{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T22:12:21Z","timestamp":1791843141944,"version":"4.3.4"},"update-to":[{"DOI":"10.1371\/journal.ppat.1008216","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,1,10]],"date-time":"2020-01-10T00:00:00Z","timestamp":1578614400000}}],"reference-count":74,"publisher":"Public Library of Science (PLoS)","issue":"12","license":[{"start":{"date-parts":[[2019,12,30]],"date-time":"2019-12-30T00:00:00Z","timestamp":1577664000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"crossref","award":["1138860"],"award-info":[{"award-number":["1138860"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"crossref","award":["FL170100022"],"award-info":[{"award-number":["FL170100022"]}],"id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"crossref","award":["1037304"],"award-info":[{"award-number":["1037304"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"crossref","award":["1045156"],"award-info":[{"award-number":["1045156"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"crossref","award":["1042072"],"award-info":[{"award-number":["1042072"]}],"id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["www.plospathogens.org"],"crossmark-restriction":false},"short-container-title":["PLoS Pathog"],"DOI":"10.1371\/journal.ppat.1008216","type":"journal-article","created":{"date-parts":[[2019,12,30]],"date-time":"2019-12-30T13:47:52Z","timestamp":1577713672000},"page":"e1008216","update-policy":"https:\/\/doi.org\/10.1371\/journal.ppat.corrections_policy","source":"Crossref","is-referenced-by-count":80,"title":["Novel RNA viruses associated with Plasmodium vivax in human malaria and Leucocytozoon parasites in avian disease"],"prefix":"10.1371","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5602-6600","authenticated-orcid":true,"given":"Justine","family":"Charon","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Matthew J.","family":"Grigg","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John-Sebastian","family":"Eden","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7414-9604","authenticated-orcid":true,"given":"Kim A.","family":"Piera","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hafsa","family":"Rana","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Timothy","family":"William","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karrie","family":"Rose","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4751-1831","authenticated-orcid":true,"given":"Miles P.","family":"Davenport","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicholas M.","family":"Anstey","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9596-3552","authenticated-orcid":true,"given":"Edward C.","family":"Holmes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2019,12,30]]},"reference":[{"key":"ppat.1008216.ref001","doi-asserted-by":"crossref","first-page":"151","DOI":"10.1007\/s11084-010-9194-1","article-title":"Defining life: the virus viewpoint","volume":"40","author":"P Forterre","year":"2010","journal-title":"Orig Life Evol Biosph"},{"key":"ppat.1008216.ref002","doi-asserted-by":"crossref","first-page":"e368","DOI":"10.1371\/journal.pbio.0040368","article-title":"The marine viromes of four oceanic regions","volume":"4","author":"FE Angly","year":"2006","journal-title":"PLoS Biol"},{"key":"ppat.1008216.ref003","doi-asserted-by":"crossref","first-page":"1795","DOI":"10.1126\/science.1127404","article-title":"Metagenomic analysis of coastal RNA virus communities","volume":"312","author":"AI Culley","year":"2006","journal-title":"Science"},{"key":"ppat.1008216.ref004","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1038\/nature06735","article-title":"Biodiversity and biogeography of phages in modern stromatolites and thrombolites","volume":"452","author":"C Desnues","year":"2008","journal-title":"Nature"},{"key":"ppat.1008216.ref005","doi-asserted-by":"crossref","first-page":"425","DOI":"10.1038\/nature19094","article-title":"Uncovering