{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,16]],"date-time":"2026-10-16T07:26:33Z","timestamp":1792135593976,"version":"4.4.0"},"reference-count":89,"publisher":"Public Library of Science (PLoS)","issue":"6","license":[{"start":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T00:00:00Z","timestamp":1687392000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","award":["(201606330071)"],"award-info":[{"award-number":["(201606330071)"]}],"id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["(20H03057)"],"award-info":[{"award-number":["(20H03057)"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014446","name":"Tula Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014446","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100014446","name":"Tula Foundation","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100014446","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"abstract":"<jats:p>Sea lice, the major ectoparasites of fish, have significant economic impacts on wild and farmed finfish, and have been implicated in the decline of wild salmon populations. As blood-feeding arthropods, sea lice may also be reservoirs for viruses infecting fish. However, except for two groups of negative-strand RNA viruses within the order <jats:italic>Mononegavirales<\/jats:italic>, nothing is known about viruses of sea lice. Here, we used transcriptomic data from three key species of sea lice (<jats:italic>Lepeophtheirus salmonis<\/jats:italic>, <jats:italic>Caligus clemensi<\/jats:italic>, and <jats:italic>Caligus rogercresseyi<\/jats:italic>) to identify 32 previously unknown RNA viruses. The viruses encompassed all the existing phyla of RNA viruses, with many placed in deeply branching lineages that likely represent new families and genera. Importantly, the presence of canonical virus-derived small interfering RNAs (viRNAs) indicates that most of these viruses infect sea lice, even though in some cases their closest classified relatives are only known to infect plants or fungi. We also identified both viRNAs and PIWI-interacting RNAs (piRNAs) from sequences of a bunya-like and two qin-like viruses in <jats:italic>C<\/jats:italic>. <jats:italic>rogercresseyi<\/jats:italic>. Our analyses showed that most of the viruses found in <jats:italic>C<\/jats:italic>. <jats:italic>rogercresseyi<\/jats:italic> occurred in multiple life stages, spanning from planktonic to parasitic stages. Phylogenetic analysis revealed that many of the viruses infecting sea lice were closely related to those that infect a wide array of eukaryotes with which arthropods associate, including fungi and parasitic tapeworms, implying that over evolutionary time there has been cross-phylum and cross-kingdom switching of viruses between arthropods and other eukaryotes. Overall, this study greatly expands our view of virus diversity in crustaceans, identifies viruses that infect and replicate in sea lice, and provides evidence that over evolutionary time, viruses have switched between arthropods and eukaryotic hosts in other phyla and kingdoms.<\/jats:p>","DOI":"10.1371\/journal.ppat.1011386","type":"journal-article","created":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T18:50:53Z","timestamp":1687459853000},"page":"e1011386","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":14,"title":["Divergent RNA viruses infecting sea lice, major ectoparasites of fish"],"prefix":"10.1371","volume":"19","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-3131-4884","authenticated-orcid":true,"given":"Tianyi","family":"Chang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian P. V.","family":"Hunt","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junya","family":"Hirai","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0372-0033","authenticated-orcid":true,"given":"Curtis A.","family":"Suttle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2023,6,22]]},"reference":[{"key":"ppat.1011386.ref001","doi-asserted-by":"crossref","first-page":"86","DOI":"10.1016\/j.parint.2014.10.006","article-title":"Instar growth and molt increments in Lepeophtheirus salmonis (Copepoda: Caligidae) chalimus larvae","volume":"64","author":"C Eichner","year":"2015","journal-title":"Parasitol