Koonin EV, Dolja VV, Krupovic M, Varsani A, Wolf YI, Yutin N, et al. Global organization and proposed megataxonomy of the virus world. Microbiol Mol Biol Rev. 2020;84:e00061–19.
Wilhelm S, Bird J, Bonifer K, Calfee B, Chen T, Coy S, et al. A student’s guide to giant viruses infecting small eukaryotes: from acanthamoeba to zooxanthellae. Viruses. 2017;9:46.
Fischer MG. Giant viruses come of age. Curr Opin Microbiol. 2016;31:50–57.
Aylward FO, Moniruzzaman M. Viral complexity. Biomolecules. 2022;12:1061.
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.
Moniruzzaman M, Weinheimer AR, Martinez-Gutierrez CA, Aylward FO. Widespread endogenization of giant viruses shapes genomes of green algae. Nature. 2020;588:141–5.
Guglielmini J, Woo AC, 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. 2019;116:19585–92.
Blanc-Mathieu R, Dahle H, Hofgaard A, Brandt D, Ban H, Kalinowski J, et al. A persistent giant algal virus, with a unique morphology, encodes an unprecedented number of genes involved in energy metabolism. J Virol. 2021;95:e02446–20.
Moniruzzaman M, Martinez-Gutierrez CA, Weinheimer AR, Aylward FO. Dynamic genome evolution and complex virocell metabolism of globally-distributed giant viruses. Nat Commun. 2020;11:1710.
Rodrigues RAL, Arantes TS, Oliveira GP, Dos Santos Silva LK, Abrahão JS. The complex nature of tupanviruses. Adv Virus Res. 2019;103:135–66.
Moreau H, Piganeau G, Desdevises Y, Cooke R, Derelle E, Grimsley N. Marine prasinovirus genomes show low evolutionary divergence and acquisition of protein metabolism genes by horizontal gene transfer. J Virol. 2010;84:12555–63.
Ha AD, Moniruzzaman M, Aylward FO. High transcriptional activity and diverse functional repertoires of hundreds of giant viruses in a coastal marine system. mSystems. 2021;6:e0029321.
Yutin N, Koonin EV. Proteorhodopsin genes in giant viruses. Biol Direct. 2012;7:34.
Rozenberg A, Oppermann J, Wietek J, Fernandez Lahore RG, Sandaa R-A, Bratbak G, et al. Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses. Curr Biol. 2020;30:4910–4920.e5.
Needham DM, Yoshizawa S, Hosaka T, Poirier C, Choi CJ, Hehenberger E, et al. A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators. Proc Natl Acad Sci. 2019;116:20574–83.
Koonin EV, Yutin N. Evolution of the large nucleocytoplasmic DNA viruses of eukaryotes and convergent origins of viral gigantism. Adv Virus Res. 2019;103:167–202.
Karki S, Moniruzzaman M, Aylward FO. Comparative genomics and environmental distribution of large dsDNA viruses in the family asfarviridae. Fronti Microbiol.
Weynberg KD, Allen MJ, Wilson WH. Marine prasinoviruses and their tiny plankton hosts: a review. Viruses. 2017;9.
Claverie J-M, Abergel C. Mimiviridae: an expanding family of highly diverse large dsDNA viruses infecting a wide phylogenetic range of aquatic eukaryotes. Viruses. 2018;10:506.
Rosenwasser S, Ziv C, van Creveld SG, Vardi A. Virocell metabolism: metabolic innovations during host–virus interactions in the ocean. Trends Microbiol. 821-32.
Forterre P. Manipulation of cellular syntheses and the nature of viruses: the virocell concept. C R Chim. 2011;14:392–9.
Chen F, Suttle CA, Short SM. Genetic diversity in marine algal virus communities as revealed by sequence analysis of DNA polymerase genes. Appl Environ Microbiol. 1996;62:2869–74.
Short SM, Suttle CA. Sequence analysis of marine virus communities reveals that groups of related algal viruses are widely distributed in nature. Appl Environ Microbiol. 2002;68:1290–6.
Monier A, Larsen JB, Sandaa R-A, Bratbak G, Claverie J-M, Ogata H. Marine mimivirus relatives are probably large algal viruses. Virol J. 2008;5:12.
Monier A, Claverie J-M, Ogata H. Taxonomic distribution of large DNA viruses in the sea. Genome Biol. 2008;9:R106.
Endo H, Blanc-Mathieu R, Li Y, Salazar G, Henry N, Labadie K, et al. Biogeography of marine giant viruses reveals their interplay with eukaryotes and ecological functions. Nat Ecol Evol. 2020;4:1639–49.