Earth\u2019s virome","volume":"536","author":"D Paez-Espino","year":"2016","journal-title":"Nature"},{"key":"ppat.1008216.ref006","doi-asserted-by":"crossref","first-page":"356","DOI":"10.1038\/nature04160","article-title":"Viruses in the sea","volume":"437","author":"CA Suttle","year":"2005","journal-title":"Nature"},{"key":"ppat.1008216.ref007","doi-asserted-by":"crossref","first-page":"1168","DOI":"10.1016\/j.cell.2018.02.043","article-title":"Using metagenomics to characterize an expanding virosphere","volume":"172","author":"Y-Z Zhang","year":"2018","journal-title":"Cell"},{"key":"ppat.1008216.ref008","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1016\/0169-4758(88)90023-3","article-title":"Viruses of parasitic protozoa","volume":"4","author":"MA Miles","year":"1988","journal-title":"Parasitol Today"},{"key":"ppat.1008216.ref009","doi-asserted-by":"crossref","first-page":"289","DOI":"10.1046\/j.1365-2958.1997.5721933.x","article-title":"Virus-like, double-stranded RNAs in the parasitic protozoan Cryptosporidium parvum","volume":"26","author":"NV Khramtsov","year":"1997","journal-title":"Mol Microbiol"},{"key":"ppat.1008216.ref010","doi-asserted-by":"crossref","first-page":"189","DOI":"10.1016\/0166-6851(88)90003-5","article-title":"Purification and characterization of the Giardia lamblia double-stranded RNA virus","volume":"28","author":"RL Miller","year":"1988","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1008216.ref011","doi-asserted-by":"crossref","first-page":"9572","DOI":"10.1073\/pnas.85.24.9572","article-title":"LR1: a candidate RNA virus of Leishmania","volume":"85","author":"PI Tarr","year":"1988","journal-title":"Proc Natl Acad Sci USA"},{"key":"ppat.1008216.ref012","doi-asserted-by":"crossref","first-page":"3697","DOI":"10.1016\/S0021-9258(19)83679-7","article-title":"A linear double-stranded RNA in Trichomonas vaginalis","volume":"260","author":"AL Wang","year":"1985","journal-title":"J Biol Chem"},{"key":"ppat.1008216.ref013","doi-asserted-by":"crossref","first-page":"269","DOI":"10.1016\/0166-6851(86)90132-5","article-title":"Discovery of a specific double-stranded RNA virus in Giardia lamblia","volume":"21","author":"AL Wang","year":"1986","journal-title":"Mol Biochem Parasitol"},{"key":"ppat.1008216.ref014","doi-asserted-by":"crossref","first-page":"5979","DOI":"10.1073\/pnas.86.15.5979","article-title":"Characterization of a RNA virus from the parasite Leishmania","volume":"86","author":"G Widmer","year":"1989","journal-title":"Proc Natl Acad Sci USA"},{"key":"ppat.1008216.ref015","doi-asserted-by":"crossref","first-page":"e00715","DOI":"10.1128\/genomeA.00715-16","article-title":"A novel bunyavirus-like virus of trypanosomatid protist parasites","volume":"4","author":"NS Akopyants","year":"2016","journal-title":"Genome Announce"},{"key":"ppat.1008216.ref016","doi-asserted-by":"crossref","first-page":"E506","DOI":"10.1073\/pnas.1717806115","article-title":"Viral discovery and diversity in trypanosomatid protozoa with a focus on relatives of the human parasite","volume":"115","author":"D Grybchuk","year":"2018","journal-title":"Proc Natl Acad Sci USA"},{"key":"ppat.1008216.ref017","first-page":"e00713","article-title":"A narnavirus-like element from the trypanosomatid protozoan parasite Leptomonas seymouri","volume":"4","author":"L-F Lye","year":"2016","journal-title":"Genome Announce"},{"key":"ppat.1008216.ref018","doi-asserted-by":"crossref","first-page":"3827","DOI":"10.1007\/s00705-017-3559-y","article-title":"Leptomonas seymouri narna-like virus 1 and not leishmaniaviruses detected in kala-azar samples from India","volume":"162","author":"S Sukla","year":"2017","journal-title":"Arch Virol"},{"key":"ppat.1008216.ref019","unstructured":"Padma TV. Russian doll disease is a virus inside a parasite inside a fly. New Scientist. August 10th, 2015. https:\/\/www.newscientist.com\/article\/dn28020-russian-doll-disease-is-a-virus-inside-a-parasite-inside-a-fly\/."