{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T19:37:20Z","timestamp":1765568240116,"version":"3.48.0"},"reference-count":61,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T00:00:00Z","timestamp":1765497600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000893","name":"Simons Foundation","doi-asserted-by":"publisher","award":["735007"],"award-info":[{"award-number":["735007"]}],"id":[{"id":"10.13039\/100000893","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000076","name":"Directorate for Biological Sciences","doi-asserted-by":"publisher","award":["IOS1922958"],"award-info":[{"award-number":["IOS1922958"]}],"id":[{"id":"10.13039\/100000076","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS One"],"abstract":"<jats:p>\n                    DNA methylation can epigenetically alter gene expression and serve as a mechanism for genomic stabilization. Advancements in long-read sequencing technology have allowed for increased exploration into the methylation profiles of various organisms, including viruses. Studies into the\n                    <jats:italic>Nucleocytoviricota<\/jats:italic>\n                    phylum of giant dsDNA viruses have revealed unique strategies for genomic methylation. However, given the diversity across this phylum, further inquiries into specific lineages are necessary.\n                    <jats:italic>Kratosvirus quantuckense<\/jats:italic>\n                    (formerly known as Aureococcus anophagefferens Virus, AaV) is predicted to encode six distinct methyltransferases, which bear homology to other methyltransferases across the many clades of\n                    <jats:italic>Nucleocytoviricota<\/jats:italic>\n                    . We found that the virus\u2019 DNA is methylated with high consistency, including nine different motifs targeted for DNA adenine methylation. Methylation levels varied depending on the associated motif. Likewise, distinct motifs were enriched within unique genomic regions. Collectively our data suggest that each methyltransferase targets unique DNA regions, suggesting they have varying functionality. This work reveals an array of methyltransferase activity in\n                    <jats:italic>Kratosvirus quantuckense<\/jats:italic>\n                    and implicates the importance of DNA methylation to the\n                    <jats:italic>Nucleocytoviricota<\/jats:italic>\n                    infection cycle.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0330887","type":"journal-article","created":{"date-parts":[[2025,12,12]],"date-time":"2025-12-12T18:38:17Z","timestamp":1765564697000},"page":"e0330887","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":0,"title":["Epigenome analysis of an algae-infecting giant virus reveals a unique methylation motif catalogue"],"prefix":"10.1371","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7194-6819","authenticated-orcid":true,"given":"Alexander 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in Nitrogen-, but Not in Phosphorus-Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences","volume":"9","author":"S Mager","year":"2018","journal-title":"Front Plant Sci"},{"issue":"9","key":"pone.0330887.ref003","doi-asserted-by":"crossref","first-page":"2825","DOI":"10.1093\/nar\/gkn121","article-title":"Presence and role of cytosine methylation in DNA viruses of animals","volume":"36","author":"K Hoelzer","year":"2008","journal-title":"Nucleic Acids Res"},{"issue":"11","key":"pone.0330887.ref004","doi-asserted-by":"crossref","first-page":"818","DOI":"10.1016\/j.tig.2019.07.007","article-title":"DNA Methylation: Shared and Divergent Features across Eukaryotes","volume":"35","author":"RJ Schmitz","year":"2019","journal-title":"Trends Genet"},{"issue":"3","key":"pone.0330887.ref005","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1002\/bies.20342","article-title":"N6-methyladenine: the other methylated base of DNA","volume":"28","author":"D Ratel","year":"2006","journal-title":"Bioessays"},{"issue":"1","key":"pone.0330887.ref006","doi-asserted-by":"crossref","first-page":"4249","DOI":"10.1038\/s41467-021-24425-w","article-title":"Tissue-specific 5-hydroxymethylcytosine landscape of the human genome","volume":"12","author":"B He","year":"2021","journal-title":"Nat Commun"},{"issue":"1","key":"pone.0330887.ref007","doi-asserted-by":"crossref","first-page":"1072","DOI":"10.1038\/s41467-022-28471-w","article-title":"Bacterial