{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,12]],"date-time":"2026-10-12T22:12:20Z","timestamp":1791843140444,"version":"4.3.4"},"update-to":[{"DOI":"10.1371\/journal.pgen.1006537","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,1,23]],"date-time":"2017-01-23T00:00:00Z","timestamp":1485129600000}}],"reference-count":68,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2017,1,6]],"date-time":"2017-01-06T00:00:00Z","timestamp":1483660800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000051","name":"National Human Genome Research Institute","doi-asserted-by":"publisher","award":["U54HG003079"],"award-info":[{"award-number":["U54HG003079"]}],"id":[{"id":"10.13039\/100000051","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Foundation for Barnes-Jewish Hospital (US)"},{"DOI":"10.13039\/501100006049","name":"Comisi\u00f3n Sectorial de Investigaci\u00f3n Cient\u00edfica","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100006049","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["www.plosgenetics.org"],"crossmark-restriction":false},"short-container-title":["PLoS Genet"],"DOI":"10.1371\/journal.pgen.1006537","type":"journal-article","created":{"date-parts":[[2017,1,9]],"date-time":"2017-01-09T15:01:36Z","timestamp":1483974096000},"page":"e1006537","update-policy":"https:\/\/doi.org\/10.1371\/journal.pgen.corrections_policy","source":"Crossref","is-referenced-by-count":121,"title":["Genomes of Fasciola hepatica from the Americas Reveal Colonization with Neorickettsia Endobacteria Related to the Agents of Potomac Horse and Human Sennetsu Fevers"],"prefix":"10.1371","volume":"13","author":[{"given":"Samantha N.","family":"McNulty","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3950-9982","authenticated-orcid":true,"given":"Jose F.","family":"Tort","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7767-4922","authenticated-orcid":true,"given":"Gabriel","family":"Rinaldi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2963-1303","authenticated-orcid":false,"given":"Kerstin","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce A.","family":"Rosa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3856-3920","authenticated-orcid":true,"given":"Pablo","family":"Smircich","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Santiago","family":"Fontenla","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young-Jun","family":"Choi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6680-8972","authenticated-orcid":true,"given":"Rahul","family":"Tyagi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kymberlie","family":"Hallsworth-Pepin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2218-597X","authenticated-orcid":false,"given":"Victoria H.","family":"Mann","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lakshmi","family":"Kammili","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia S.","family":"Latham","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nicolas","family":"Dell\u2019Oca","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernanda","family":"Dominguez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Carlos","family":"Carmona","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter U.","family":"Fischer","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1765-0002","authenticated-orcid":true,"given":"Paul J.","family":"Brindley","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Makedonka","family":"Mitreva","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2017,1,6]]},"reference":[{"issue":"3","key":"ref1","doi-asserted-by":"crossref","first-page":"466","DOI":"10.1128\/CMR.00012-09","article-title":"Food-borne trematodiases","volume":"22","author":"J Keiser","year":"2009","journal-title":"Clin Microbiol Rev"},{"issue":"7","key":"ref2","doi-asserted-by":"crossref","first-page":"e2865","DOI":"10.1371\/journal.pntd.0002865","article-title":"The global burden of disease study 2010: interpretation and implications for the neglected tropical diseases","volume":"8","author":"PJ Hotez","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"issue":"12","key":"ref3","doi-asserted-by":"crossref","first-page":"e1001920","DOI":"10.1371\/journal.pmed.1001920","article-title":"World Health Organization Estimates