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
Pritham, E. J., Putliwala, T. & Feschotte, C. Mavericks, a novel class of giant transposable elements widespread in eukaryotes and related to DNA viruses. Gene 390, 3–17 (2007).
Google Scholar
Kapitonov, V. V. & Jurka, J. Self-synthesizing DNA transposons in eukaryotes. Proc. Natl Acad. Sci. USA 103, 4540–4545 (2006).
Google Scholar
Krupovic, M. & Koonin, E. V. Polintons: a hotbed of eukaryotic virus, transposon and plasmid evolution. Nat. Rev. Microbiol. 13, 105–115 (2015).
Google Scholar
Koonin, E. V., Krupovic, M. & Yutin, N. Evolution of double-stranded DNA viruses of eukaryotes: from bacteriophages to transposons to giant viruses. Ann. N. Y. Acad. Sci. 1341, 10–24 (2015).
Google Scholar
Yutin, N., Raoult, D. & Koonin, E. V. Virophages, polintons, and transpovirons: a complex evolutionary network of diverse selfish genetic elements with different reproduction strategies. Virol. J. 10, 158 (2013).
Google Scholar
Krupovic, M., Bamford, D. H. & Koonin, E. V. Conservation of major and minor jelly-roll capsid proteins in Polinton (Maverick) transposons suggests that they are bona fide viruses. Biol. Direct 9, 6 (2014).
Google Scholar
Yutin, N., Shevchenko, S., Kapitonov, V., Krupovic, M. & Koonin, E. V. A novel group of diverse Polinton-like viruses discovered by metagenome analysis. BMC Biol. 13, 95 (2015).
Google Scholar
Bellas, C. M. & Sommaruga, R. Polinton-like viruses are abundant in aquatic ecosystems. Microbiome 9, 13 (2021).
Google Scholar
Pagarete, A., Grébert, T., Stepanova, O., Sandaa, R.-A. & Bratbak, G. Tsv-N1: a novel DNA algal virus that infects Tetraselmis striata. Viruses 7, 3937–3953 (2015).
Google Scholar
Bekliz, M., Colson, P. & La Scola, B. The expanding family of virophages. Viruses 8, 317 (2016).
Google Scholar
Fischer, M. G. The virophage family Lavidaviridae. Curr. Issues Mol. Biol. https://doi.org/10.21775/cimb.040.001 (2021).
Desnues, C. et al. Provirophages and transpovirons as the diverse mobilome of giant viruses. Proc. Natl Acad. Sci. USA 109, 18078–18083 (2012).
Google Scholar
Campos, R. K. et al. Samba virus: a novel mimivirus from a giant rain forest, the Brazilian Amazon. Virol. J. 11, 95 (2014).
Google Scholar
Gaia, M. et al. Broad spectrum of mimiviridae virophage allows its isolation using a mimivirus reporter. PLoS ONE 8, e61912 (2013).
Google Scholar
Hackl, T., Duponchel, S., Barenhoff, K., Weinmann, A. & Fischer, M. G. Virophages and retrotransposons colonize the genomes of a heterotrophic flagellate. eLife 10, e72674 (2021).
Google Scholar
Yau, S. et al. Virophage control of Antarctic algal host-virus dynamics. Proc. Natl Acad. Sci. USA 108, 6163–6168 (2011).
Google Scholar
Gong, C. et al. Novel virophages discovered in a freshwater lake in China. Front. Microbiol. 7, 5 (2016).
Google Scholar
Zhou, J. et al. Three novel virophage genomes discovered from Yellowstone Lake metagenomes. J. Virol. 89, 1278–1285 (2014).
Google Scholar
Yutin, N., Kapitonov, V. V. & Koonin, E. V. A new family of hybrid virophages from an animal gut metagenome. Biol. Direct 10, 19 (2015).
Google Scholar
Stough, J. M. A. et al. Genome and environmental activity of a Chrysochromulina parva virus and its virophages. Front. Microbiol. 10, 703 (2019).
Google Scholar
La Scola, B. et al. The virophage as a unique parasite of the giant mimivirus. Nature 455, 100–104 (2008).
Google Scholar
Fischer, M. G. & Suttle, C. A. A virophage at the origin of large DNA transposons. Science 332, 231–234 (2011).
