{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,12]],"date-time":"2026-09-12T05:34:13Z","timestamp":1789191253956,"version":"build-2803163510"},"reference-count":52,"publisher":"Springer Science and Business Media LLC","issue":"1","license":[{"start":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T00:00:00Z","timestamp":1606262400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"},{"start":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T00:00:00Z","timestamp":1606262400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0"}],"funder":[{"name":"USDA-ARS","award":["8042-32000-100-00-D"],"award-info":[{"award-number":["8042-32000-100-00-D"]}]}],"content-domain":{"domain":["link.springer.com"],"crossmark-restriction":false},"short-container-title":["Parasites Vectors"],"published-print":{"date-parts":[[2020,12]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:sec>\n                <jats:title>Background<\/jats:title>\n                <jats:p><jats:italic>Blastocystis<\/jats:italic> sp. is one of the most common enteric parasites of humans and animals worldwide. It is well recognized that this ubiquitous protist displays a remarkable degree of genetic diversity in the <jats:italic>SSU<\/jats:italic> rRNA gene, which is currently the main gene used for defining <jats:italic>Blastocystis<\/jats:italic> subtypes. Yet, full-length reference sequences of this gene are available for only 16 subtypes of <jats:italic>Blastocystis<\/jats:italic> in part because of the technical difficulties associated with obtaining these sequences from complex samples.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Methods<\/jats:title>\n                <jats:p>We have developed a method using Oxford Nanopore MinION long-read sequencing and universal eukaryotic primers to produce full-length (&gt;\u20091800\u00a0bp) <jats:italic>SSU<\/jats:italic> rRNA gene sequences for <jats:italic>Blastocystis<\/jats:italic>. Seven <jats:italic>Blastocystis<\/jats:italic> specimens representing five subtypes (ST1, ST4, ST10, ST11, and ST14) obtained both from cultures and feces were used for validation.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>We demonstrate that this method can be used to produce highly accurate full-length sequences from both cultured and fecal DNA isolates. Full-length sequences were successfully obtained from all five subtypes including ST11 for which no full-length reference sequence currently exists and for an isolate that contained mixed ST10\/ST14.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>The suitability of the use of MinION long-read sequencing technology to successfully generate full-length <jats:italic>Blastocystis SSU<\/jats:italic> rRNA gene sequences was demonstrated. The ability to produce full-length <jats:italic>SSU<\/jats:italic> rRNA gene sequences is key in understanding the role of genetic diversity in important aspects of <jats:italic>Blastocystis<\/jats:italic> biology such as transmission, host specificity, and pathogenicity.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Graphical Abstract<\/jats:title>\n                \n              <\/jats:sec>","DOI":"10.1186\/s13071-020-04484-6","type":"journal-article","created":{"date-parts":[[2020,11,25]],"date-time":"2020-11-25T12:05:53Z","timestamp":1606305953000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":26,"title":["Use of Oxford Nanopore MinION to generate full-length sequences of the Blastocystis small subunit (SSU) rRNA gene"],"prefix":"10.1186","volume":"13","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6405-883X","authenticated-orcid":false,"given":"Jenny G.","family":"Maloney","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4571-7641","authenticated-orcid":false,"given":"Aleksey","family":"Molokin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1386-6255","authenticated-orcid":false,"given":"Monica","family":"Santin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2020,11,25]]},"reference":[{"key":"4484_CR1","doi-asserted-by":"publisher","DOI":"10.1016\/j.rvsc.2020.09.031","author":"JSY Hublin","year":"2020","unstructured":"Hublin JSY, Maloney JG, Santin M. Blastocystis in domesticated and wild mammals and birds. Res Vet Sci. 2020. https:\/\/doi.org\/10.1016\/j.rvsc.2020.09.031.","journal-title":"Res Vet Sci"},{"key":"4484_CR2","doi-asserted-by":"publisher","first-page":"365","DOI":"10.1186\/s13071-020-04225-9","volume":"13","author":"I Mohammadpour","year":"2020","unstructured":"Mohammadpour I, Bozorg-Ghalati F, Gazzonis AL, Manfredi MT, Motazedian MH, Mohammadpour N. First molecular subtyping and phylogeny of Blastocystis sp. isolated from domestic and synanthropic animals (dogs, cats and brown rats) in southern Iran. Parasites Vectors. 2020;13:365.","journal-title":"Parasites Vectors"},{"key":"4484_CR3","doi-asserted-by":"publisher","first-page":"164","DOI":"10.1186\/1471-2334-14-164","volume":"14","author":"D EL Safadi","year":"2014","unstructured":"EL Safadi D, Gaayeb L, Meloni D, Cian A, Poirier P, Wawrzyniak I, et al. Children of Senegal River Basin show the highest prevalence of Blastocystis sp. ever observed worldwide. BMC Infect Dis. 2014;14:164.","journal-title":"BMC Infect Dis"},{"key":"4484_CR4","doi-asserted-by":"publisher","first-page":"524","DOI":"10.1128\/JCM.02520-15","volume":"54","author":"LO Andersen","year":"2016","unstructured":"Andersen LO, Stensvold CR. Blastocystis in health and disease: are we moving from a clinical to a public health perspective? J Clin Microbiol. 2016;54:524\u20138.","journal-title":"J Clin Microbiol"},{"key":"4484_CR5","doi-asserted-by":"publisher","first-page":"772","DOI":"10.1016\/j.parint.2016.05.007","volume":"65","author":"SSR Ajjampur","year":"2016","unstructured":"Ajjampur SSR, Tan KSW. Pathogenic mechanisms in Blastocystis spp.\u2014interpreting results from in vitro and in vivo studies. Parasitol Int. 2016;65:772\u20139.","journal-title":"Parasitol Int"},{"key":"4484_CR6","doi-asserted-by":"publisher","first-page":"156","DOI":"10.1016\/j.actatropica.2015.05.004","volume":"148","author":"RD Casero","year":"2015","unstructured":"Casero RD, Mongi F, S\u00e1nchez A, Ram\u00edrez JD. Blastocystis and urticaria: examination of subtypes and morphotypes in an unusual clinical manifestation. Acta Trop. 2015;148:156\u201361.","journal-title":"Acta Trop"},{"key":"4484_CR7","first-page":"1900241","volume":"43","author":"L Reh","year":"2019","unstructured":"Reh L, Muadica AS, K\u00f6ster PC, Balasegaram S, Verlander NQ, Ch\u00e9rcoles ER, et al. Substantial prevalence of enteroparasites Cryptosporidium spp., Giardia duodenalis and Blastocystis sp. in asymptomatic schoolchildren in Madrid, Spain, November 2017 to June 2018. Euro Surveill. 2019;43:1900241.","journal-title":"Euro Surveill"},{"key":"4484_CR8","doi-asserted-by":"publisher","first-page":"566","DOI":"10.1186\/s13071-019-3814-z","volume":"12","author":"L Rojas-Vel\u00e1zquez","year":"2019","unstructured":"Rojas-Vel\u00e1zquez L, Maloney JG, Molokin A, Mor\u00e1n P, Serrano-V\u00e1zquez A, Gonz\u00e1lez E, et al. Use of next-generation amplicon sequencing to study Blastocystis genetic diversity in a rural human population from Mexico. Parasites Vectors. 