Orcutt B, D’Angelo T, Jungbluth SP, Huber JA, Sylvan JB. Microbial life in oceanic crust. OSF Preprints, 2020; https://doi.org/10.31219/osf.io/2wxe6.
Koonin EV. On the origin of cells and viruses: primordial virus world scenario. Ann NY Acad Sci. 2009;1178:47–64.
Nigro OD, Jungbluth SP, Lin HT, Hsieh CC, Miranda JA, Schvarcz CR, et al. Viruses in the oceanic basement. MBio. 2017;8:1–15.
Wheat CG, Jannasch HW, Kastner M, Hulme S, Cowen J, Edwards KJ, et al. Fluid sampling from oceanic borehole observatories: design and methods for CORK activities (1990–2010). 2011. In Fisher AT, Tsuji T, Petronotis K, and the Expedition 327 Scientists, Proc. IODP, 327: Tokyo (Integrated Ocean Drilling Program Management International, Inc.). https://doi.org/10.2204/iodp.proc.327.109.2011.
Koonin EV, Yutin N Evolution of the large nucleocytoplasmic DNA viruses of eukaryotes and convergent origins of viral gigantism. Advances in Virus Research. 2019. Elsevier, pp 167–202.
Koonin EV, Senkevich TG, Dolja VV. The ancient Virus World and evolution of cells. Biol Direct. 2006;1:29.
Shinn GL, Bullard BL. Ultrastructure of Meelsvirus: A nuclear virus of arrow worms (phylum Chaetognatha) producing giant “tailed” virions. PLoS One. 2018;13:e0203282.
Wilhelm SW, Bird JT, Bonifer KS, Calfee BC, Chen T, Coy SR, et al. A student’s guide to giant viruses infecting small eukaryotes: From Acanthamoeba to Zooxanthellae. Viruses. 2017;9:46–63.
Schulz F, Roux S, Paez-Espino D, Jungbluth S, Walsh DA, Denef VJ, et al. Giant virus diversity and host interactions through global metagenomics. Nature. 2020;578:432–6.
Google Scholar
Moniruzzaman M, Martinez-Gutierrez CA, Weinheimer AR, Aylward FO. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nat Commun. 2020;11:1–11.
Martínez Martínez J, Swan BK, Wilson WH. Marine viruses, a genetic reservoir revealed by targeted viromics. ISME J. 2014;8:1079–88.
Khalil JYB, Robert S, Reteno DG, Andreani J, Raoult D, La Scola B. High-throughput isolation of giant viruses in liquid medium using automated flow cytometry and fluorescence staining. Front Microbiol. 2016;7:1–9.
Wilson WH, Gilg IC, Moniruzzaman M, Field EK, Koren S, Lecleir GR, et al. Genomic exploration of individual giant ocean viruses. ISME J. 2017;11:1736–45.
Roux S, Chan LK, Egan R, Malmstrom RR, McMahon KD, Sullivan MB. Ecogenomics of virophages and their giant virus hosts assessed through time series metagenomics. Nat Commun. 2017;8:1–12.
Schulz F, Alteio L, Goudeau D, Blanchard J, Woyke T, Ryan EM, et al. Hidden diversity of soil giant viruses. Nat Commun. 2018;9:1–9.
Bäckström D, Yutin N, Jørgensen SL, Dharamshi J, Homa F, Zaremba-Niedwiedzka K, et al. Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism. mBio. 2019;10:e02497-18.
Martínez JM, Martinez-Hernandez F, Martinez-Garcia M. Single-virus genomics and beyond. Nat Rev Microbiol. 2020;18:705–16.
Schulz F, Yutin N, Ivanova NN, Ortega DR, Lee TK, Vierheilig J, et al. Giant viruses with an expanded complement of translation system components. Science (80-). 2017;356:82 LP–85.