Bellec L, Grimsley N, Derelle E, Moreau H, Desdevises Y. Abundance, spatial distribution and genetic diversity of Ostreococcus tauri viruses in two different environments. Environ Microbiol Rep. 2010;2:313–21.
Hingamp P, Grimsley N, Acinas SG, Clerissi C, Subirana L, Poulain J, et al. Exploring nucleo-cytoplasmic large DNA viruses in Tara Oceans microbial metagenomes. ISME J. 2013;7:1678–95.
Sorensen G, Baker AC, Hall MJ, Munn CB, Schroeder DC. Novel virus dynamics in an Emiliania huxleyi bloom. Journal of Plankton Research. 2009;31:787–91.
Wilson WH, Tarran GA, Schroeder D, Cox M, Oke J, Malin G. Isolation of viruses responsible for the demise of an Emiliania huxleyi bloom in the English Channel. J Marine Biol Assoc United Kingdom. 2002;82:369–77.
Lehahn Y, Koren I, Schatz D, Frada M, Sheyn U, Boss E, et al. Decoupling physical from biological processes to assess the impact of viruses on a mesoscale algal bloom. Curr Biol. 2014;24:2041–6.
Tarutani K, Nagasaki K, Yamaguchi M. Viral impacts on total abundance and clonal composition of the harmful bloom-forming phytoplankton Heterosigma akashiwo. Appl Environ Microbiol. 2000;66:4916–20.
Sandaa RA, Heldal M, Castberg T, Thyrhaug R, Bratbak G. Isolation and characterization of two viruses with large genome size infecting Chrysochromulina ericina (Prymnesiophyceae) and Pyramimonas orientalis (Prasinophyceae). Virology. 2001;290:272–80.
Brussaard CP, Short SM, Frederickson CM, Suttle CA. Isolation and phylogenetic analysis of novel viruses infecting the phytoplankton Phaeocystis globosa (Prymnesiophyceae). Appl Environ Microbiol. 2004;70:3700–5.
Kaneko H, Blanc-Mathieu R, Endo H, Chaffron S, Delmont TO, Gaia M, et al. Eukaryotic virus composition can predict the efficiency of carbon export in the global ocean. iScience. 2020;24:102002.
Laber CP, Hunter JE, Carvalho F, Collins JR, Hunter EJ, Schieler BM, et al. Coccolithovirus facilitation of carbon export in the North Atlantic. Nat Microbiol. 2018;3:537–47.
Kavagutti VS, Bulzu P-A, Chiriac CM, Salcher MM, Mukherjee I, Shabarova T, et al. High-resolution metagenomic reconstruction of the freshwater spring bloom. Microbiome. 2023;11:1–24.
Thurber RV, Haynes M, Breitbart M, Wegley L, Rohwer F. Laboratory procedures to generate viral metagenomes. Nat Protoc. 2009;4:470–83.
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.
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.
Gaïa M, Meng L, Pelletier E, Forterre P, Vanni C, Fernandez-Guerra A, et al. Mirusviruses link herpesviruses to giant viruses. Nature. 2023. doi.org/10.1038/s41586-023-05962-4
Biller SJ, Berube PM, Dooley K, Williams M, Satinsky BM, Hackl T, et al. Marine microbial metagenomes sampled across space and time. Scientific Data. 2018;5:1–7.
Chow CET, Suttle CA. Biogeography of Viruses in the Sea. Annu Rev Virol. 2015;2:41–66.
Endo H, Ogata H, Suzuki K. Contrasting biogeography and diversity patterns between diatoms and haptophytes in the central Pacific Ocean. Sci Rep. 2018;8:1–13.
Sow SLS, Trull TW, Bodrossy L. Oceanographic fronts shape phaeocystis assemblages: a high-resolution 18S rRNA gene survey from the ice-edge to the equator of the South Pacific. Front Microbiol. 2020;11:1847.
Schvarcz CR, Steward GF. A giant virus infecting green algae encodes key fermentation genes. Virology. 2018;518:423–33.
Chelkha N, Levasseur A, Pontarotti P, Raoult D, Scola BL, Colson P. A Phylogenomic study of acanthamoeba polyphaga draft genome sequences suggests genetic exchanges with giant viruses. Front Microbiol. 2018;9:2098.
Fischer MG, Allen MJ, Wilson WH, Suttle CA. Giant virus with a remarkable complement of genes infects marine zooplankton. Proc Natl Acad Sci USA. 2010;107:19508–13.
Abrahão J, Silva L, Silva LS, Khalil JYB, Rodrigues R, Arantes T, et al. Tailed giant Tupanvirus possesses the most complete translational apparatus of the known virosphere. Nat Commun. 2018;9:1–12.