2019;12:566.","journal-title":"Parasites Vectors"},{"key":"4484_CR9","doi-asserted-by":"publisher","first-page":"130","DOI":"10.1186\/1756-3305-5-130","volume":"5","author":"L Lee","year":"2012","unstructured":"Lee L, Chye T, Karmacharya B, Govind S. Blastocystis sp.: waterborne zoonotic organism, a possibility? Parasites Vectors. 2012;5:130.","journal-title":"Parasites Vectors"},{"key":"4484_CR10","doi-asserted-by":"publisher","first-page":"e2541","DOI":"10.7717\/peerj.2541","volume":"4","author":"SA Noradilah","year":"2016","unstructured":"Noradilah SA, Lee IL, Anuar TS, Salleh FM, Manap SNAA, Mohtar NSHM, et al. Occurrence of Blastocystis sp. in water catchments at Malay villages and Aboriginal settlement during wet and dry seasons in Peninsular Malaysia. PeerJ. 2016;4:e2541.","journal-title":"PeerJ"},{"key":"4484_CR11","doi-asserted-by":"publisher","first-page":"837","DOI":"10.2166\/wh.2019.045","volume":"17","author":"E Javanmard","year":"2019","unstructured":"Javanmard E, Rahimi HM, Niyyati M, Aghdaei HA, Sharifdini M, Mirjalali H, et al. Molecular analysis of Blastocystis sp. and its subtypes from treated wastewater routinely used for irrigation of vegetable farmlands in Iran. J Water Health. 2019;17:837\u201344.","journal-title":"J Water Health"},{"key":"4484_CR12","doi-asserted-by":"publisher","first-page":"398","DOI":"10.1038\/380398a0","volume":"380","author":"JD Silberman","year":"1996","unstructured":"Silberman JD, Sogin ML, Leipe DD, Clark CG. Human parasite finds taxonomic home. Nature. 1996;380:398.","journal-title":"Nature"},{"key":"4484_CR13","doi-asserted-by":"publisher","first-page":"42","DOI":"10.1111\/j.1550-7408.2002.tb00339.x","volume":"49","author":"N Arisue","year":"2002","unstructured":"Arisue N, Hashimoto T, Yoshikawa H, Nakamura Y, Nakamura G, Nakamura F, et al. Phylogenetic position of Blastocystis hominis and of stramenopiles inferred from multiple molecular sequence data. J Eukaryot Microbiol. 2002;49:42\u201353.","journal-title":"J Eukaryot Microbiol"},{"key":"4484_CR14","doi-asserted-by":"publisher","first-page":"229","DOI":"10.1016\/j.pt.2019.12.009","volume":"36","author":"CR Stensvold","year":"2020","unstructured":"Stensvold CR, Clark CG. Pre-empting Pandora\u2019s box: Blastocystis subtypes revisited. Trends Parasitol. 2020;36:229\u201332.","journal-title":"Trends Parasitol"},{"key":"4484_CR15","doi-asserted-by":"publisher","first-page":"e00138","DOI":"10.1016\/j.parepi.2020.e00138","volume":"9","author":"JG Maloney","year":"2020","unstructured":"Maloney JG, Molokin A, da Cunha MJR, Cury MC, Santin M. Blastocystis subtype distribution in domestic and captive wild bird species from Brazil using next generation amplicon sequencing. Parasite Epidemiol Control. 2020;9:e00138.","journal-title":"Parasite Epidemiol Control"},{"key":"4484_CR16","doi-asserted-by":"publisher","first-page":"544335","DOI":"10.3389\/fcimb.2020.544335","volume":"10","author":"Z Lhotsk\u00e1","year":"2020","unstructured":"Lhotsk\u00e1 Z, Jirk\u016f M, Hlo\u017ekov\u00e1 O, Bro\u017eov\u00e1 K, Jirsov\u00e1 D, Stensvold CR, et al. A study on the prevalence and subtype diversity of the intestinal protist Blastocystis sp. in a gut-healthy human population in the Czech Republic. Front Cell Infect Microbiol. 