},{"key":"ppat.1008216.ref020","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1016\/j.actatropica.2016.11.028","article-title":"Viruses of parasites as actors in the parasite-host relationship: A \u201cm\u00e9nage \u00e0 trois\u201d","volume":"166","author":"A G\u00f3mez-Arreaza","year":"2017","journal-title":"Acta Tropica"},{"key":"ppat.1008216.ref021","doi-asserted-by":"crossref","first-page":"e48418","DOI":"10.1371\/journal.pone.0048418","article-title":"Endobiont viruses sensed by the human host\u2014beyond conventional antiparasitic therapy","volume":"7","author":"RN Fichorova","year":"2012","journal-title":"PLoS One"},{"key":"ppat.1008216.ref022","doi-asserted-by":"crossref","first-page":"533","DOI":"10.1016\/j.bjorl.2015.07.014","article-title":"Correlation between presence of Leishmania RNA virus 1 and clinical characteristics of nasal mucosal leishmaniosis","volume":"81","author":"MM Ito","year":"2015","journal-title":"Braz J Otorhinol"},{"key":"ppat.1008216.ref023","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1126\/science.1199326","article-title":"Leishmania RNA virus controls the severity of mucocutaneous leishmaniasis","volume":"331","author":"A Ives","year":"2011","journal-title":"Science"},{"key":"ppat.1008216.ref024","doi-asserted-by":"crossref","first-page":"11998","DOI":"10.1073\/pnas.1615085113","article-title":"Tilting the balance between RNA interference and replication eradicates Leishmania RNA virus 1 and mitigates the inflammatory response","volume":"113","author":"EA Brettmann","year":"2016","journal-title":"Proc Natl Acad Sci USA"},{"key":"ppat.1008216.ref025","doi-asserted-by":"crossref","first-page":"e2836","DOI":"10.1371\/journal.pntd.0002836","article-title":"Leishmania aethiopica field isolates bearing an endosymbiontic dsRNA virus induce pro-inflammatory cytokine response","volume":"8","author":"H Zangger","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"key":"ppat.1008216.ref026","doi-asserted-by":"crossref","first-page":"112","DOI":"10.1093\/infdis\/jiv354","article-title":"Association of the endobiont double-stranded RNA virus LRV1 with treatment failure for human Leishmaniasis caused by Leishmania braziliensis in Peru and Bolivia","volume":"213","author":"V Adaui","year":"2016","journal-title":"J Infect Dis"},{"key":"ppat.1008216.ref027","doi-asserted-by":"crossref","first-page":"105","DOI":"10.1093\/infdis\/jiv355","article-title":"Presence of Leishmania RNA Virus 1 in Leishmania guyanensis increases the risk of first-line treatment failure and symptomatic relapse","volume":"213","author":"E Bourreau","year":"2016","journal-title":"J Infect Dis"},{"key":"ppat.1008216.ref028","doi-asserted-by":"crossref","first-page":"1959","DOI":"10.1007\/s00705-009-0513-7","article-title":"Cryspovirus: a new genus of protozoan viruses in the family Partitiviridae","volume":"154","author":"ML Nibert","year":"2009","journal-title":"Arch Virol"},{"key":"ppat.1008216.ref029","doi-asserted-by":"crossref","first-page":"1051","DOI":"10.1016\/j.ijpara.2007.11.005","article-title":"Fecundity of Cryptosporidium parvum is correlated with intracellular levels of the viral symbiont CPV","volume":"38","author":"MC Jenkins","year":"2008","journal-title":"Int J Parasitol"},{"key":"ppat.1008216.ref030","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1016\/0035-9203(62)90137-2","article-title":"Electron microscope studies of motile stages of malaria parasites. III. The ookinetes of Haemamoeba and Plasmodium","volume":"56","author":"PC Garnham","year":"1962","journal-title":"Trans R Soc Trop Med Hyg"},{"key":"ppat.1008216.ref031","unstructured":"WHO. 2018. World Health Organization. World Malaria Report 2018."