Google Scholar
Gaia, M. et al. Zamilon, a novel virophage with Mimiviridae host specificity. PLoS ONE 9, e94923 (2014).
Google Scholar
Mougari, S. et al. Guarani virophage, a new Sputnik-like isolate from a Brazilian lake. Front. Microbiol. 10, 1003 (2019).
Google Scholar
Sheng, Y., Wu, Z., Xu, S. & Wang, Y. Isolation and identification of a large green alga virus (Chlorella Virus XW01) of Mimiviridae and its virophage (Chlorella Virus Virophage SW01) by using unicellular green algal cultures. J. Virol. 96, e02114–e02121 (2022).
Google Scholar
Baudoux, A. C. & Brussaard, C. P. D. Characterization of different viruses infecting the marine harmful algal bloom species Phaeocystis globosa. Virology 341, 80–90 (2005).
Google Scholar
Santini, S. et al. Genome of Phaeocystis globosa virus PgV-16T highlights the common ancestry of the largest known DNA viruses infecting eukaryotes. Proc. Natl Acad. Sci. USA 110, 10800–10805 (2013).
Google Scholar
Tarutani, K., Nagasaki, K. & Yamaguchi, M. Virus adsorption process determines virus susceptibility in Heterosigma akashiwo (Raphidophyceae). Aquat. Microb. Ecol. 42, 209–213 (2006).
Google Scholar
Gann, E. R., Gainer, P. J., Reynolds, T. B. & Wilhelm, S. W. Influence of light on the infection of Aureococcus anophagefferens CCMP 1984 by a ‘giant virus’. PLoS ONE 15, e0226758 (2020).
Google Scholar
Van Etten, J. L., Burbank, D. E., Xia, Y. & Meints, R. H. Growth cycle of a virus, PBCV-1, that infects Chlorella-like algae. Virology 126, 117–125 (1983).
Google Scholar
Boyer, M. et al. Mimivirus shows dramatic genome reduction after intraamoebal culture. Proc. Natl Acad. Sci. USA 108, 10296–10301 (2011).
Google Scholar
Desnues, C. & Raoult, D. Inside the lifestyle of the virophage. Intervirology 53, 293–303 (2010).
Google Scholar
Sobhy, H., Scola, B. L., Pagnier, I., Raoult, D. & Colson, P. Identification of giant Mimivirus protein functions using RNA interference. Front. Microbiol. 6, 345 (2015).
Google Scholar
Fischer, M. G. & Hackl, T. Host genome integration and giant virus-induced reactivation of the virophage mavirus. Nature 540, 288–291 (2016).
Google Scholar
Wodarz, D. Evolutionary dynamics of giant viruses and their virophages. Ecol. Evol. 3, 2103–2115 (2013).
Google Scholar
Farr, G. A., Zhang, L. & Tattersall, P. Parvoviral virions deploy a capsid-tethered lipolytic enzyme to breach the endosomal membrane during cell entry. Proc. Natl Acad. Sci. USA 102, 17148–17153 (2005).
Google Scholar
Suhre, K., Audic, S. & Claverie, J.-M. Mimivirus gene promoters exhibit an unprecedented conservation among all eukaryotes. Proc. Natl Acad. Sci. USA 102, 14689–14693 (2005).
Google Scholar
Legendre, M. et al. mRNA deep sequencing reveals 75 new genes and a complex transcriptional landscape in Mimivirus. Genome Res. 20, 664–674 (2010).
Google Scholar
Smith, D. R., Arrigo, K. R., Alderkamp, A.-C. & Allen, A. E. Massive difference in synonymous substitution rates among mitochondrial, plastid, and nuclear genes of Phaeocystis algae. Mol. Phylogenet. Evol. 71, 36–40 (2014).
Google Scholar
Krupovic, M., Kuhn, J. H. & Fischer, M. G. A classification system for virophages and satellite viruses. Arch. Virol. 161, 233–247 (2016).
Google Scholar
Suplatov, D. A., Besenmatter, W., Svedas, V. K. & Svendsen, A. Bioinformatic analysis of alpha/beta-hydrolase fold enzymes reveals subfamily-specific positions responsible for discrimination of amidase and lipase activities. Protein Eng. Des. Sel. 25, 689–697 (2012).