Int"},{"key":"ppat.1011386.ref002","doi-asserted-by":"crossref","first-page":"101","DOI":"10.1016\/S0044-8486(02)00512-4","article-title":"Life cycle of Caligus rogercresseyi, (Copepoda: Caligidae) parasite of Chilean reared salmonids","volume":"220","author":"L Gonz\u00e1lez","year":"2003","journal-title":"Aquaculture"},{"key":"ppat.1011386.ref003","doi-asserted-by":"crossref","first-page":"1304","DOI":"10.1016\/j.icesjms.2006.04.017","article-title":"A review of the biology and genetics of sea lice","volume":"63","author":"K. Boxaspen","year":"2006","journal-title":"ICES J Mar Sci"},{"key":"ppat.1011386.ref004","doi-asserted-by":"crossref","first-page":"3385","DOI":"10.1098\/rspb.2009.0771","article-title":"How sea lice from salmon farms may cause wild salmonid declines in Europe and North America and be a threat to fishes elsewhere","volume":"276","author":"MJ Costello","year":"2009","journal-title":"Proc R Soc B Biol Sci"},{"key":"ppat.1011386.ref005","doi-asserted-by":"crossref","first-page":"1255","DOI":"10.1139\/f2012-063","article-title":"A widespread decrease in productivity of sockeye salmon (Oncorhynchus nerka) populations in western North America","volume":"69","author":"RM Peterman","year":"2012","journal-title":"Can J Fish Aquat Sci"},{"key":"ppat.1011386.ref006","doi-asserted-by":"crossref","first-page":"1507","DOI":"10.1139\/cjfas-2017-0127","article-title":"Canada\u2019s Wild Salmon Policy: an assessment of conservation progress in British Columbia","volume":"74","author":"MHH Price","year":"2017","journal-title":"Can J Fish Aquat Sci"},{"key":"ppat.1011386.ref007","doi-asserted-by":"crossref","first-page":"1772","DOI":"10.1126\/science.1148744","article-title":"Declining wild salmon populations in relation to parasites from farm salmon","volume":"318","author":"M Krko\u0161ek","year":"2007","journal-title":"Science"},{"key":"ppat.1011386.ref008","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1111\/jfb.13325","article-title":"Reduced growth in wild juvenile sockeye salmon Oncorhynchus nerka infected with sea lice","volume":"91","author":"SC Godwin","year":"2017","journal-title":"J Fish Biol"},{"key":"ppat.1011386.ref009","doi-asserted-by":"crossref","first-page":"155","DOI":"10.3354\/dao02414","article-title":"Vector potential of the salmon louse Lepeophtheirus salmonis in the transmission of infectious haematopoietic necrosis virus (IHNV)","volume":"97","author":"E Jakob","year":"2011","journal-title":"Dis Aquat Organ"},{"key":"ppat.1011386.ref010","doi-asserted-by":"crossref","first-page":"e112517","DOI":"10.1371\/journal.pone.0112517","article-title":"Genomic characterization and phylogenetic position of two new species in Rhabdoviridae infecting the parasitic copepod, salmon louse (Lepeophtheirus salmonis).","volume":"9","author":"AL \u00d8kland","year":"2014","journal-title":"PLoS ONE"},{"key":"ppat.1011386.ref011","doi-asserted-by":"crossref","first-page":"675","DOI":"10.1007\/s00705-018-04119-3","article-title":"Genomic characterization, phylogenetic position and in situ localization of a novel putative mononegavirus in Lepeophtheirus salmonis","volume":"164","author":"AL \u00d8kland","year":"2019","journal-title":"Arch Virol"},{"key":"ppat.1011386.ref012","first-page":"1","article-title":"The evolution, diversity, and host associations of rhabdoviruses","author":"B Longdon","year":"2015","journal-title":"Virus Evol."},{"key":"ppat.1011386.ref013","doi-asserted-by":"crossref","first-page":"1657","DOI":"10.1007\/s00705-018-3768-z","article-title":"The complete genome sequence of CrRV-Ch01, a new member of the family Rhabdoviridae in the parasitic copepod Caligus rogercresseyi present on farmed Atlantic salmon (Salmo salar) in Chile.","volume":"163","author":"AL \u00d8kland","year":"2018","journal-title":"Arch Virol"},{"key":"ppat.1011386.ref014","doi-asserted-by":"crossref","first-page":"14030","DOI":"10.1038\/s41598-017-14282-3","article-title":"RNAi-mediated treatment of two vertically transmitted rhabdovirus infecting the salmon louse (Lepeophtheirus salmonis).","volume":"7","author":"A-C \u00d8verg\u00e5rd","year":"2017","journal-title":"Sci Rep"},{"key":"ppat.1011386.ref015","doi-asserted-by":"crossref","first-page":"1127","DOI":"10.1111\/mpp.12466","article-title":"Deep sequencing