},{"key":"ppat.1008216.ref032","doi-asserted-by":"crossref","first-page":"377","DOI":"10.1128\/CMR.00051-10","article-title":"Epidemiology and infectivity of Plasmodium falciparum and Plasmodium vivax gametocytes in relation to malaria control and elimination","volume":"24","author":"T Bousema","year":"2011","journal-title":"Clin Micro Rev"},{"key":"ppat.1008216.ref033","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1093\/cid\/ciy065","article-title":"Age-related clinical spectrum of Plasmodium knowlesi malaria and predictors of severity","volume":"67","author":"MJ Grigg","year":"2018","journal-title":"Clin Infect Dis"},{"key":"ppat.1008216.ref034","first-page":"e00680","article-title":"High-resolution metatranscriptomics reveals the ecological dynamics of mosquito-associated RNA viruses in Western Australia","volume":"91","author":"M Shi","year":"2017","journal-title":"J Virol"},{"key":"ppat.1008216.ref035","doi-asserted-by":"crossref","first-page":"499","DOI":"10.1002\/prot.22458","article-title":"Structure is three to ten times more conserved than sequence\u2014a study of structural response in protein cores","volume":"77","author":"K Illerg\u00e5rd","year":"2009","journal-title":"Proteins"},{"key":"ppat.1008216.ref036","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1038\/nprot.2015.053","article-title":"The Phyre2 web portal for protein modeling, prediction and analysis","volume":"10","author":"LA Kelley","year":"2015","journal-title":"Nat Protocol"},{"key":"ppat.1008216.ref037","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1007\/s00705-011-1126-5","article-title":"A member of the virus family Narnaviridae from the plant pathogenic oomycete Phytophthora infestans","volume":"157","author":"G Cai","year":"2012","journal-title":"Arch Virol"},{"key":"ppat.1008216.ref038","doi-asserted-by":"crossref","first-page":"e02381","DOI":"10.1128\/JVI.02381-16","article-title":"Dinucleotide composition in animal RNA Viruses is shaped more by virus family than by host species","volume":"91","author":"F Di Giallonardo","year":"2017","journal-title":"J Virol"},{"key":"ppat.1008216.ref039","doi-asserted-by":"crossref","first-page":"89","DOI":"10.1186\/1756-3305-4-89","article-title":"The dominant Anopheles vectors of human malaria in the Asia-Pacific region: occurrence data, distribution maps and bionomic pr\u00e9cis","volume":"4","author":"ME Sinka","year":"2011","journal-title":"Parasit Vectors"},{"key":"ppat.1008216.ref040","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.1008216.ref041","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/1471-2148-4-2","article-title":"A molecular timescale of eukaryote evolution and the rise of complex multicellular life","volume":"4","author":"SB Hedges","year":"2004","journal-title":"BMC Evol Biol"},{"key":"ppat.1008216.ref042","doi-asserted-by":"crossref","first-page":"267","DOI":"10.1038\/nrg2323","article-title":"Rates of evolutionary change in viruses: patterns and determinants","volume":"9","author":"S Duffy","year":"2008","journal-title":"Nat Rev Genet"},{"key":"ppat.1008216.ref043","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.1008216.ref044","doi-asserted-by":"crossref","first-page":"e00711","DOI":"10.1128\/genomeA.00711-16","article-title":"A narnavirus in the trypanosomatid protist plant pathogen Phytomonas serpens","volume":"4","author":"NS Akopyants","year":"2016","journal-title":"Genome Announce"},{"key":"ppat.1008216.ref045","doi-asserted-by":"crossref","first-page":"2525","DOI":"10.1099\/vir.0.013086-0","article-title":"Molecular characterization of the plant virus genus Ourmiavirus and evidence of inter-kingdom reassortment of viral genome segments as its possible route of origin","volume":"90","author":"M Rastgou","year":"2009","journal-title":"J Gen Virol"},{"key":"ppat.1008216.ref046","doi-asserted-by":"crossref","DOI":"10.1002\/9780470015902.a0023269","article-title":"Capsid-less