Google Scholar
Burt, A. & Koufopanou, V. Homing endonuclease genes: the rise and fall and rise again of a selfish element. Curr. Opin. Genet. Dev. 14, 609–615 (2004).
Google Scholar
Sullivan, M. B. DNA extraction of cesium chloride-purified viruses using wizard prep columns. Protocols https://doi.org/10.17504/protocols.io.c26yhd (2016).
González-Domínguez, J. & Schmidt, B. ParDRe: faster parallel duplicated reads removal tool for sequencing studies. Bioinformatics 32, 1562–1564 (2016).
Google Scholar
Guillard, R. R. L. Culture of phytoplankton for feeding marine invertebrates. In Culture of Marine Invertebrate Animals: Proceedings—1st Conference on Culture of Marine Invertebrate Animals Greenport (eds Smith, W. L., & Chanley, M. H.) 29– 60 (Springer, 1975).
Cottrell, M. & Suttle, C. Wide-spread occurrence and clonal variation in viruses which cause lysis of a cosmopolitan, eukaryotic marine phytoplankter Micromonas pusilla. Mar. Ecol. Prog. Ser. 78, 1–9 (1991).
Google Scholar
Krueger, F., James, F., Ewels, P., Afyounian, E. & Schuster-Boeckler, B. FelixKrueger/TrimGalore: v0.6.7 – DOI via Zenodo. https://doi.org/10.5281/zenodo.5127899 (2021).
Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455–477 (2012).
Google Scholar
Schneider, C. A., Rasband, W. S. & Eliceiri, K. W. NIH Image to ImageJ: 25 years of image analysis. Nat. Methods 9, 671–675 (2012).
Google Scholar
Patel, A. et al. Virus and prokaryote enumeration from planktonic aquatic environments by epifluorescence microscopy with SYBR Green I. Nat. Protoc. 2, 269–276 (2007).
Google Scholar
Bolte, S. & Cordelières, F. P. A guided tour into subcellular colocalization analysis in light microscopy. J. Microsc. 224, 213–232 (2006).
Google Scholar
Brussaard, C. P. D. Optimization of procedures for counting viruses by flow cytometry. Appl. Environ. Microbiol. 70, 1506–1513 (2004).
Google Scholar
Kirzner, S., Barak, E. & Lindell, D. Variability in progeny production and virulence of cyanophages determined at the single-cell level. Environ. Microbiol. Rep. 8, 605–613 (2016).
Google Scholar
Ziv, I. et al. A perturbed ubiquitin landscape distinguishes between ubiquitin in trafficking and in proteolysis. Mol. Cell. Proteomics 10, M111.009753 (2011).
HaileMariam, M. et al. S-Trap, an ultrafast sample-preparation approach for shotgun proteomics. J. Proteome Res. 17, 2917–2924 (2018).
Google Scholar
Rappsilber, J., Mann, M. & Ishihama, Y. Protocol for micro-purification, enrichment, pre-fractionation and storage of peptides for proteomics using StageTips. Nat. Protoc. 2, 1896–1906 (2007).
Google Scholar
Kong, A. T., Leprevost, F. V., Avtonomov, D. M., Mellacheruvu, D. & Nesvizhskii, A. I. MSFragger: ultrafast and comprehensive peptide identification in mass spectrometry-based proteomics. Nat. Methods 14, 513–520 (2017).
Google Scholar
Li, W. & Godzik, A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 22, 1658–1659 (2006).
Google Scholar
Lechner, M. et al. Proteinortho: detection of (Co-)orthologs in large-scale analysis. BMC Bioinformatics 12, 124 (2011).
Google Scholar
Buchfink, B., Reuter, K. & Drost, H.-G. Sensitive protein alignments at tree-of-life scale using DIAMOND. Nat. Methods 18, 366–368 (2021).
Google Scholar
Cox, J. et al. Accurate proteome-wide label-free quantification by delayed normalization and maximal peptide ratio extraction termed MaxLFQ. Mol. Cell. Proteomics 13, 2513–2526 (2014).
Google Scholar
Mirdita, M. et al. ColabFold: making protein folding accessible to all. Nat. Methods 19, 679–682 (2022).
Jumper, J. et al. Highly accurate protein structure prediction with AlphaFold. Nature 596, 583–589 (2021).