of mycovirus-derived small RNAs from Botrytis species","volume":"18","author":"L Donaire","year":"2016","journal-title":"Mol Plant Pathol"},{"key":"ppat.1011386.ref016","doi-asserted-by":"crossref","first-page":"855","DOI":"10.1017\/S0031182019001689","article-title":"Small RNAs in parasitic nematodes\u2013forms and functions","volume":"147","author":"C Britton","year":"2020","journal-title":"Parasitology"},{"key":"ppat.1011386.ref017","doi-asserted-by":"crossref","first-page":"9343","DOI":"10.1093\/nar\/gkz678","article-title":"Highly efficacious antiviral protection of plants by small interfering RNAs identified in vitro","volume":"47","author":"S Gago-Zachert","year":"2019","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011386.ref018","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1002\/eji.201242806","article-title":"Host defense against DNA virus infection in shrimp is mediated by the siRNA pathway: cellular immune response","volume":"43","author":"T Huang","year":"2013","journal-title":"Eur J Immunol"},{"key":"ppat.1011386.ref019","doi-asserted-by":"crossref","first-page":"e1002210","DOI":"10.1371\/journal.pbio.1002210","article-title":"The discovery, distribution, and evolution of viruses associated with Drosophila melanogaster","volume":"13","author":"CL Webster","year":"2015","journal-title":"PLoS Biol"},{"key":"ppat.1011386.ref020","doi-asserted-by":"crossref","first-page":"3477","DOI":"10.1093\/nar\/gkw044","article-title":"Sequence-independent characterization of viruses based on the pattern of viral small RNAs produced by the host","volume":"44","author":"ERGR Aguiar","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011386.ref021","doi-asserted-by":"crossref","first-page":"e24758","DOI":"10.1371\/journal.pone.0024758","article-title":"Discovery of DNA viruses in wild-caught mosquitoes using small RNA high throughput sequencing","volume":"6","author":"M Ma","year":"2011","journal-title":"PLoS ONE"},{"key":"ppat.1011386.ref022","doi-asserted-by":"crossref","first-page":"13","DOI":"10.1016\/j.ibmb.2019.04.008","article-title":"Small RNA responses of Culex mosquitoes and cell lines during acute and persistent virus infection","volume":"109","author":"C R\u00fcckert","year":"2019","journal-title":"Insect Biochem Mol Biol"},{"key":"ppat.1011386.ref023","doi-asserted-by":"crossref","first-page":"271","DOI":"10.3390\/v11030271","article-title":"Mosquito small RNA responses to West Nile and insect-specific virus infections in Aedes and Culex mosquito cells","volume":"11","author":"G G\u00f6ertz","year":"2019","journal-title":"Viruses"},{"key":"ppat.1011386.ref024","doi-asserted-by":"crossref","first-page":"11473","DOI":"10.1128\/JVI.01695-15","article-title":"Viral small-RNA analysis of Bombyx mori larval midgut during persistent and pathogenic cytoplasmic polyhedrosis virus infection","volume":"89","author":"A Zografidis","year":"2015","journal-title":"J Virol"},{"key":"ppat.1011386.ref025","doi-asserted-by":"crossref","first-page":"e00158","DOI":"10.1128\/JVI.00158-17","article-title":"A diverse range of novel RNA viruses in geographically distinct honey bee populations","volume":"91","author":"EJ Remnant","year":"2017","journal-title":"J Virol"},{"key":"ppat.1011386.ref026","doi-asserted-by":"crossref","first-page":"176","DOI":"10.1016\/j.virol.2014.02.012","article-title":"Characterization of viral siRNA populations in honey bee colony collapse disorder","volume":"454\u2013455","author":"N Chejanovsky","year":"2014","journal-title":"Virology"},{"key":"ppat.1011386.ref027","doi-asserted-by":"crossref","first-page":"vez061","DOI":"10.1093\/ve\/vez061","article-title":"A new lineage of segmented RNA viruses infecting animals","volume":"6","author":"DJ Obbard","year":"2020","journal-title":"Virus Evol"},{"key":"ppat.1011386.ref028","doi-asserted-by":"crossref","first-page":"D708","DOI":"10.1093\/nar\/gkx932","article-title":"Virus taxonomy: the database of the International Committee on Taxonomy of Viruses (ICTV).","volume":"46","author":"EJ Lefkowitz","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"ppat.1011386.ref029","doi-asserted-by":"crossref","first-page":"e00061","DOI":"10.1128\/MMBR.00061-19","article-title":"Global organization and proposed megataxonomy of