N4-methylcytosine as an epigenetic mark in eukaryotic DNA","volume":"13","author":"F Rodriguez","year":"2022","journal-title":"Nat Commun"},{"issue":"5980","key":"pone.0330887.ref008","doi-asserted-by":"crossref","first-page":"916","DOI":"10.1126\/science.1186366","article-title":"Genome-wide evolutionary analysis of eukaryotic DNA methylation","volume":"328","author":"A Zemach","year":"2010","journal-title":"Science"},{"issue":"5524","key":"pone.0330887.ref009","doi-asserted-by":"crossref","first-page":"2077","DOI":"10.1126\/science.1059745","article-title":"Requirement of CHROMOMETHYLASE3 for maintenance of CpXpG methylation","volume":"292","author":"AM Lindroth","year":"2001","journal-title":"Science"},{"issue":"12","key":"pone.0330887.ref010","doi-asserted-by":"crossref","first-page":"950","DOI":"10.1016\/j.cels.2022.11.005","article-title":"The sound of silence: Transgene silencing in mammalian cell engineering","volume":"13","author":"A Cabrera","year":"2022","journal-title":"Cell Syst"},{"issue":"5","key":"pone.0330887.ref011","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1016\/0168-9525(89)90054-1","article-title":"The great GATC: DNA methylation in E. coli","volume":"5","author":"F Barras","year":"1989","journal-title":"Trends Genet"},{"key":"pone.0330887.ref012","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2014.00115","article-title":"Helicobacter pylori DNA methyltransferases and the epigenetic field effect in cancerization","volume":"5","author":"R Sitaraman","year":"2014","journal-title":"Frontiers in Microbiology"},{"issue":"3","key":"pone.0330887.ref013","doi-asserted-by":"crossref","DOI":"10.1128\/mBio.00873-21","article-title":"Nutrient Loading and Viral Memory Drive Accumulation of Restriction Modification Systems in Bloom-Forming Cyanobacteria","volume":"12","author":"SE Papoulis","year":"2021","journal-title":"mBio"},{"key":"pone.0330887.ref014","doi-asserted-by":"crossref","first-page":"1129437","DOI":"10.3389\/fmicb.2023.1129437","article-title":"Bacterial DNA methyltransferase: A key to the epigenetic world with lessons learned from proteobacteria","volume":"14","author":"Q Gao","year":"2023","journal-title":"Front Microbiol"},{"key":"pone.0330887.ref015","doi-asserted-by":"crossref","first-page":"11301","DOI":"10.1038\/ncomms11301","article-title":"Characterization of eukaryotic DNA N(6)-methyladenine by a highly sensitive restriction enzyme-assisted sequencing","volume":"7","author":"G-Z Luo","year":"2016","journal-title":"Nat Commun"},{"issue":"4","key":"pone.0330887.ref016","doi-asserted-by":"crossref","first-page":"879","DOI":"10.1016\/j.cell.2015.04.010","article-title":"N6-methyldeoxyadenosine marks active transcription start sites in Chlamydomonas","volume":"161","author":"Y Fu","year":"2015","journal-title":"Cell"},{"issue":"6580","key":"pone.0330887.ref017","doi-asserted-by":"crossref","first-page":"515","DOI":"10.1126\/science.abe7489","article-title":"Critical assessment of DNA adenine methylation in eukaryotes using quantitative deconvolution","volume":"375","author":"Y Kong","year":"2022","journal-title":"Science"},{"key":"pone.0330887.ref018","article-title":"Adenine DNA methylation associated to transcription is widespread across eukaryotes","author":"P Romero Charria","year":"2024","journal-title":"bioRxiv"},{"key":"pone.0330887.ref019","article-title":"SMRT Sequencing of Paramecium Bursaria Chlorella Virus-1 Reveals Diverse Methylation Stability in Adenines Targeted by Restriction Modification Systems","volume":"11","author":"SR Coy","year":"2020","journal-title":"Frontiers in Microbiology"},{"issue":"1","key":"pone.0330887.ref020","doi-asserted-by":"crossref","DOI":"10.1038\/s41467-020-16414-2","article-title":"The DNA methylation landscape of giant viruses","volume":"11","author":"S Jeudy","year":"2020","journal-title":"Nature Communications"},{"issue":"16","key":"pone.0330887.ref021","doi-asserted-by":"crossref","first-page":"8114","DOI":"10.1128\/JVI.00486-06","article-title":"Virion-associated restriction endonucleases of chloroviruses","volume":"80","author":"IV Agarkova","year":"2006","journal-title":"J Virol"},{"issue":"1","key":"pone.0330887.ref022","doi-asserted-by":"crossref","first-page":"138","DOI":"10.1016\/j.pep.2006.04.002","article-title":"Cloning of