RNA viruses","author":"VV Dolja","year":"2012","journal-title":"eLS"},{"key":"ppat.1008216.ref047","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/B978-0-12-394315-6.00006-4","article-title":"The family Narnaviridae: simplest of RNA viruses","volume":"86","author":"BI Hillman","year":"2013","journal-title":"Adv Virus Res"},{"key":"ppat.1008216.ref048","doi-asserted-by":"crossref","first-page":"918","DOI":"10.1016\/j.pt.2016.08.014","article-title":"Why do some primate malarias relapse?","volume":"32","author":"NJ White","year":"2016","journal-title":"Trends Parasitol"},{"key":"ppat.1008216.ref049","doi-asserted-by":"crossref","first-page":"e0165340","DOI":"10.1371\/journal.pone.0165340","article-title":"Submicroscopic and asymptomatic Plasmodium parasitaemia associated with significant risk of anaemia in Papua, Indonesia","volume":"11","author":"Z Pava","year":"2016","journal-title":"PLoS One"},{"key":"ppat.1008216.ref050","doi-asserted-by":"crossref","first-page":"e1004558","DOI":"10.1371\/journal.ppat.1004558","article-title":"Parasite biomass-related inflammation, endothelial activation, microvascular dysfunction and disease severity in vivax malaria","volume":"11","author":"BE Barber","year":"2015","journal-title":"PLoS Pathog"},{"key":"ppat.1008216.ref051","doi-asserted-by":"crossref","first-page":"131","DOI":"10.1179\/000349803125002977","article-title":"Use of a rapid, single-round, multiplex PCR to detect malarial parasites and identify the species present","volume":"97","author":"D Padley","year":"2003","journal-title":"Ann Trop Med Parasitol"},{"key":"ppat.1008216.ref052","doi-asserted-by":"crossref","first-page":"4173","DOI":"10.1128\/JCM.00811-09","article-title":"Spurious amplification of a Plasmodium vivax small-subunit RNA gene by use of primers currently used to detect P. knowlesi","volume":"47","author":"M Imwong","year":"2009","journal-title":"J Clin Micro"},{"key":"ppat.1008216.ref053","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.1008216.ref054","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.1008216.ref055","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 Meth"},{"key":"ppat.1008216.ref056","first-page":"644","article-title":"Full-length transcriptome assembly from RNA-Seq data without a reference genome","volume":"29","author":"MG Grabherr","journal-title":"Nat Biotech 2011"},{"key":"ppat.1008216.ref057","doi-asserted-by":"crossref","first-page":"323","DOI":"10.1186\/1471-2105-12-323","article-title":"RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome","volume":"12","author":"B Li","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"ppat.1008216.ref058","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1038\/nmeth.3176","article-title":"Fast and sensitive protein alignment using DIAMOND","volume":"12","author":"B Buchfink","year":"2015","journal-title":"Nat Meth"},{"key":"ppat.1008216.ref059","doi-asserted-by":"crossref","unstructured":"Wickham H. 2009. ggplot2: Elegant Graphics for Data Analysis. Springer.","DOI":"10.1007\/978-0-387-98141-3"},{"key":"ppat.1008216.ref060","doi-asserted-by":"crossref","first-page":"1647","DOI":"10.1093\/bioinformatics\/bts199","article-title":"Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data","volume":"28","author":"M Kearse","year":"2012","journal-title":"Bioinformatics"},{"key":"ppat.1008216.ref061","doi-asserted-by":"crossref","first-page":"173","DOI":"10.1038\/nmeth.1818","article-title":"HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment","volume":"9","author":"M Remmert","year":"2012","journal-title":"Nat Meth"},{"key":"ppat.1008216.ref062","doi-asserted-by":"crossref","first-page":"951","DOI":"10.1093\/bioinformatics\/bti125","article-title":"Protein homology detection by HMM-HMM comparison","volume":"21","author":"J