the virus world","volume":"84","author":"EV Koonin","year":"2020","journal-title":"Microbiol Mol Biol Rev"},{"key":"ppat.1011386.ref030","first-page":"e02329","article-title":"Origins and evolution of the global RNA virome","volume":"9","author":"YI Wolf","year":"2018","journal-title":"mBio"},{"key":"ppat.1011386.ref031","doi-asserted-by":"crossref","first-page":"1530","DOI":"10.1093\/molbev\/msaa015","article-title":"IQ-TREE 2: new models and efficient methods for phylogenetic inference in the genomic era","volume":"37","author":"BQ Minh","year":"2020","journal-title":"Mol Biol Evol"},{"key":"ppat.1011386.ref032","doi-asserted-by":"crossref","first-page":"587","DOI":"10.1038\/nmeth.4285","article-title":"ModelFinder: fast model selection for accurate phylogenetic estimates","volume":"14","author":"S Kalyaanamoorthy","year":"2017","journal-title":"Nat Methods"},{"key":"ppat.1011386.ref033","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/s41577-018-0071-x","article-title":"Small RNA-based antimicrobial immunity","volume":"19","author":"Z Guo","year":"2019","journal-title":"Nat Rev Immunol"},{"key":"ppat.1011386.ref034","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1038\/s41597-021-00842-w","article-title":"Chromosome-scale genome assembly of the sea louse Caligus rogercresseyi by SMRT sequencing and Hi-C analysis","volume":"8","author":"C Gallardo-Esc\u00e1rate","year":"2021","journal-title":"Sci Data"},{"key":"ppat.1011386.ref035","first-page":"255","article-title":"The importance of small planktonic copepods and their roles in pelagic marine food webs","volume":"43","author":"J. Turner","year":"2004","journal-title":"Zool Stud"},{"key":"ppat.1011386.ref036","doi-asserted-by":"crossref","first-page":"e41244","DOI":"10.7554\/eLife.41244","article-title":"Control of RNA viruses in mosquito cells through the acquisition of vDNA and endogenous viral elements","volume":"8","author":"M Tassetto","year":"2019","journal-title":"eLife"},{"key":"ppat.1011386.ref037","doi-asserted-by":"crossref","first-page":"e05378","DOI":"10.7554\/eLife.05378","article-title":"Unprecedented genomic diversity of RNA viruses in arthropods reveals the ancestry of negative-sense RNA viruses","volume":"4","author":"C-X Li","year":"2015","journal-title":"eLife"},{"key":"ppat.1011386.ref038","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1038\/nature20167","article-title":"Redefining the invertebrate RNA virosphere","volume":"540","author":"M Shi","year":"2016","journal-title":"Nature"},{"key":"ppat.1011386.ref039","doi-asserted-by":"crossref","first-page":"e1008224","DOI":"10.1371\/journal.ppat.1008224","article-title":"Re-assessing the diversity of negative strand RNA viruses in insects","volume":"15","author":"S K\u00e4fer","year":"2019","journal-title":"PLoS Pathog"},{"key":"ppat.1011386.ref040","first-page":"e00039","article-title":"Abundant and diverse RNA viruses in insects revealed by RNA-seq analysis: ecological and evolutionary implications","volume":"5","author":"H Wu","year":"2020","journal-title":"mSystems"},{"key":"ppat.1011386.ref041","doi-asserted-by":"crossref","first-page":"1375","DOI":"10.1073\/pnas.1216595110","article-title":"Molecular and microscopic evidence of viruses in marine copepods","volume":"110","author":"DS Dunlap","year":"2013","journal-title":"Proc Natl Acad Sci"},{"key":"ppat.1011386.ref042","author":"R-L Roennfeldt","year":"2013"},{"key":"ppat.1011386.ref043","doi-asserted-by":"crossref","first-page":"1220","DOI":"10.1111\/fwb.12938","article-title":"Distribution of circular single-stranded DNA viruses associated with benthic amphipods of genus Diporeia in the Laurentian Great Lakes","volume":"62","author":"KSI Bistolas","year":"2017","journal-title":"Freshw Biol"},{"key":"ppat.1011386.ref044","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1016\/j.jglr.2013.06.006","article-title":"Investigation of viruses in Diporeia spp. from the Laurentian Great Lakes and Owasco Lake as potential stressors of declining populations","volume":"39","author":"I Hewson","year":"2013","journal-title":"J Gt Lakes Res"},{"key":"ppat.1011386.ref045","doi-asserted-by":"crossref","first-page":"1605","DOI":"10.4319\/lo.2013.58.5.1605","article-title":"Metagenomic identification, seasonal