Fisher A, Wheat CG, Becker K, Cowen J, Orcutt BN, Hulme SM, et al. Design, deployment, and status of borehole observatory systems used for single-hole and cross-hole experiments, IODP Expedition 327, eastern flank of Juan de Fuca Ridge. Proc Integr Ocean Drill Program; Juan Fuca Ridge flank Hydrogeol Exped 327 riserless Drill Platf from to Victoria, Br Columbia (Canada); Sites U1362, U1301, 1027, U1363; 5 July-5 Sept 2010. 2011;327:38.
Jungbluth SP, Grote J, Lin HT, Cowen JP, Rappé MS. Microbial diversity within basement fluids of the sediment-buried Juan de Fuca Ridge flank. ISME J. 2013;7:161–72.
Google Scholar
Jungbluth SP, Bowers RM, Lin HT, Cowen JP, Rappé MS. Novel microbial assemblages inhabiting crustal fluids within mid-ocean ridge flank subsurface basalt. ISME J. 2016;10:2033–47.
Google Scholar
Jungbluth SP, Amend JP, Rappé MS. Metagenome sequencing and 98 microbial genomes from Juan de Fuca Ridge flank subsurface fluids. Sci data. 2017;4:1–11.
Brussaard CPD. Optimization of procedures for counting viruses by flow cytometry. Appl Environ Microbiol. 2004;70:1506–13.
Google Scholar
Dean FB, Hosono S, Fang L, Wu X, Faruqi AF, Bray-Ward P, et al. Comprehensive human genome amplification using multiple displacement amplification. Proc Natl Acad Sci. 2002;99:5261–6.
Google Scholar
Labonté JM, Swan BK, Poulos B, Luo H, Koren S, Hallam SJ, et al. Single-cell genomics-based analysis of virus-host interactions in marine surface bacterioplankton. ISME J. 2015;9:2386–99.
Bolger AM, Lohse M, Usadel B. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics. 2014;30:2114–20.
Google Scholar
Bushnell B, Rood J. BBTools. Dep Energy Jt Genome Institute, Walnut Creek, CA 2014.
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19:455–77.
Google Scholar
Nurk S, Bankevich A, Antipov D, Gurevich AA, Korobeynikov A, Lapidus A, et al. Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol. 2013;20:714–37.
Google Scholar
Besemer J, Lomsadze A, Borodovsky M. GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions. Nucleic Acids Res. 2001;29:2607–18.
Google Scholar
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol. 1990;215:403–10.
Google Scholar
Goodacre N, Aljanahi A, Nandakumar S, Mikailov M, Khan AS, Delwart E, et al. A reference viral database (RVDB) to enhance bioinformatics analysis of high-throughput sequencing for novel virus detection. mSphere. 2018;3:e00069–18.
McGinnis S, Madden TL. BLAST: at the core of a powerful and diverse set of sequence analysis tools. Nucleic Acids Res. 2004;32:W20–W25.
Google Scholar
Sullivan MJ, Petty NK, Beatson SA. Easyfig: a genome comparison visualizer. Bioinformatics. 2011;27:1009–10.
Google Scholar
Johnson LS, Eddy SR, Portugaly E. Hidden Markov model speed heuristic and iterative HMM search procedure. BMC Bioinformatics. 2010;11:431.
Colson P, De Lamballerie X, Yutin N, Asgari S, Bigot Y, Bideshi DK, et al. “Megavirales”, a proposed new order for eukaryotic nucleocytoplasmic large DNA viruses. Arch Virol. 2013;158:2517–21.
Yutin N, Wolf YI, Raoult D, Koonin EV. Eukaryotic large nucleo-cytoplasmic DNA viruses: Clusters of orthologous genes and reconstruction of viral genome evolution. Virol J. 2009;6:1–13.
Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol. 2013;30:772–80.
Google Scholar
Capella-Gutiérrez S, Silla-Martínez JM, Gabaldón T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics. 2009;25:1972–3.
Nguyen L-T, Schmidt HA, von Haeseler A, Minh BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2014;32:268–74.