S\u00f6ding","year":"2005","journal-title":"Bioinformatics"},{"key":"ppat.1008216.ref063","doi-asserted-by":"crossref","first-page":"1539","DOI":"10.1089\/cmb.2009.0046","article-title":"Categorizing host-dependent RNA viruses by principal component analysis of their codon usage preferences","volume":"16","author":"M-W Su","year":"2009","journal-title":"J Comp Biol"},{"key":"ppat.1008216.ref064","doi-asserted-by":"crossref","first-page":"38","DOI":"10.1186\/1745-6150-3-38","article-title":"CAIcal: a combined set of tools to assess codon usage adaptation","volume":"3","author":"P Puigb\u00f2","year":"2008","journal-title":"Biol Direct"},{"key":"ppat.1008216.ref065","doi-asserted-by":"crossref","first-page":"567","DOI":"10.1006\/jmbi.2000.4315","article-title":"Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes","volume":"305","author":"A Krogh","year":"2001","journal-title":"J Mol Biol"},{"key":"ppat.1008216.ref066","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1007\/978-1-59745-515-2_5","article-title":"InterPro and InterProScan: Tools for protein sequence classification and comparison","volume":"396","author":"N Mulder","year":"2007","journal-title":"Meth Mol Biol"},{"key":"ppat.1008216.ref067","article-title":"Magic-BLAST, an accurate DNA and RNA-seq aligner for long and short reads","author":"GM Boratyn","year":"2018","journal-title":"bioRxiv"},{"key":"ppat.1008216.ref068","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.1008216.ref069","doi-asserted-by":"crossref","first-page":"540","DOI":"10.1093\/oxfordjournals.molbev.a026334","article-title":"Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis","volume":"17","author":"J Castresana","year":"2000","journal-title":"Mol Biol Evol"},{"key":"ppat.1008216.ref070","doi-asserted-by":"crossref","first-page":"2422","DOI":"10.1093\/molbev\/msx149","article-title":"SMS: Smart Model Selection in PhyML","volume":"34","author":"V Lefort","year":"2017","journal-title":"Mol Biol Evol"},{"key":"ppat.1008216.ref071","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 Meth"},{"key":"ppat.1008216.ref072","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1007\/978-1-59745-251-9_6","article-title":"Estimating Maximum Likelihood Phylogenies with PhyML","volume":"537","author":"S Guindon","year":"2009","journal-title":"Meth Mol Biol"},{"key":"ppat.1008216.ref073","doi-asserted-by":"crossref","first-page":"268","DOI":"10.1093\/molbev\/msu300","article-title":"IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies","volume":"32","author":"L-T Nguyen","year":"2015","journal-title":"Mol Biol Evol"},{"key":"ppat.1008216.ref074","doi-asserted-by":"crossref","first-page":"657","DOI":"10.1016\/j.ijpara.2018.02.003","article-title":"Primers targeting mitochondrial genes of avian haemosporidians: PCR detection and differential DNA amplification of parasites belonging to different genera","volume":"48","author":"MA Pacheco","year":"2018","journal-title":"Int J Parasitol"}],"updated-by":[{"DOI":"10.1371\/journal.ppat.1008216","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2020,1,10]],"date-time":"2020-01-10T00:00:00Z","timestamp":1578614400000}}],"container-title":["PLOS Pathogens"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1008216","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,2,14]],"date-time":"2021-02-14T09:12:37Z","timestamp":1613293957000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.ppat.1008216"}},"subtitle":[],"editor":[{"given":"Oliver","family":"Billker","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2019,12,30]]},"references-count":74,"journal-issue":{"issue":"12","published-online":{"date-parts":[[2019,12,30]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.ppat.1008216","relation":{"has-review":[{"id-type":"doi","id":"10.3410\/f.737143724.793597086","asserted-by":"object"}]},"ISSN":["1553-7374"],"issn-type":[{"value":"1553-7374","type":"electronic"}],"subject":[],"published":{"date-parts":[[2019,12,30]]}}}