of the Global and Regional Disease Burden of 11 Foodborne Parasitic Diseases, 2010: A Data Synthesis","volume":"12","author":"PR Torgerson","year":"2015","journal-title":"PLoS Med"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"786195","DOI":"10.1155\/2015\/786195","article-title":"Fascioliasis: An Ongoing Zoonotic Trematode Infection","volume":"2015","author":"M Nyindo","year":"2015","journal-title":"Biomed Res Int"},{"issue":"3","key":"ref5","doi-asserted-by":"crossref","first-page":"326","DOI":"10.1017\/S0031182013001662","article-title":"Recent advances in the diagnosis, impact on production and prediction of Fasciola hepatica in cattle","volume":"141","author":"J Charlier","year":"2014","journal-title":"Parasitology"},{"issue":"3","key":"ref6","doi-asserted-by":"crossref","first-page":"245","DOI":"10.1017\/S0022149X09222528","article-title":"Redial generations of Fasciola hepatica: a review","volume":"83","author":"D Rondelaud","year":"2009","journal-title":"J Helminthol"},{"issue":"2","key":"ref7","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1016\/0014-4894(83)90073-5","article-title":"<italic>Fasciola hepatica<\/italic>: migration of newly excysted juveniles in resistant rats","volume":"56","author":"DJ Burden","year":"1983","journal-title":"Experimental parasitology"},{"issue":"3","key":"ref8","doi-asserted-by":"crossref","first-page":"481","DOI":"10.4269\/ajtmh.2012.11-0448","article-title":"Burden of <italic>Fasciola hepatica<\/italic> Infection among children from Paucartambo in Cusco, Peru","volume":"86","author":"M Lopez","year":"2012","journal-title":"The American journal of tropical medicine and hygiene"},{"key":"ref9","first-page":"389","article-title":"La infecci\u00f3n por <italic>Fasciola Hep\u00e1tica<\/italic> en el Per\u00fa: una enfermedad emergente","volume":"27","author":"L Marcos","year":"2007","journal-title":"Revista de Gastroenterolog\u00eda del Per\u00fa"},{"issue":"1","key":"ref10","doi-asserted-by":"crossref","first-page":"32","DOI":"10.3947\/ic.2013.45.1.32","article-title":"Praziquantel treatment in trematode and cestode infections: an update","volume":"45","author":"JY Chai","year":"2013","journal-title":"Infection & chemotherapy"},{"key":"ref11","article-title":"Current Threat of Triclabendazole Resistance in <italic>Fasciola hepatica<\/italic>","author":"JM Kelley","year":"2016","journal-title":"Trends Parasitol"},{"issue":"1","key":"ref12","doi-asserted-by":"crossref","first-page":"e0004361","DOI":"10.1371\/journal.pntd.0004361","article-title":"Treatment Failure after Multiple Courses of Triclabendazole among Patients with Fascioliasis in Cusco, Peru: A Case Series","volume":"10","author":"MM Cabada","year":"2016","journal-title":"PLoS Negl Trop Dis"},{"issue":"10","key":"ref13","first-page":"1330","article-title":"Resistant human fasciolasis: report of four patients","volume":"142","author":"LC Gil","year":"2014","journal-title":"Rev Med Chil"},{"key":"ref14","article-title":"Germs within worms: localization of <italic>Neorickettsia sp<\/italic>. within life cycle stages of digenean <italic>plagiorchis elegans<\/italic>","author":"SE Greiman","year":"2016","journal-title":"Applied and environmental microbiology"},{"issue":"6","key":"ref15","doi-asserted-by":"crossref","first-page":"e98453","DOI":"10.1371\/journal.pone.0098453","article-title":"Large scale screening of digeneans for <italic>Neorickettsia<\/italic> endosymbionts using real-time PCR reveals new <italic>Neorickettsia<\/italic> genotypes, host associations and geographic records","volume":"9","author":"SE Greiman","year":"2014","journal-title":"PLoS One"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"253","DOI":"10.1016\/B978-0-12-398457-9.00003-2","article-title":"Neorickettsial endosymbionts of the digenea: diversity, transmission and distribution","volume":"79","author":"JA Vaughan","year":"2012","journal-title":"Adv Parasitol"},{"issue":"9","key":"ref17","doi-asserted-by":"crossref","first-page":"1061","DOI":"10.1093\/bioinformatics\/btm071","article-title":"CEGMA: a pipeline to accurately annotate core genes in eukaryotic genomes","volume":"23","author":"G Parra","year":"2007","journal-title":"Bioinformatics"},{"issue":"10","key":"ref18","doi-asserted-by":"crossref","first-page":"R107","DOI":"10.1186\/gb-2011-12-10-r107","article-title":"The