Price MN, Dehal PS, Arkin AP. FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol. 2009;26:1641–50.
Google Scholar
Kalyaanamoorthy S, Minh BQ, Wong TKF, Von Haeseler A, Jermiin LS. ModelFinder: fast model selection for accurate phylogenetic estimates. Nat Methods. 2017;14:587–9.
Google Scholar
Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun. 2018;9:1–8.
Guindon S, Dufayard JF, Lefort V, Anisimova M, Hordijk W, Gascuel O. New algorithms and methods to estimate maximum-likelihood phylogenies: Assessing the performance of PhyML 3.0. Syst Biol. 2010;59:307–21.
Google Scholar
Emms DM, Kelly S. OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy. Genome Biol. 2015;16:157.
Barrett P, Hunter J, Miller JT, Hsu J-C, Greenfield P matplotlib–A Portable Python Plotting Package. Astron. data Anal. Softw. Syst. XIV. 2005. p 91.
Lex A, Gehlenborg N, Strobelt H, Vuillemot R, Pfister H. UpSet: visualization of intersecting sets. IEEE Trans Vis Comput Graph. 2014;20:1983–92.
Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res. 1997;25:955.
Google Scholar
Laslett D, Canback B. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Nucleic Acids Res. 2004;32:11–16.
Google Scholar
Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol. 2018;35:1547.
Google Scholar
Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–7.
Google Scholar
Chen IMA, Markowitz VM, Chu K, Palaniappan K, Szeto E, Pillay M, et al. IMG/M: Integrated genome and metagenome comparative data analysis system. Nucleic Acids Res. 2017;45:D507–D516.
Google Scholar
Markowitz VM, Chen I-MA, Palaniappan K, Chu K, Szeto E, Grechkin Y, et al. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 2012;40:D115–D122.
Google Scholar
Quast C, Pruesse E, Yilmaz P, Gerken J, Schweer T, Yarza P, et al. The SILVA ribosomal RNA gene database project: improved data processing and web-based tools. Nucleic Acids Res. 2012;41:D590–D596.
Yutin N, Wolf YI, Koonin EV. Origin of giant viruses from smaller DNA viruses not from a fourth domain of cellular life. Virology. 2014;466–467:38–52.
Mihara T, Koyano H, Hingamp P, Grimsley N, Goto S, Ogata H Taxon richness of “Megaviridae” exceeds those of bacteria and archaea in the ocean. Microbes Environ. 2018; ME17203.
Gallot-Lavallée L, Blanc G. A glimpse of nucleo-cytoplasmic large DNA virus biodiversity through the eukaryotic genomics window. Viruses. 2017;9:17.
Aylward FO, Moniruzzaman M, Ha AD, Koonin EV. A phylogenomic framework for charting the diversity and evolution of giant viruses. PLOS Biol. 2021;19:e3001430.
Google Scholar
Andreani J, Verneau J, Raoult D, Levasseur A, La, Scola B. Deciphering viral presences: two novel partial giant viruses detected in marine metagenome and in a mine drainage metagenome. Virol J. 2018;15:66.
Koonin EV, Yutin N. Multiple evolutionary origins of giant viruses. F1000Research. 2018;7:1840.
Abrahao JS, Araujo R, Colson P, La, Scola B. The analysis of translation-related gene set boosts debates around origin and evolution of mimiviruses. PLoS Genet. 2017;13:e1006532.
Filée J, Chandler M. Gene exchange and the origin of giant viruses. Intervirology. 2010;53:354–61.
Koonin EV, Yutin N. Nucleo‐cytoplasmic large DNA viruses (NCLDV) of eukaryotes. eLS. 2012. https://doi.org/10.1002/9780470015902.a0023268.
Abergel C, Rudinger-Thirion J, Giegé R, Claverie J-M. Virus-encoded aminoacyl-tRNA synthetases: structural and functional characterization of mimivirus TyrRS and MetRS. J Virol. 2007;81:12406–17.