2020;10:544335.","journal-title":"Front Cell Infect Microbiol"},{"key":"4484_CR17","doi-asserted-by":"publisher","first-page":"327","DOI":"10.1128\/CMR.15.3.327-328.2002","volume":"15","author":"GS Visvesvara","year":"2002","unstructured":"Visvesvara GS, Garcia LS. Culture of protozoan parasites. Clin Microbiol Rev. 2002;15:327\u20138.","journal-title":"Clin Microbiol Rev"},{"key":"4484_CR18","doi-asserted-by":"publisher","first-page":"1097","DOI":"10.1111\/1755-0998.12324","volume":"14","author":"AS Mikheyev","year":"2014","unstructured":"Mikheyev AS, Tin MMY. A first look at the Oxford nanopore MinION sequencer. Mol Ecol Resour. 2014;14:1097\u2013102.","journal-title":"Mol Ecol Resour"},{"key":"4484_CR19","doi-asserted-by":"publisher","first-page":"338","DOI":"10.1038\/nbt.4060","volume":"36","author":"M Jain","year":"2018","unstructured":"Jain M, Koren S, Miga KH, Quick J, Rand AC, Sasani TA, et al. Nanopore sequencing and assembly of a human genome with ultra-long reads. Nat Biotechnol. 2018;36:338\u201345.","journal-title":"Nat Biotechnol"},{"key":"4484_CR20","doi-asserted-by":"publisher","first-page":"100","DOI":"10.3389\/fevo.2020.00100","volume":"8","author":"IE Knot","year":"2020","unstructured":"Knot IE, Zouganelis GD, Weedall GD, Wich SA, Rae R. DNA barcoding of nematodes using the MinION. Front Ecol Evol. 2020;8:100.","journal-title":"Front Ecol Evol"},{"key":"4484_CR21","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/s41598-018-26334-3","volume":"8","author":"LR Runtuwene","year":"2018","unstructured":"Runtuwene LR, Tuda JSB, Mongan AE, Makalowski W, Frith MC, Imwong M, et al. Nanopore sequencing of drug-resistance-associated genes in malaria parasites Plasmodium falciparum. Sci Rep. 2018;8:1\u201313.","journal-title":"Sci Rep"},{"key":"4484_CR22","first-page":"1","volume":"8","author":"P Orsini","year":"2018","unstructured":"Orsini P, Minervini CF, Cumbo C, Anelli L, Zagaria A, Minervini A, et al. Design and MinION testing of a nanopore targeted gene sequencing panel for chronic lymphocytic leukemia. Sci Rep. 2018;8:1\u201310.","journal-title":"Sci Rep"},{"key":"4484_CR23","doi-asserted-by":"publisher","first-page":"giz006","DOI":"10.1093\/gigascience\/giz006","volume":"8","author":"H Krehenwinkel","year":"2019","unstructured":"Krehenwinkel H, Pomerantz A, Henderson JB, Kennedy SR, Lim JY, Swamy V, et al. Nanopore sequencing of long ribosomal DNA amplicons enables portable and simple biodiversity assessments with high phylogenetic resolution across broad taxonomic scale. Gigascience. 2019;8:giz006.","journal-title":"Gigascience"},{"key":"4484_CR24","doi-asserted-by":"publisher","first-page":"205","DOI":"10.1007\/s00436-010-2244-9","volume":"109","author":"M Sant\u00edn","year":"2011","unstructured":"Sant\u00edn M, G\u00f3mez-Mu\u00f1oz MT, Solano-Aguilar G, Fayer R. Development of a new PCR protocol to detect and subtype Blastocystis spp. from humans and animals. Parasitol Res. 2011;109:205\u201312.","journal-title":"Parasitol Res"},{"key":"4484_CR25","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1016\/j.meegid.2019.04.013","volume":"73","author":"JG Maloney","year":"2019","unstructured":"Maloney JG, Molokin A, Santin M. Next generation amplicon sequencing improves detection of Blastocystis mixed subtype infections. Infect Genet Evol. 2019;73:119\u201325.","journal-title":"Infect Genet Evol"},{"key":"4484_CR26","doi-asserted-by":"publisher","first-page":"491","DOI":"10.1016\/0378-1119(88)90066-2","volume":"71","author":"L