Meng L, Endo H, Blanc-Mathieu R, Chaffron S, Hernández-Velázquez R, Kaneko H, et al. Quantitative assessment of nucleocytoplasmic large DNA virus and host interactions predicted by co-occurrence analyses. mSphere. 2021;6:e01298–20.
Moniruzzaman M, Wurch LL, Alexander H, Dyhrman ST, Gobler CJ, Wilhelm SW. Virus-host relationships of marine single-celled eukaryotes resolved from metatranscriptomics. Nat Commun. 2017;8:16054.
Massana R Picoeukaryotes. Encyclopedia of Microbiology (Third Edition). 2009. Academic Press, pp 674-88.
Derelle E, Monier A, Cooke R, Worden AZ, Grimsley NH, Moreau H. Diversity of viruses infecting the green microalga ostreococcus lucimarinus. J Virol. 2015;89:5812–21.
Bellec L, Grimsley N, Desdevises Y. Isolation of prasinoviruses of the green unicellular algae Ostreococcus spp. on a worldwide geographical scale. Appl Environ Microbiol. 2010;76:96–101.
Santini S, Jeudy S, Bartoli J, Poirot O, Lescot M, Abergel C, 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. 2013;110:10800–5.
Gallot-Lavallée L, Blanc G, Claverie JM. Comparative genomics of chrysochromulina ericina virus and other microalga-infecting large DNA viruses highlights their intricate evolutionary relationship with the established mimiviridae family. J Virol. 2017;91:e00230–17.
Stough JMA, Yutin N, Chaban YV, Moniruzzaman M, Gann ER, Pound HL, et al. Genome and environmental activity of a chrysochromulina parva virus and its virophages. Front Microbiol. 2019;10:703.
Farzad R, Ha AD, Aylward FO. Diversity and genomics of giant viruses in the North Pacific Subtropical Gyre. Front Microbiol. 2022;13:1021923.
Chaudhary C, Saeedi H, Costello MJ. Bimodality of latitudinal gradients in marine species richness. Trends Ecol Evol. 2016;31:670–6.
Chown SL, Sinclair BJ, Leinaas HP, Gaston KJ. Hemispheric asymmetries in biodiversity—a serious matter for ecology. PLoS Biol. 2004;2:e406.
Ibarbalz FM, et al. Global trends in marine plankton diversity across kingdoms of Life. Cell. 2019;179:1084–1097.e21.
Hillebrand H. Strength, slope and variability of marine latitudinal gradients. Marine Ecology Progress Series. 2004;273:251–67.
Tittensor DP, Mora C, Jetz W, Lotze HK, Ricard D, Berghe EV, et al. Global patterns and predictors of marine biodiversity across taxa. Nature. 2010;466:1098–101.
Li T, Philander SGH. On the seasonal cycle of the equatorial atlantic ocean. J Clim. 1997;10:813–7.
Edwards KF, Steward GF, Schvarcz CR. Making sense of virus size and the tradeoffs shaping viral fitness. Ecol Lett. 2021;24:363–73.
Longhurst AR. Ecological Geography of the Sea. 2010. Elsevier.
Yutin N, Koonin EV. Hidden evolutionary complexity of nucleo-cytoplasmic large DNA viruses of eukaryotes. Virol J. 2012;9:1–18.
Raoult D, Audic S, Robert C, Abergel C, Renesto P, Ogata H, et al. The 1.2-megabase genome sequence of Mimivirus. Science. 2004;306:1344–50.
Saini HK, Fischer D. Structural and functional insights into Mimivirus ORFans. BMC Genomics. 2007;8:115.
Abrahão JS, Araújo 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.
Silva LCF, Almeida GMF, Assis FL, Albarnaz JD, Boratto PVM, Dornas FP, et al. Modulation of the expression of mimivirus-encoded translation-related genes in response to nutrient availability during Acanthamoeba castellanii infection. Front Microbiol. 2015;6:539.
Behrenfeld MJ, Kolber ZS. Widespread iron limitation of phytoplankton in the south pacific ocean. Science. 1999;283:840–3.
Revilla Y, Cebrián A, Baixerás E, Martínez C, Viñuela E, Salas ML. Inhibition of apoptosis by the African swine fever virus Bcl-2 homologue: role of the BH1 domain. Virology. 1997;228:400–4.
Bidle KD, Kwityn CJ. Assessing the role of caspase activity and metacaspase expression on viral susceptibility of the coccolithophore, emiliania huxleyi (haptophyta). J Phycol. 2012;48:1079–89.
Du J, Wang L, Wang Y, Shen J, Pan C, Meng Y, et al. Autophagy and apoptosis induced by Chinese giant salamander (Andrias davidianus) iridovirus (CGSIV). Vet Microbiol. 2016;195:87–95.