dynamics, and potential transmission mechanisms of a Daphnia-associated single-stranded DNA virus in two temperate lakes","volume":"58","author":"I Hewson","year":"2013","journal-title":"Limnol Oceanogr"},{"key":"ppat.1011386.ref046","doi-asserted-by":"crossref","first-page":"509","DOI":"10.3389\/fmicb.2020.00509","article-title":"Virome analysis of aphid populations that infest the Barley field: the discovery of two novel groups of Nege\/Kita-like viruses and other novel RNA viruses","volume":"11","author":"H Kondo","year":"2020","journal-title":"Front Microbiol"},{"key":"ppat.1011386.ref047","doi-asserted-by":"crossref","first-page":"8448","DOI":"10.1038\/s41598-021-87122-0","article-title":"Metagenomic shotgun sequencing reveals host species as an important driver of virome composition in mosquitoes","volume":"11","author":"P Thongsripong","year":"2021","journal-title":"Sci Rep"},{"key":"ppat.1011386.ref048","doi-asserted-by":"crossref","first-page":"768","DOI":"10.3390\/v13050768","article-title":"Virome diversity among mosquito populations in a sub-urban region of Marseille, France.","volume":"13","author":"A Nebbak","year":"2021","journal-title":"Viruses"},{"key":"ppat.1011386.ref049","doi-asserted-by":"crossref","first-page":"121","DOI":"10.1186\/s40168-019-0734-2","article-title":"Stable distinct core eukaryotic viromes in different mosquito species from Guadeloupe, using single mosquito viral metagenomics","volume":"7","author":"C Shi","year":"2019","journal-title":"Microbiome"},{"key":"ppat.1011386.ref050","doi-asserted-by":"crossref","first-page":"e68353","DOI":"10.7554\/eLife.68353","article-title":"Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay","volume":"10","author":"J Batson","year":"2021","journal-title":"eLife"},{"key":"ppat.1011386.ref051","doi-asserted-by":"crossref","first-page":"1606","DOI":"10.1073\/pnas.0911353107","article-title":"Virus discovery by deep sequencing and assembly of virus-derived small silencing RNAs","volume":"107","author":"Q Wu","year":"2010","journal-title":"Proc Natl Acad Sci"},{"key":"ppat.1011386.ref052","doi-asserted-by":"crossref","first-page":"R592","DOI":"10.1016\/j.cub.2019.04.057","article-title":"The phylogeny and evolutionary history of arthropods","volume":"29","author":"G Giribet","year":"2019","journal-title":"Curr Biol"},{"key":"ppat.1011386.ref053","article-title":"Entomophthovirus: an insect-derived iflavirus that infects a behavior manipulating fungal pathogen of dipterans","author":"MC Coyle","year":"2018","journal-title":"BioRxiv"},{"key":"ppat.1011386.ref054","doi-asserted-by":"crossref","first-page":"713","DOI":"10.3390\/v10120713","article-title":"Transcriptional and small RNA responses of the white mold fungus Sclerotinia sclerotiorum to infection by a virulence-attenuating hypovirus","volume":"10","author":"S-Y Lee Marzano","year":"2018","journal-title":"Viruses"},{"key":"ppat.1011386.ref055","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1002\/jobm.201700325","article-title":"Identification of virus-derived siRNAs and their targets in RBSDV-infected rice by deep sequencing","volume":"58","author":"Y Lan","year":"2018","journal-title":"J Basic Microbiol"},{"key":"ppat.1011386.ref056","doi-asserted-by":"crossref","first-page":"19268","DOI":"10.1038\/s41598-019-55547-3","article-title":"Plant virome reconstruction and antiviral RNAi characterization by deep sequencing of small RNAs from dried leaves","volume":"9","author":"V Golyaev","year":"2019","journal-title":"Sci Rep"},{"key":"ppat.1011386.ref057","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1016\/j.virol.2009.07.005","article-title":"Deep-sequencing of plant viral small RNAs reveals effective and widespread targeting of viral genomes","volume":"392","author":"L Donaire","year":"2009","journal-title":"Virology"},{"key":"ppat.1011386.ref058","doi-asserted-by":"crossref","first-page":"e02124","DOI":"10.1128\/JVI.02124-18","article-title":"Endogenous viral elements are widespread in arthropod genomes and commonly give rise to PIWI-interacting RNAs","volume":"93","author":"AM Ter Horst","year":"2019","journal-title":"J Virol"},{"key":"ppat.1011386.ref059","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1146\/annurev-phyto-030320-041346","article-title":"Deep