draft genome of the carcinogenic human liver fluke <italic>Clonorchis sinensis<\/italic>","volume":"12","author":"X Wang","year":"2011","journal-title":"Genome Biol"},{"key":"ref19","doi-asserted-by":"crossref","DOI":"10.1038\/ncomms5378","article-title":"The <italic>Opisthorchis viverrini<\/italic> genome provides insights into life in the bile duct","volume":"5","author":"ND Young","year":"2014","journal-title":"Nature communications"},{"issue":"1","key":"ref20","doi-asserted-by":"crossref","first-page":"e54732","DOI":"10.1371\/journal.pone.0054732","article-title":"The carcinogenic liver fluke, <italic>Clonorchis sinensis<\/italic>: new assembly, reannotation and analysis of the genome and characterization of tissue transcriptomes","volume":"8","author":"Y Huang","year":"2013","journal-title":"PLoS One"},{"issue":"1","key":"ref21","doi-asserted-by":"crossref","first-page":"e1455","DOI":"10.1371\/journal.pntd.0001455","article-title":"A Systematically Improved High Quality Genome and Transcriptome of the Human Blood Fluke <italic>Schistosoma mansoni<\/italic>","volume":"6","author":"AV Protasio","year":"2012","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"ref22","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s00239-002-2434-x","article-title":"The evolution of enzyme specificity in <italic>Fasciola spp<\/italic>","volume":"57","author":"JA Irving","year":"2003","journal-title":"J Mol Evol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1007\/978-1-4419-8414-2_8","article-title":"The phylogeny, structure and function of trematode cysteine proteases, with particular emphasis on the <italic>Fasciola hepatica<\/italic> cathepsin L family","volume":"712","author":"C Stack","year":"2011","journal-title":"Adv Exp Med Biol"},{"key":"ref24","doi-asserted-by":"crossref","first-page":"227","DOI":"10.1186\/1471-2164-11-227","article-title":"Survey of transcripts expressed by the invasive juvenile stage of the liver fluke <italic>Fasciola hepatica<\/italic>","volume":"11","author":"M Cancela","year":"2010","journal-title":"BMC Genomics"},{"issue":"10","key":"ref25","doi-asserted-by":"crossref","first-page":"1461","DOI":"10.1016\/j.biochi.2008.04.020","article-title":"A distinctive repertoire of cathepsins is expressed by juvenile invasive <italic>Fasciola hepatica<\/italic>","volume":"90","author":"M Cancela","year":"2008","journal-title":"Biochimie"},{"key":"ref26","doi-asserted-by":"crossref","DOI":"10.1074\/mcp.M700560-MCP200","article-title":"Proteomics and phylogenetic analysis of the cathepsin L protease family of the helminth pathogen <italic>Fasciola hepatica<\/italic>: expansion of a repertoire of virulence-associated factors","volume":"7","author":"MW Robinson","year":"2008","journal-title":"Mol Cell Proteomics"},{"issue":"1","key":"ref27","doi-asserted-by":"crossref","first-page":"e369","DOI":"10.1371\/journal.pntd.0000369","article-title":"The Importance of pH in Regulating the Function of the <italic>Fasciola hepatica<\/italic> Cathepsin L1 Cysteine Protease","volume":"3","author":"J Lowther","year":"2009","journal-title":"PLoS Negl Trop Dis"},{"issue":"4","key":"ref28","doi-asserted-by":"crossref","first-page":"e1012","DOI":"10.1371\/journal.pntd.0001012","article-title":"Collagenolytic activities of the major secreted cathepsin L peptidases involved in the virulence of the helminth pathogen, <italic>Fasciola hepatica<\/italic>","volume":"5","author":"MW Robinson","year":"2011","journal-title":"PLoS Negl Trop Dis"},{"key":"ref29","doi-asserted-by":"crossref","DOI":"10.1016\/j.molbiopara.2009.04.005","article-title":"The major cathepsin L secreted by the invasive juvenile <italic>Fasciola hepatica<\/italic> prefers proline in the S2 subsite and can cleave collagen","volume":"167","author":"I Corvo","year":"2009","journal-title":"Mol Biochem Parasitol"},{"issue":"12","key":"ref30","doi-asserted-by":"crossref","first-page":"e1414","DOI":"10.1371\/journal.pntd.0001414","article-title":"Tracing of the Bile-chemotactic migration of juvenile <italic>Clonorchis sinensis<\/italic> in rabbits by PET-CT","volume":"5","author":"TI Kim","year":"2011","journal-title":"PLoS Negl Trop