Google Scholar
Yoshihisa T. Handling tRNA introns, archaeal way and eukaryotic way. Front Genet. 2014;5:213.
Ivarsson M, Schnürer A, Bengtson S, Neubeck A. Anaerobic fungi: a potential source of biological H2 in the oceanic crust. Front Microbiol. 2016;7:1–8.
Ivarsson M, Bengtson S, Neubeck A. The igneous oceanic crust e Earth’ s largest fungal habitat? Fungal Ecol. 2016;20:249–55.
Quemener M, Mara P, Schubotz F, Beaudoin D, Li W, Pachiadaki M, et al. Meta‐omics highlights the diversity, activity and adaptations of fungi in deep oceanic crust. Environ Microbiol. 2020;22:3950–67.
Google Scholar
Drake H, Ivarsson M. The role of anaerobic fungi in fundamental biogeochemical cycles in the deep biosphere. Fungal Biol Rev. 2017;32:20–25.
Bengtson S, Rasmussen B, Ivarsson M, Muhling J, Broman C, Marone F, et al. Fungus-like mycelial fossils in 2.4-billion-year-old vesicular basalt. Nat Publ Gr. 2017;1:1–6.
Suzuki N. An introduction to fungal viruses. In Encyclopedia of Virology. Bamford DH, Zuckerman M. editors. 431–42. Oxford: Academic Press; 2021.
Ivarsson M, Broman C, Holmström SJM, Ahlbom M, Lindblom S, Holm NG. Putative fossilized fungi from the lithified volcaniclastic apron of Gran Canaria, Spain. Astrobiology. 2011;11:633–50.
Google Scholar
Bengtson S, Ivarsson M, Astolfo A, Belivanova V, Broman C, Marone F, et al. Deep‐biosphere consortium of fungi and prokaryotes in Eocene subseafloor basalts. Geobiology. 2014;12:489–96.
Google Scholar
Hirayama H, Abe M, Miyazaki J, Sakai S, Nagano Y, Takai K Data report: cultivation of microorganisms from basaltic rock and sediment cores from the North Pond on the western flank of the Mid-Atlantic Ridge, IODP Expedition 336 1. 2015; 336.
Ivarsson M, Bengtson S, Skogby H, Lazor P, Broman C A Fungal-Prokaryotic Consortium at the Basalt-Zeolite Interface in Subseafloor A Fungal-Prokaryotic Consortium at the Basalt-Zeolite Interface in Subseafloor Igneous Crust. 2015.
Khan HA, Telengech P, Kondo H, Bhatti MF, Suzuki N. Mycovirus Hunting Revealed the Presence of Diverse Viruses in a Single Isolate of the Phytopathogenic Fungus Diplodia seriata From Pakistan. Front Cell Infect Microbiol. 2022;12:913619.
García-Pedrajas MD, Cañizares MC, Sarmiento-Villamil JL, Jacquat AG, Dambolena JS. Mycoviruses in biological control: From basic research to field implementation. Phytopathology. 2019;109:1828–39.
Ghabrial SA, Castón JR, Jiang D, Nibert ML, Suzuki N. 50-plus years of fungal viruses. Virology. 2015;479:356–68.
Okada R, Ichinose S, Takeshita K, Urayama S, Fukuhara T, Komatsu K, et al. Molecular characterization of a novel mycovirus in Alternaria alternata manifesting two-sided effects: Down-regulation of host growth and up-regulation of host plant pathogenicity. Virology. 2018;519:23–32.
Google Scholar
Shah UA, Kotta-Loizou I, Fitt BDL, Coutts RHA. Mycovirus-induced hypervirulence of Leptosphaeria biglobosa enhances systemic acquired resistance to Leptosphaeria maculans in Brassica napus. Mol Plant-Microbe Interact. 2020;33:98–107.
Google Scholar
Hillman BI, Annisa A, Suzuki N. Viruses of plant-interacting fungi. Adv Virus Res. 2018;100:99–116.
Google Scholar
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