Google Scholar
O’Connell, J. et al. NxTrim: optimized trimming of Illumina mate pair reads. Bioinformatics 31, 2035–2037 (2015).
Google Scholar
Li, D., Liu, C.-M., Luo, R., Sadakane, K. & Lam, T.-W. MEGAHIT: an ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph. Bioinformatics 31, 1674–1676 (2015).
Google Scholar
Luo, R. et al. SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler. GigaScience 1, 2047-217X-1–18 (2012).
Chevreux, B., Wetter, T. & Suhai, S. Genome sequence assembly using trace signals and additional sequence information. In Proc. German Conference on Bioinformatics 45–56 (Fachgruppe Bioinformatik, 1999).
Deng, Z. & Delwart, E. ContigExtender: a new approach to improving de novo sequence assembly for viral metagenomics data. BMC Bioinformatics 22, 119 (2021).
Google Scholar
Walker, B. J. et al. Pilon: an integrated tool for comprehensive microbial variant detection and genome assembly improvement. PLoS ONE 9, e112963 (2014).
Google Scholar
Eddy, S. R. Accelerated profile HMM searches. PLoS Comput. Biol. 7, e1002195 (2011).
Google Scholar
Katoh, K., Misawa, K., Kuma, K. & Miyata, T. MAFFT: a novel method for rapid multiple sequence alignment based on fast Fourier transform. Nucleic Acids Res. 30, 3059–3066 (2002).
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
Hoang, D. T., Chernomor, O., von Haeseler, A., Minh, B. Q. & Vinh, L. S. UFBoot2: improving the ultrafast bootstrap approximation. Mol. Biol. Evol. 35, 518–522 (2018).
Google Scholar
Kozlov, A. M., Darriba, D., Flouri, T., Morel, B. & Stamatakis, A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 35, 4453–4455 (2019).
Google Scholar
Barbera, P. et al. EPA-ng: massively parallel evolutionary placement of genetic sequences. Syst. Biol. 68, 365–369 (2019).
Google Scholar
Capella-Gutiérrez, S., Silla-Martínez, J. M. & Gabaldón, T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 25, 1972–1973 (2009).
Google Scholar
Steinegger, M. & Söding, J. MMseqs2 enables sensitive protein sequence searching for the analysis of massive data sets. Nat. Biotechnol. 35, 1026–1028 (2017).
Google Scholar
Steinegger, M. et al. HH-suite3 for fast remote homology detection and deep protein annotation. BMC Bioinformatics 20, 473 (2019).
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
Bolduc, B. et al. vConTACT: an iVirus tool to classify double-stranded DNA viruses that infect Archaea and Bacteria. PeerJ 5, e3243 (2017).
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
Heger, A. & Holm, L. Rapid automatic detection and alignment of repeats in protein sequences. Proteins 41, 224–237 (2000).
Google Scholar
Chase, E., Desnues, C. & Blanc, G. Integrated viral elements unveil the dual lifestyle of Tetraselmis spp. polinton-like viruses. Virus Evol. 8, veac068 (2022).
Egge, E. S., Eikrem, W. & Edvardsen, B. Deep-branching novel lineages and high diversity of haptophytes in the Skagerrak (Norway) uncovered by 454 pyrosequencing. J. Eukaryot. Microbiol. 62, 121–140 (2015).
Google Scholar
Hovde, B. T. et al. Chrysochromulina: genomic assessment and taxonomic diagnosis of the type species for an oleaginous algal clade. Algal Res. 37, 307–319 (2019).
Google Scholar
Andersen, R. A., Bailey, J. C., Decelle, J. & Probert, I. Phaeocystis rex sp. nov. (Phaeocystales, Prymnesiophyceae): a new solitary species that produces a multilayered scale cell covering. Eur. J. Phycol. 50, 207–222 (2015).
Google Scholar
Stepanova, O. A. Black Sea algal viruses. Russ. J. Mar. Biol. 42, 123–127 (2016).
Google Scholar
Alarcón-Schumacher, T., Guajardo-Leiva, S., Antón, J. & Díez, B. Elucidating viral communities during a phytoplankton bloom on the West Antarctic Peninsula. Front. Microbiol. 10, 1014 (2019).
Google Scholar
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