Dis"},{"issue":"1","key":"ref31","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.molbiopara.2009.11.006","article-title":"A family of cathepsin F cysteine proteases of <italic>Clonorchis sinensis<\/italic> is the major secreted proteins that are expressed in the intestine of the parasite","volume":"170","author":"JM Kang","year":"2010","journal-title":"Mol Biochem Parasitol"},{"issue":"2","key":"ref32","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1016\/j.biochi.2007.08.013","article-title":"Differential use of protease families for invasion by schistosome cercariae","volume":"90","author":"J Dvo\u0159\u00e1k","year":"2008","journal-title":"Biochimie"},{"issue":"D1","key":"ref33","doi-asserted-by":"crossref","first-page":"D343","DOI":"10.1093\/nar\/gkv1118","article-title":"Twenty years of the MEROPS database of proteolytic enzymes, their substrates and inhibitors","volume":"44","author":"ND Rawlings","year":"2016","journal-title":"Nucleic acids research"},{"key":"ref34","doi-asserted-by":"crossref","first-page":"32796","DOI":"10.1038\/srep32796","article-title":"Across intra-mammalian stages of the liver fluke <italic>Fasciola hepatica<\/italic>: a proteomic study","volume":"6","author":"LS Di Maggio","year":"2016","journal-title":"Scientific reports"},{"issue":"7443","key":"ref35","doi-asserted-by":"crossref","first-page":"57","DOI":"10.1038\/nature12031","article-title":"The genomes of four tapeworm species reveal adaptations to parasitism","volume":"496","author":"IJ Tsai","year":"2013","journal-title":"Nature"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1152\/physiol.00054.2005","article-title":"From bacteria to man: archaic proton-dependent peptide transporters at work","volume":"21","author":"H Daniel","year":"2006","journal-title":"Physiology (Bethesda)"},{"issue":"1","key":"ref37","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1128\/CVI.00338-07","article-title":"Leucine Aminopeptidase Is an Immunodominant Antigen of <italic>Fasciola hepatica<\/italic> Excretory and Secretory Products in Human Infections","volume":"15","author":"A Marcilla","year":"2008","journal-title":"Clinical and Vaccine Immunology: CVI"},{"issue":"4","key":"ref38","doi-asserted-by":"crossref","first-page":"387","DOI":"10.1016\/j.ijpara.2009.12.006","article-title":"Acetate formation in the energy metabolism of parasitic helminths and protists","volume":"40","author":"AG Tielens","year":"2010","journal-title":"Int J Parasitol"},{"issue":"6 Pt 1","key":"ref39","doi-asserted-by":"crossref","first-page":"980","DOI":"10.1016\/j.biotechadv.2015.05.004","article-title":"Cracking the nodule worm code advances knowledge of parasite biology and biotechnology to tackle major diseases of livestock","volume":"33","author":"R Tyagi","year":"2015","journal-title":"Biotechnology advances"},{"issue":"2","key":"ref40","doi-asserted-by":"crossref","first-page":"e21","DOI":"10.1371\/journal.pgen.0020021","article-title":"Comparative genomics of emerging human ehrlichiosis agents","volume":"2","author":"JC Dunning Hotopp","year":"2006","journal-title":"PLoS Genet"},{"issue":"18","key":"ref41","doi-asserted-by":"crossref","first-page":"6076","DOI":"10.1093\/nar\/gkp642","article-title":"Analysis of complete genome sequence of <italic>Neorickettsia risticii<\/italic>: causative agent of Potomac horse fever","volume":"37","author":"M Lin","year":"2009","journal-title":"Nucleic acids research"},{"issue":"22","key":"ref42","doi-asserted-by":"crossref","first-page":"5898","DOI":"10.1128\/JB.00632-10","article-title":"Proteomic analysis of <italic>Neorickettsia sennetsu<\/italic> surface-exposed proteins and porin activity of the major surface protein P51","volume":"192","author":"K Gibson","year":"2010","journal-title":"J Bacteriol"},{"issue":"6","key":"ref43","doi-asserted-by":"crossref","first-page":"e20884","DOI":"10.1371\/journal.pone.0020884","article-title":"<italic>Francisella tularensis<\/italic> 2-C-Methyl-D-Erythritol 4-Phosphate Cytidylyltransferase: Kinetic Characterization and Phosphoregulation","volume":"6","author":"A Tsang","year":"2011","journal-title":"PLoS One"},{"issue":"1","key":"ref44","first-page":"1","article-title":"Concurrent transcriptional profiling of <italic>Dirofilaria immitis<\/italic> and its <italic>Wolbachia<\/italic> endosymbiont throughout the nematode life cycle reveals coordinated gene expression","volume":"15","author":"AN Luck","year":"2014","journal-title":"BMC Genomics"},{"issue":"4","key":"ref45","doi-asserted-by":"crossref","first-page":"e121","DOI":"10.1371\/journal.pbio.0030121","article-title":"The <italic>Wolbachia<\/italic> genome of <italic>Brugia malayi<\/italic>: endosymbiont evolution within a human pathogenic nematode","volume":"3","author":"J Foster","year":"2005","journal-title":"PLoS Biol"},{"issue":"1\u20133","key":"ref46","doi-asserted-by":"crossref","first-page":"4","DOI":"10.1016\/S0014-5793(03)00483-6","article-title":"Microbial isoprenoid biosynthesis and human gammadelta T cell activation","volume":"544","author":"M Eberl","year":"2003","journal-title":"FEBS letters"},{"issue":"2","key":"ref47","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1111\/j.1462-2920.2004.00683.x","article-title":"<italic>Neorickettsia risticii<\/italic> is vertically transmitted in the trematode Acanthatrium oregonense and horizontally transmitted to bats","volume":"7","author":"KE Gibson","year":"2005","journal-title":"Environmental microbiology"},{"issue":"5","key":"ref48","doi-asserted-by":"crossref","first-page":"e1174","DOI":"10.1371\/journal.pntd.0001174","article-title":"Tissue and stage-specific distribution of <italic>Wolbachia<\/italic> in <italic>Brugia malayi<\/italic>","volume":"5","author":"K Fischer","year":"2011","journal-title":"PLoS Negl Trop Dis"},{"key":"ref49","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1007\/978-1-4939-0915-5_1","article-title":"Form and function in the digenea","volume":"766","author":"RC Peoples","year":"2014","journal-title":"Adv Exp Med Biol"},{"issue":"2","key":"ref50","doi-asserted-by":"crossref","first-page":"182","DOI":"10.1016\/0014-4894(82)90125-4","article-title":"<italic>Borrelia crocidurae<\/italic>: venereal transfer in Egyptian <italic>Ornithodoros erraticus<\/italic> ticks","volume":"54","author":"MS Gaber","year":"1982","journal-title":"Exp Parasitol"},{"issue":"5","key":"ref51","doi-asserted-by":"crossref","first-page":"433","DOI":"10.1177\/104063870101300514","article-title":"Equine monocytic Ehrlichiosis (Potomac horse fever) in horses in Uruguay and southern Brazil","volume":"13","author":"F Dutra","year":"2001","journal-title":"J Vet Diagn Invest"},{"issue":"3","key":"ref52","doi-asserted-by":"crossref","first-page":"286","DOI":"10.1128\/CMR.4.3.286","article-title":"The tribe <italic>Ehrlichieae<\/italic> and ehrlichial diseases","volume":"4","author":"Y Rikihisa","year":"1991","journal-title":"Clin Microbiol Rev"},{"issue":"2","key":"ref53","doi-asserted-by":"crossref","first-page":"190","DOI":"10.4269\/ajtmh.2009.81.190","article-title":"<italic>Sennetsu neorickettsiosis<\/italic>: a probable fish-borne cause of fever rediscovered in Laos","volume":"81","author":"PN Newton","year":"2009","journal-title":"Am J Trop Med Hyg"},{"issue":"2","key":"ref54","doi-asserted-by":"crossref","first-page":"187","DOI":"10.4269\/ajtmh.2009.81.187","article-title":"Sennetsu neorickettsiosis: a potentially prevalent, treatable, acutely incapacitating tropical infectious disease","volume":"81","author":"DH Walker","year":"2009","journal-title":"Am J Trop Med Hyg"},{"issue":"5","key":"ref55","doi-asserted-by":"crossref","first-page":"375","DOI":"10.1038\/nrmicro1866","article-title":"Emerging and re-emerging rickettsioses: endothelial cell infection and early disease events","volume":"6","author":"DH Walker","year":"2008","journal-title":"Nat Rev Microbiol"},{"key":"ref56","doi-asserted-by":"crossref","first-page":"20316","DOI":"10.1038\/srep20316","article-title":"<italic>Dictyocaulus viviparus<\/italic> genome, variome and transcriptome elucidate lungworm biology and support future intervention","volume":"6","author":"SN McNulty","year":"2016","journal-title":"Scientific reports"},{"issue":"4","key":"ref57","doi-asserted-by":"crossref","first-page":"1513","DOI":"10.1073\/pnas.1017351108","article-title":"High-quality draft assemblies of mammalian genomes from massively parallel sequence data","volume":"108","author":"S Gnerre","year":"2011","journal-title":"Proc Natl Acad Sci U S A"},{"key":"ref58","article-title":"Genome of