Schrad JR, Abrahão JS, Cortines JR, Parent KN. Structural and proteomic characterization of the initiation of giant virus infection. Cell. 2020;181:1046–1061.e6.
Lartigue A, Burlat B, Coutard B, Chaspoul F, Claverie J-M, Abergel C. The megavirus chilensis Cu,Zn-superoxide dismutase: the first viral structure of a typical cellular copper chaperone-independent hyperstable dimeric enzyme. J Virol. 2015;89:824–32.
Van Etten JL, Meints RH. Giant viruses infecting algae. Annu Rev Microbiol. 1999;53:447–94.
Furuta M, Schrader JO, Schrader HS, Kokjohn TA, Nyaga S, McCullough AK, et al. Chlorella virus PBCV-1 encodes a homolog of the bacteriophage T4 UV damage repair gene denV. Appl Environ Microbiol. 1997;63:1551–6.
Redrejo-Rodríguez M, Ishchenko A, Saparbaev MK, Salas ML, Salas J. African swine fever virus AP endonuclease is a redox-sensitive enzyme that repairs alkylating and oxidative damage to DNA. Virology. 2009;390:102–9.
Manandhar M, Boulware KS, Wood RD. The ERCC1 and ERCC4 (XPF) genes and gene products. Gene. 2015;569:153.
Wilson WH, Gilg IC, Duarte A, Ogata H. Development of DNA mismatch repair gene, MutS, as a diagnostic marker for detection and phylogenetic analysis of algal Megaviruses. Virology. 2014;466-467:123–8.
Ogata H, Ray J, Toyoda K, Sandaa R-A, Nagasaki K, Bratbak G, et al. Two new subfamilies of DNA mismatch repair proteins (MutS) specifically abundant in the marine environment. ISME J. 2011;5:1143–51.
Piacente F, De Castro C, Jeudy S, Molinaro A, Salis A, Damonte G, et al. Giant virus megavirus chilensis encodes the biosynthetic pathway for uncommon acetamido sugars. J Biol Chem. 2014;289:24428–39.
Parakkottil Chothi M, Duncan GA, Armirotti A, Abergel C, Gurnon JR, Van Etten JL, et al. Identification of an L-rhamnose synthetic pathway in two nucleocytoplasmic large DNA viruses. J Virol. 2010;84:8829–38.
Rodrigues RAL, dos Santos Silva LK, Dornas FP, de Oliveira DB, Magalhães TFF, Santos DA, et al. Mimivirus fibrils are important for viral attachment to the microbial world by a diverse glycoside interaction repertoire. J Virol. 2015;89:11812.
Geslin C, Gaillard M, Flament D, Rouault K, Le Romancer M, Prieur D, et al. Analysis of the first genome of a hyperthermophilic marine virus-like particle, PAV1, isolated from Pyrococcus abyssi. J Bacteriol. 2007;189:4510–9.
Rose SL, Fulton JM, Brown CM, Natale F, Van Mooy BAS, Bidle KD. Isolation and characterization of lipid rafts in Emiliania huxleyi: a role for membrane microdomains in host-virus interactions. Environ Microbiol. 2014;16:1150–66.
Aylward FO, Moniruzzaman M. ViralRecall-A Flexible command-line tool for the detection of giant virus signatures in ’Omic Data. Viruses. 2021;13:150.
Olm MR, Brown CT, Brooks B, Banfield JF. dRep: a tool for fast and accurate genomic comparisons that enables improved genome recovery from metagenomes through de-replication. ISME J. 2017;11:2864–8.
Weinheimer AR, Aylward FO. Infection strategy and biogeography distinguish cosmopolitan groups of marine jumbo bacteriophages. ISME J. 2022;16:1657–67.
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.
Minh BQ, Schmidt HA, Chernomor O, Schrempf D, Woodhams MD, von Haeseler A, et al. IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era. Mol Biol Evol. 2020;37:1530–4.
Lemos LN, Fulthorpe RR, Triplett EW, Roesch LFW. Rethinking microbial diversity analysis in the high throughput sequencing era. J Microbiol Methods. 2011;86:42–51.
Schlitzer R. Data analysis and visualization with ocean data view. doi.org/10.1016/s0098-3004(02)00040-7.
Hyatt D, Chen G-L, LoCascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010;11:1–11.
Huerta-Cepas J, Szklarczyk D, Heller D, Hernández-Plaza A, Forslund SK, Cook H, et al. eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses. Nucleic Acids Res. 2018;47:D309–D314.
Mistry J, Chuguransky S, Williams L, Qureshi M, Salazar GA, Sonnhammer ELL, et al. Pfam: the protein families database in 2021. Nucleic Acids Res. 2020;49:D412–D419.
Read more here: Source link