roots and splendid boughs of the global plant virome","volume":"58","author":"VV Dolja","year":"2020","journal-title":"Annu Rev Phytopathol"},{"key":"ppat.1011386.ref060","doi-asserted-by":"crossref","first-page":"36","DOI":"10.1016\/j.virusres.2017.10.020","article-title":"Metagenomics reshapes the concepts of RNA virus evolution by revealing extensive horizontal virus transfer","volume":"244","author":"VV Dolja","year":"2018","journal-title":"Virus Res"},{"key":"ppat.1011386.ref061","doi-asserted-by":"crossref","first-page":"18","DOI":"10.1016\/j.jip.2014.05.002","article-title":"The ability to cause infection in a pathogenic fungus uncovers a new biological feature of honey bee viruses","volume":"120","author":"Z Li","year":"2014","journal-title":"J Invertebr Pathol"},{"key":"ppat.1011386.ref062","doi-asserted-by":"crossref","first-page":"e1006215","DOI":"10.1371\/journal.ppat.1006215","article-title":"Comparative analysis estimates the relative frequencies of co-divergence and cross-species transmission within viral families","volume":"13","author":"JL Geoghegan","year":"2017","journal-title":"PLoS Pathog"},{"key":"ppat.1011386.ref063","doi-asserted-by":"crossref","first-page":"1755","DOI":"10.1038\/s41396-020-0642-2","article-title":"Characterization of viruses in a tapeworm: phylogenetic position, vertical transmission, and transmission to the parasitized host","volume":"14","author":"MA Hahn","year":"2020","journal-title":"ISME J"},{"key":"ppat.1011386.ref064","first-page":"103","article-title":"Potential origins of fish toti-like viruses in invertebrates","author":"AJ Tighe","year":"2022","journal-title":"J Gen Virol"},{"key":"ppat.1011386.ref065","first-page":"4","article-title":"Hidden diversity and evolution of viruses in market fish","author":"JL Geoghegan","year":"2018","journal-title":"Virus Evol"},{"key":"ppat.1011386.ref066","doi-asserted-by":"crossref","first-page":"1063","DOI":"10.3390\/v13061063","article-title":"Comparative molecular characterization of novel and known piscine toti-like viruses","volume":"13","author":"L Sandlund","year":"2021","journal-title":"Viruses"},{"key":"ppat.1011386.ref067","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1007\/s10126-011-9398-z","article-title":"Genomic resources for sea lice: analysis of ESTs and mitochondrial genomes","volume":"14","author":"M Yasuike","year":"2012","journal-title":"Mar Biotechnol"},{"key":"ppat.1011386.ref068","doi-asserted-by":"crossref","first-page":"9","DOI":"10.1016\/j.cbd.2014.01.003","article-title":"High-throughput SNP discovery and transcriptome expression profiles from the salmon louse Caligus rogercresseyi (Copepoda: Caligidae).","volume":"10","author":"G Nu\u00f1ez-Acu\u00f1a","year":"2014","journal-title":"Comp Biochem Physiol Part D Genomics Proteomics"},{"key":"ppat.1011386.ref069","doi-asserted-by":"crossref","first-page":"1953","DOI":"10.1007\/s10980-017-0557-0","article-title":"Network analysis reveals strong seasonality in the dispersal of a marine parasite and identifies areas for coordinated management","volume":"32","author":"F Samsing","year":"2017","journal-title":"Landsc Ecol"},{"key":"ppat.1011386.ref070","doi-asserted-by":"crossref","first-page":"195","DOI":"10.3354\/meps230195","article-title":"Mortality of marine planktonic copepods: global rates and patterns","volume":"230","author":"AG Hirst","year":"2002","journal-title":"Mar Ecol Prog Ser"},{"key":"ppat.1011386.ref071","doi-asserted-by":"crossref","first-page":"115","DOI":"10.3354\/dao023115","article-title":"Taura syndrome in Penaeus vannamei: demonstration of a viral etiology","volume":"23","author":"H Kw","year":"1995","journal-title":"Dis Aquat Organ"},{"key":"ppat.1011386.ref072","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1126\/science.285.5424.110","article-title":"Replication of subgenomic hepatitis C virus RNAs in a hepatoma cell line","volume":"285","author":"V Lohmann","year":"1999","journal-title":"Science"},{"key":"ppat.1011386.ref073","article-title":"Ribosome-linked mRNA-rRNA chimeras reveal active novel virus host associations","author":"JC