Nt.CviQII nicking endonuclease and its cognate methyltransferase: M.CviQII methylates AG sequences","volume":"49","author":"S Chan","year":"2006","journal-title":"Protein Expr Purif"},{"issue":"1","key":"pone.0330887.ref023","doi-asserted-by":"crossref","first-page":"2285","DOI":"10.1038\/s41467-018-04698-4","article-title":"Diversity and evolution of the emerging Pandoraviridae family","volume":"9","author":"M Legendre","year":"2018","journal-title":"Nat Commun"},{"key":"pone.0330887.ref024","doi-asserted-by":"crossref","first-page":"648731","DOI":"10.3389\/fmicb.2021.648731","article-title":"Marseilleviruses: an update in 2021","volume":"12","author":"D Sahmi-Bounsiar","year":"2021","journal-title":"Front Microbiol"},{"key":"pone.0330887.ref025","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1016\/j.virol.2014.06.031","article-title":"Genome of brown tide virus (AaV), the little giant of the Megaviridae, elucidates NCLDV genome expansion and host-virus coevolution","author":"M Moniruzzaman","year":"2014","journal-title":"Virology"},{"key":"pone.0330887.ref026","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2023.1284617","article-title":"Kratosvirus quantuckense: the history and novelty of an algal bloom disrupting virus and a model for giant virus research","volume":"14","author":"AR Truchon","year":"2023","journal-title":"Frontiers in Microbiology"},{"key":"pone.0330887.ref027","doi-asserted-by":"crossref","unstructured":"Gann ER. ASP12A Recipe for Culturing Aureococcus Anophagefferens. https:\/\/protocols.io. 2016.","DOI":"10.17504\/protocols.io.f3ybqpw"},{"key":"pone.0330887.ref028","doi-asserted-by":"crossref","unstructured":"Coy SR, Wilhelm SW. Concentrating viruses by tangential flow filtration. https:\/\/protocols.io. 2020.","DOI":"10.17504\/protocols.io.bbagiibw"},{"key":"pone.0330887.ref029","unstructured":"Chase EE, Truchon AR, Coy SR, Wilhelm SW. Aureococcus anophagefferens virus (AaV)\/Kratosvirus quantuckense viral particle count by SYBR green staining and flow cytometry (CytoFLEX S flow cytometer Beckman Coulter) V.2. https:\/\/www.protocols.io. 2023."},{"issue":"7","key":"pone.0330887.ref030","doi-asserted-by":"crossref","DOI":"10.1128\/mra.00282-22","article-title":"Closed, Circular Genome Sequence of Aureococcus anophagefferens Virus, a Lytic Virus of a Brown Tide-Forming Alga","volume":"11","author":"AR Truchon","year":"2022","journal-title":"Microbiol Resour Announc"},{"key":"pone.0330887.ref031","unstructured":"Bonito C. A PyTorch basecaller for Oxford Nanopore reads. 2019."},{"issue":"16","key":"pone.0330887.ref032","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"pone.0330887.ref033","article-title":"Nanomotif: Leveraging DNA Methylation Motifs for Genome Recovery and Host Association of Plasmids in Metagenomes from Complex Microbial Communities","volume":"7","year":"2024","journal-title":"Bioinformatics"},{"key":"pone.0330887.ref034"},{"issue":"15","key":"pone.0330887.ref035","doi-asserted-by":"crossref","first-page":"1972","DOI":"10.1093\/bioinformatics\/btp348","article-title":"trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses","volume":"25","year":"2009","journal-title":"Bioinformatics"},{"key":"pone.0330887.ref036"},{"key":"pone.0330887.ref037","doi-asserted-by":"crossref","DOI":"10.1093\/nar\/gkac975","article-title":"REBASE: a database for DNA restriction and modification: enzymes, genes and genomes","volume":"51","author":"RJ Roberts","year":"2023","journal-title":"Nucleic Acids Res"},{"issue":"1","key":"pone.0330887.ref038","doi-asserted-by":"crossref","first-page":"418","DOI":"10.1093\/nar\/gkg069","article-title":"REBASE: restriction enzymes and methyltransferases","volume":"31","author":"RJ Roberts","year":"2003","journal-title":"Nucleic Acids Res"},{"issue":"23","key":"pone.0330887.ref039","doi-asserted-by":"crossref","first-page":"9823","DOI":"10.1093\/nar\/17.23.9823","article-title":"Sequence motifs characteristic of DNA[cytosine-N4]methyltransferases: similarity to adenine and cytosine-C5 DNA-methylases","volume":"17","author":"S Klimasauskas","year":"1989","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"pone.0330887.ref040","doi-asserted-by":"crossref","first-page":"1805","DOI":"10.1093\/nar\/gkg274","article-title":"A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes","volume":"31","author":"RJ Roberts","year":"2003","journal-title":"Nucleic Acids Res"},{"issue":"7","key":"pone.0330887.ref041","doi-asserted-by":"crossref","first-page":"2421","DOI":"10.1093\/nar\/17.7.2421","article-title":"Predictive motifs derived from cytosine methyltransferases","volume":"17","author":"J P\u00f3sfai","year":"1989","journal-title":"Nucleic Acids Res"},{"key":"pone.0330887.ref042","doi-asserted-by":"crossref","first-page":"2047","DOI":"10.3389\/fmicb.2020.02047","article-title":"Structural and Proteomic Studies of the Aureococcus anophagefferens Virus Demonstrate a Global Distribution of Virus-Encoded Carbohydrate Processing","volume":"11","author":"ER Gann","year":"2020","journal-title":"Front Microbiol"},{"issue":"3","key":"pone.0330887.ref043","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1038\/s41559-019-0810-9","article-title":"Diversity of cytosine methylation across the fungal tree of life","volume":"3","author":"AJ Bewick","year":"2019","journal-title":"Nat Ecol Evol"},{"key":"pone.0330887.ref044","doi-asserted-by":"crossref","first-page":"752","DOI":"10.3389\/fmicb.2018.00752","article-title":"Infection by a Giant Virus (AaV) Induces Widespread Physiological Reprogramming in Aureococcus anophagefferens CCMP1984 - A Harmful Bloom Algae","volume":"9","author":"M Moniruzzaman","year":"2018","journal-title":"Front Microbiol"},{"issue":"20","key":"pone.0330887.ref045","doi-asserted-by":"crossref","first-page":"5351","DOI":"10.1093\/nar\/20.20.5351","article-title":"Characterization of Chlorella virus PBCV-1 CviAII restriction and modification system","volume":"20","author":"Y Zhang","year":"1992","journal-title":"Nucleic Acids Res"},{"issue":"4587","key":"pone.0330887.ref046","doi-asserted-by":"crossref","first-page":"994","DOI":"10.1126\/science.219.4587.994","article-title":"Virus infection of culturable chlorella-like algae and dlevelopment of a plaque assay","volume":"219","author":"JL VAN Etten","year":"1983","journal-title":"Science"},{"issue":"5615","key":"pone.0330887.ref047","doi-asserted-by":"crossref","first-page":"2033","DOI":"10.1126\/science.1081867","article-title":"A giant virus in amoebae","volume":"299","author":"B La Scola","year":"2003","journal-title":"Science"},{"issue":"1","key":"pone.0330887.ref048","doi-asserted-by":"crossref","first-page":"94","DOI":"10.1016\/0042-6822(84)90150-8","article-title":"The role of DNA methylation in virus replication: inhibition of frog virus 3 replication by 5-azacytidine","volume":"138","author":"R Goorha","year":"1984","journal-title":"Virology"},{"issue":"2","key":"pone.0330887.ref049","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/j.virol.2013.04.018","article-title":"Evaluation of higher plant virus resistance genes in the green alga, Chlorella variabilis NC64A, during the early phase of infection with Paramecium bursaria chlorella virus-1","volume":"442","author":"JM Rowe","year":"2013","journal-title":"Virology"},{"issue":"4","key":"pone.0330887.ref050","doi-asserted-by":"crossref","first-page":"407","DOI":"10.1038\/nmeth.4184","article-title":"Detecting DNA cytosine methylation using nanopore sequencing","volume":"14","author":"JT Simpson","year":"2017","journal-title":"Nat Methods"},{"issue":"1","key":"pone.0330887.ref051","doi-asserted-by":"crossref","first-page":"3438","DOI":"10.1038\/s41467-021-23778-6","article-title":"Systematic benchmarking of tools for CpG methylation detection from nanopore sequencing","volume":"12","author":"ZW-S Yuen","year":"2021","journal-title":"Nat Commun"},{"issue":"9","key":"pone.0330887.ref052","doi-asserted-by":"crossref","first-page":"620","DOI":"10.1038\/s41576-025-00822-5","article-title":"Computational analysis of DNA methylation from long-read sequencing","volume":"26","author":"Y Fu","year":"2025","journal-title":"Nat Rev Genet"},{"issue":"2","key":"pone.0330887.ref053","article-title":"Growth condition-dependent differences in methylation imply transiently differentiated DNA methylation states in Escherichia coli","volume":"13","author":"GL Breckell","year":"2022","journal-title":"G3 Genes|Genomes|Genetics"},{"key":"pone.0330887.ref054","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1016\/j.virol.2014.07.023","article-title":"Attenuation of virus production at high multiplicities of infection in Aureococcus anophagefferens","author":"CM 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