
Google Scholar
Kang, D. D. et al. MetaBAT 2: an adaptive binning algorithm for robust and efficient genome reconstruction from metagenome assemblies. PeerJ 7, e7359 (2019).
Google Scholar
Sieber, C. M. K. et al. Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy. Nat. Microbiol. 3, 836–843 (2018).
Google Scholar
Chen, I.-M. A. et al. IMG/M v.5.0: an integrated data management and comparative analysis system for microbial genomes and microbiomes. Nucleic Acids Res. 47, D666–D677 (2019).
Google Scholar
Jones, P. et al. InterProScan 5: genome-scale protein function classification. Bioinformatics 30, 1236–1240 (2014).
Google Scholar
Biswas, A., Staals, R. H. J., Morales, S. E., Fineran, P. C. & Brown, C. M. CRISPRDetect: a flexible algorithm to define CRISPR arrays. BMC Genomics 17, 356 (2016).
Google Scholar
Fu, L., Niu, B., Zhu, Z., Wu, S. & Li, W. CD-HIT: accelerated for clustering the next-generation sequencing data. Bioinformatics 28, 3150–3152 (2012).
Google Scholar
Bland, C. et al. CRISPR recognition tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics 8, 209 (2007).
Google Scholar
Li, H. & Durbin, R. Fast and accurate short read alignment with Burrows-Wheeler transform. Bioinformatics 25, 1754–1760 (2009).
Google Scholar
Danecek, P. et al. Twelve years of SAMtools and BCFtools. Gigascience 10, giab008 (2021).
Google Scholar
Padilha, V. A., Alkhnbashi, O. S., Shah, S. A., de Carvalho, A. C. P. L. F. & Backofen, R. CRISPRcasIdentifier: machine learning for accurate identification and classification of CRISPR-Cas systems. Gigascience 9, giaa062 (2020).
Google Scholar
Makarova, K. S. et al. An updated evolutionary classification of CRISPR-Cas systems. Nat. Rev. Microbiol. 13, 722–736 (2015).
Google Scholar
Koonin, E. V., Makarova, K. S. & Zhang, F. Diversity, classification and evolution of CRISPR-Cas systems. Curr. Opin. Microbiol. 37, 67–78 (2017).
Google Scholar
Nethery, M. A. et al. CRISPRclassify: repeat-based classification of CRISPR loci. CRISPR J. 4, 558–574 (2021).
Google Scholar
Hyatt, D. et al. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11, 119 (2010).
Google Scholar
Aramaki, T. et al. KofamKOALA: KEGG Ortholog assignment based on profile HMM and adaptive score threshold. Bioinformatics 36, 2251–2252 (2019).
Google Scholar
El-Gebali, S. et al. The Pfam protein families database in 2019. Nucleic Acids Res. 47, D427–D432 (2019).
Google Scholar
Grazziotin, A. L., Koonin, E. V. & Kristensen, D. M. Prokaryotic virus orthologous groups (pVOGs): a resource for comparative genomics and protein family annotation. Nucleic Acids Res. 45, D491–D498 (2017).
Google Scholar
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
Google Scholar
Guo, J. et al. VirSorter2: a multi-classifier, expert-guided approach to detect diverse DNA and RNA viruses. Microbiome 9, 37 (2021).
Google Scholar
Camacho, C. et al. BLAST+: architecture and applications. BMC Bioinformatics 10, 421 (2009).
Google Scholar
Buchfink, B., Xie, C. & Huson, D. H. Fast and sensitive protein alignment using DIAMOND. Nat. Methods 12, 59–60 (2014).
Google Scholar
Schulz, F. et al. Giant virus diversity and host interactions through global metagenomics. Nature 578, 432–436 (2020).
Google Scholar
Cantu, V. A. et al. PhANNs, a fast and accurate tool and web server to classify phage structural proteins. PloS Comput. Biol. 16, e1007845 (2020).
Google Scholar
Zimmermann, L. et al. A completely reimplemented MPI bioinformatics toolkit with a new HHpred server at its core. J. Mol. Biol. 430, 2237–2243 (2018).
Google Scholar
Grant, J. R. & Stothard, P. The CGView server: a comparative genomics tool for circular genomes. Nucleic Acids Res. 36, W181–W184 (2008).
Google Scholar
Bin Jang, H. et al. Taxonomic assignment of uncultivated prokaryotic virus genomes is enabled by gene-sharing networks. Nat. Biotechnol. 37, 632–639 (2019).
Google Scholar
Nepusz, T., Yu, H. & Paccanaro, A. Detecting overlapping protein complexes in protein-protein interaction networks. Nat. Methods 9, 471–472 (2012).
Google Scholar
Enright, A. J., Van Dongen, S. & Ouzounis, C. A. An efficient algorithm for large-scale detection of protein families. Nucleic Acids Res. 30, 1575–1584 (2002).
Google Scholar
Sayers, E. W. et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res. 37, D5–D15 (2009).
Google Scholar
Al-Shayeb, B. et al. Clades of huge phages from across Earth’s ecosystems. Nature 578, 425–431 (2020).
Google Scholar
Shannon, P. et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 13, 2498–2504 (2003).
Google Scholar
RStudio: Integrated Development Environment for R (RStudio Team, 2019).
R: A Language and Environment for Statistical Computing (R Core Team, 2020).
Rudis, B. & Gandy, D. waffle: create waffle chart visualizations in R (2016).
Yutin, N., Wolf, Y. I. & Koonin, E. V. Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. Virology 466-467, 38–52 (2014).
Google Scholar
Paez-Espino, D. et al. IMG/VR: a database of cultured and uncultured DNA viruses and retroviruses. Nucleic Acids Res. 45, D457–D465 (2017).
Google Scholar
Wu, F. et al. Unique mobile elements and scalable gene flow at the prokaryote–eukaryote boundary revealed by circularized Asgard archaea genomes. Nat. Microbiol. 7, 200–212 (2022).
Google Scholar
Andersson, A. F. & Banfield, J. F. Virus population dynamics and acquired virus resistance in natural microbial communities. Science 320, 1047–1050 (2008).
Google Scholar
De Anda, V. et al. Understanding the mechanisms behind the response to environmental perturbation in microbial mats: a metagenomic-network based approach. Front. Microbiol. 9, 2606 (2018).
Google Scholar
Zhang, R. et al. SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics 37, 3364–3366 (2021).
Google Scholar
Guglielmini, J., Woo, A. C., Krupovic, M., Forterre, P. & Gaia, M. Diversification of giant and large eukaryotic dsDNA viruses predated the origin of modern eukaryotes. Proc. Natl Acad. Sci. USA 116, 19585–19592 (2019).
Google Scholar
Katoh, K. & Standley, D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol. Biol. Evol. 30, 772–780 (2013).
Google Scholar
Minh, B. Q. et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol. Biol. Evol. 37, 1530–1534 (2020).
Google Scholar
Kalyaanamoorthy, S., Minh, B. Q., Wong, T. K. F., von Haeseler, A. & Jermiin, L. S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat. Methods 14, 587–589 (2017).
Google Scholar
Edgar, R. C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 32, 1792–1797 (2004).
Google Scholar
Letunic, I. & Bork, P. Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
Google Scholar
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