Medlin","year":"1988","unstructured":"Medlin L, Elwood HJ, Stickel S, Sogin ML. The characterization of enzymatically amplified eukaryotic 16S-like rRNA-coding regions. Gene. 1988;71:491\u20139.","journal-title":"Gene"},{"key":"4484_CR27","doi-asserted-by":"publisher","first-page":"348","DOI":"10.1128\/JCM.43.1.348-355.2005","volume":"43","author":"C No\u00ebl","year":"2005","unstructured":"No\u00ebl C, Dufernez F, Gerbod D, Edgcomb VP, Delgado-Viscogliosi P, Ho L-C, et al. Molecular phylogenies of Blastocystis isolates from different hosts: implications for genetic diversity, identification of species, and zoonosis. J Clin Microbiol. 2005;43:348\u201355.","journal-title":"J Clin Microbiol"},{"key":"4484_CR28","doi-asserted-by":"publisher","first-page":"722","DOI":"10.1101\/gr.215087.116","volume":"27","author":"S Koren","year":"2017","unstructured":"Koren S, Walenz BP, Berlin K, Miller JR, Bergman NH, Phillippy AM. Canu: scalable and accurate long-read assembly via adaptive \u03ba-mer weighting and repeat separation. Genome Res. 2017;27:722\u201336.","journal-title":"Genome Res"},{"key":"4484_CR29","unstructured":"Brian Bushnell. BBMap download | SourceForge.net. 2014."},{"key":"4484_CR30","doi-asserted-by":"publisher","first-page":"e2584","DOI":"10.7717\/peerj.2584","volume":"4","author":"T Rognes","year":"2016","unstructured":"Rognes T, Flouri T, Nichols B, Quince C, Mah\u00e9 F. VSEARCH: a versatile open source tool for metagenomics. PeerJ. 2016;4:e2584.","journal-title":"PeerJ"},{"key":"4484_CR31","doi-asserted-by":"publisher","first-page":"737","DOI":"10.1101\/gr.214270.116","volume":"27","author":"R Vaser","year":"2017","unstructured":"Vaser R, Sovi\u0107 I, Nagarajan N, \u0160iki\u0107 M. Fast and accurate de novo genome assembly from long uncorrected reads. Genome Res. 2017;27:737\u201346.","journal-title":"Genome Res"},{"key":"4484_CR32","doi-asserted-by":"publisher","first-page":"3094","DOI":"10.1093\/bioinformatics\/bty191","volume":"34","author":"H Li","year":"2018","unstructured":"Li H. Minimap2: pairwise alignment for nucleotide sequences. Bioinformatics. 2018;34:3094\u2013100.","journal-title":"Bioinformatics"},{"key":"4484_CR33","doi-asserted-by":"publisher","first-page":"733","DOI":"10.1038\/nmeth.3444","volume":"12","author":"NJ Loman","year":"2015","unstructured":"Loman NJ, Quick J, Simpson JT. A complete bacterial genome assembled de novo using only nanopore sequencing data. Nat Methods. 2015;12:733\u20135.","journal-title":"Nat Methods"},{"key":"4484_CR34","doi-asserted-by":"publisher","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","volume":"25","author":"H Li","year":"2009","unstructured":"Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment\/map format and SAMtools. Bioinformatics. 2009;25:2078\u20139.","journal-title":"Bioinformatics"},{"key":"4484_CR35","doi-asserted-by":"publisher","first-page":"263","DOI":"10.1016\/j.meegid.2011.11.002","volume":"12","author":"CR Stensvold","year":"2012","unstructured":"Stensvold CR, Alfellani M, Clark CG. Levels of genetic diversity vary dramatically between Blastocystis subtypes. Infect Genet Evol. 2012;12:263\u201373.","journal-title":"Infect Genet Evol"},{"key":"4484_CR36","doi-asserted-by":"publisher","first-page":"750","DOI":"10.1016\/j.parint.2016.04.004","volume":"65","author":"H Yoshikawa","year":"2016","unstructured":"Yoshikawa H, Koyama Y, Tsuchiya E, Takami K. Blastocystis phylogeny among various isolates from humans to insects. Parasitol Int. 2016;65:750\u20139.","journal-title":"Parasitol Int"},{"key":"4484_CR37","doi-asserted-by":"publisher","first-page":"R227","DOI":"10.1093\/hmg\/ddq416","volume":"19","author":"EE Schadt","year":"2010","unstructured":"Schadt EE, Turner S, Kasarskis A. A window into third-generation sequencing. Hum Mol Genet. 