Ignacio-Espinoza","year":"2020","journal-title":"BioRxiv"},{"key":"ppat.1011386.ref074","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ppat.1011386.ref075","doi-asserted-by":"crossref","first-page":"3211","DOI":"10.1093\/bioinformatics\/bts611","article-title":"SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data","volume":"28","author":"E Kopylova","year":"2012","journal-title":"Bioinformatics"},{"key":"ppat.1011386.ref076","doi-asserted-by":"crossref","first-page":"giz100","DOI":"10.1093\/gigascience\/giz100","article-title":"rnaSPAdes: a de novo transcriptome assembler and its application to RNA-Seq data","volume":"8","author":"E Bushmanova","year":"2019","journal-title":"GigaScience"},{"key":"ppat.1011386.ref077","doi-asserted-by":"crossref","first-page":"644","DOI":"10.1038\/nbt.1883","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"MG Grabherr","year":"2011","journal-title":"Nat Biotechnol"},{"key":"ppat.1011386.ref078","doi-asserted-by":"crossref","first-page":"3150","DOI":"10.1093\/bioinformatics\/bts565","article-title":"CD-HIT: accelerated for clustering the next-generation sequencing data","volume":"28","author":"L Fu","year":"2012","journal-title":"Bioinformatics"},{"key":"ppat.1011386.ref079","doi-asserted-by":"crossref","first-page":"772","DOI":"10.1093\/molbev\/mst010","article-title":"MAFFT multiple sequence alignment software version 7: improvements in performance and usability","volume":"30","author":"K Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"ppat.1011386.ref080","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","author":"S Capella-Gutierrez","year":"2009","journal-title":"Bioinformatics"},{"key":"ppat.1011386.ref081","doi-asserted-by":"crossref","first-page":"1189","DOI":"10.1093\/bioinformatics\/btp033","article-title":"Jalview Version 2\u2014a multiple sequence alignment editor and analysis workbench","volume":"25","author":"AM Waterhouse","year":"2009","journal-title":"Bioinformatics"},{"key":"ppat.1011386.ref082","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1093\/molbev\/msx281","article-title":"UFBoot2: improving the ultrafast bootstrap approximation","volume":"35","author":"DT Hoang","year":"2018","journal-title":"Mol Biol Evol"},{"key":"ppat.1011386.ref083","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1016\/j.margen.2019.01.005","article-title":"Characterization of the salmon louse Lepeophtheirus salmonis miRNome: sex-biased differences related to the coding and non-coding RNA interplay","volume":"45","author":"G N\u00fa\u00f1ez-Acu\u00f1a","year":"2019","journal-title":"Mar Genomics"},{"key":"ppat.1011386.ref084","doi-asserted-by":"crossref","first-page":"357","DOI":"10.1038\/nmeth.1923","article-title":"Fast gapped-read alignment with Bowtie 2","volume":"9","author":"B Langmead","year":"2012","journal-title":"Nat Methods"},{"key":"ppat.1011386.ref085","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":"ppat.1011386.ref086","doi-asserted-by":"crossref","first-page":"174","DOI":"10.1038\/s41559-017-0403-4","article-title":"Pan-arthropod analysis reveals somatic piRNAs as an ancestral defence against transposable elements","volume":"2","author":"SH Lewis","year":"2018","journal-title":"Nat Ecol Evol"},{"key":"ppat.1011386.ref087","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1038\/nmeth.4197","article-title":"Salmon provides fast and bias-aware quantification of transcript expression","volume":"14","author":"R Patro","year":"2017","journal-title":"Nat Methods"},{"key":"ppat.1011386.ref088","doi-asserted-by":"crossref","first-page":"1686","DOI":"10.21105\/joss.01686","article-title":"Welcome to the Tidyverse","volume":"4","author":"H Wickham","year":"2019","journal-title":"J Open Source Softw."},{"key":"ppat.1011386.ref089","author":"H Wickham","year":"2016"}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011386","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,6,22]],"date-time":"2023-06-22T18:51:41Z","timestamp":1687459901000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1011386"}},"subtitle":[],"editor":[{"given":"Jens H.","family":"Kuhn","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,6,22]]},"references-count":89,"journal-issue":{"issue":"6","published-online":{"date-parts":[[2023,6,22]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1011386","relation":{},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,6,22]]}}}