the human hookworm Necator americanus","author":"YT Tang","year":"2014","journal-title":"Nat Genet"},{"issue":"10","key":"ref59","doi-asserted-by":"crossref","first-page":"e3242","DOI":"10.1371\/journal.pntd.0003242","article-title":"Systems biology studies of adult <italic>paragonimus<\/italic> lung flukes facilitate the identification of immunodominant parasite antigens","volume":"8","author":"SN McNulty","year":"2014","journal-title":"PLoS Negl Trop Dis"},{"issue":"14","key":"ref60","doi-asserted-by":"crossref","first-page":"1754","DOI":"10.1093\/bioinformatics\/btp324","article-title":"Fast and accurate short read alignment with Burrows-Wheeler transform","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"issue":"2","key":"ref61","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1089\/omi.2008.0017","article-title":"Toward an online repository of Standard Operating Procedures (SOPs) for (meta)genomic annotation","volume":"12","author":"SV Angiuoli","year":"2008","journal-title":"OMICS"},{"issue":"14","key":"ref62","doi-asserted-by":"crossref","first-page":"e9","DOI":"10.1093\/bioinformatics\/btl213","article-title":"Automatic clustering of orthologs and inparalogs shared by multiple proteomes","volume":"22","author":"A Alexeyenko","year":"2006","journal-title":"Bioinformatics"},{"key":"ref63","doi-asserted-by":"crossref","first-page":"157","DOI":"10.1186\/s13059-015-0721-2","article-title":"OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthogroup inference accuracy","volume":"16","author":"DM Emms","year":"2015","journal-title":"Genome Biol"},{"issue":"5","key":"ref64","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1038\/ng.806","article-title":"A framework for variation discovery and genotyping using next-generation DNA sequencing data","volume":"43","author":"MA DePristo","year":"2011","journal-title":"Nat Genet"},{"issue":"9","key":"ref65","doi-asserted-by":"crossref","first-page":"1297","DOI":"10.1101\/gr.107524.110","article-title":"The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data","volume":"20","author":"A McKenna","year":"2010","journal-title":"Genome Res"},{"issue":"2","key":"ref66","doi-asserted-by":"crossref","first-page":"80","DOI":"10.4161\/fly.19695","article-title":"A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of <italic>Drosophila melanogaster<\/italic> strain w1118; iso-2; iso-3","volume":"6","author":"P Cingolani","year":"2012","journal-title":"Fly (Austin)"},{"key":"ref67","doi-asserted-by":"crossref","first-page":"303","DOI":"10.1186\/1756-3305-6-303","article-title":"Transmission rates of the bacterial endosymbiont, <italic>Neorickettsia risticii<\/italic>, during the asexual reproduction phase of its digenean host, Plagiorchis elegans, within naturally infected lymnaeid snails","volume":"6","author":"SE Greiman","year":"2013","journal-title":"Parasit Vectors"},{"key":"ref68","doi-asserted-by":"crossref","first-page":"71","DOI":"10.1186\/s13059-015-0632-2","article-title":"The <italic>Fasciola hepatica<\/italic> genome: gene duplication and polymorphism reveals adaptation to the host environment and the capacity for rapid evolution","volume":"16","author":"K Cwiklinski","year":"2015","journal-title":"Genome Biol"}],"updated-by":[{"DOI":"10.1371\/journal.pgen.1006537","type":"new_version","label":"New version","source":"publisher","updated":{"date-parts":[[2017,1,23]],"date-time":"2017-01-23T00:00:00Z","timestamp":1485129600000}}],"container-title":["PLOS Genetics"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pgen.1006537","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2019,9,17]],"date-time":"2019-09-17T05:26:52Z","timestamp":1568698012000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pgen.1006537"}},"subtitle":[],"editor":[{"given":"Eva H.","family":"Stukenbrock","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2017,1,6]]},"references-count":68,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2017,1,6]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pgen.1006537","relation":{"new_version":[{"id-type":"doi","id":"10.1371\/journal.pgen.1006537","asserted-by":"object"}]},"ISSN":["1553-7404"],"issn-type":[{"value":"1553-7404","type":"electronic"}],"subject":[],"published":{"date-parts":[[2017,1,6]]}}}