2010;19:R227\u201340.","journal-title":"Hum Mol Genet"},{"key":"4484_CR38","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1016\/j.cmi.2017.10.013","volume":"24","author":"J Besser","year":"2018","unstructured":"Besser J, Carleton HA, Gerner-Smidt P, Lindsey RL, Trees E. Next-generation sequencing technologies and their application to the study and control of bacterial infections. Clin Microbiol Infect. 2018;24:335\u201341.","journal-title":"Clin Microbiol Infect"},{"key":"4484_CR39","doi-asserted-by":"publisher","first-page":"27","DOI":"10.1016\/j.cell.2013.09.006","volume":"155","author":"DC Koboldt","year":"2013","unstructured":"Koboldt DC, Steinberg KM, Larson DE, Wilson RK, Mardis ER. The next-generation sequencing revolution and its impact on genomics. Cell. 2013;155:27\u201338.","journal-title":"Cell"},{"key":"4484_CR40","doi-asserted-by":"publisher","first-page":"1075","DOI":"10.12688\/f1000research.7201.1","volume":"4","author":"CLC Ip","year":"2015","unstructured":"Ip CLC, Loose M, Tyson JR, de Cesare M, Brown BL, Jain M, et al. MinION analysis and reference consortium: phase 1 data release and analysis. F1000Research. 2015;4:1075.","journal-title":"F1000Research"},{"key":"4484_CR41","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1016\/j.bdq.2015.02.001","volume":"3","author":"T Laver","year":"2015","unstructured":"Laver T, Harrison J, O\u2019Neill PA, Moore K, Farbos A, Paszkiewicz K, et al. Assessing the performance of the Oxford nanopore technologies MinION. Biomol Detect Quantif. 2015;3:1\u20138.","journal-title":"Biomol Detect Quantif"},{"key":"4484_CR42","doi-asserted-by":"publisher","first-page":"10931","DOI":"10.1038\/s41598-018-29334-5","volume":"8","author":"AD Tyler","year":"2018","unstructured":"Tyler AD, Mataseje L, Urfano CJ, Schmidt L, Antonation KS, Mulvey MR, et al. Evaluation of Oxford nanopore\u2019s MinION sequencing device for microbial whole genome sequencing applications. Sci Rep. 2018;8:10931.","journal-title":"Sci Rep"},{"key":"4484_CR43","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1016\/j.gpb.2016.05.004","volume":"14","author":"H Lu","year":"2016","unstructured":"Lu H, Giordano F, Ning Z. Oxford nanopore MinION sequencing and genome assembly. Genom Proteom Bioinform. 2016;14:265\u201379.","journal-title":"Genom Proteom Bioinform"},{"key":"4484_CR44","doi-asserted-by":"publisher","first-page":"316","DOI":"10.1111\/dgd.12608","volume":"61","author":"N Kono","year":"2019","unstructured":"Kono N, Arakawa K. Nanopore sequencing: review of potential applications in functional genomics. Dev Growth Differ. 2019;61:316\u201326.","journal-title":"Dev Growth Differ"},{"key":"4484_CR45","doi-asserted-by":"publisher","first-page":"1869","DOI":"10.1038\/s41467-019-09637-5","volume":"10","author":"R Bowden","year":"2019","unstructured":"Bowden R, Davies RW, Heger A, Pagnamenta AT, de Cesare M, Oikkonen LE, et al. Sequencing of human genomes with nanopore technology. Nat Commun. 2019;10:1869.","journal-title":"Nat Commun"},{"key":"4484_CR46","doi-asserted-by":"publisher","first-page":"129","DOI":"10.1186\/s13059-019-1727-y","volume":"20","author":"RR Wick","year":"2019","unstructured":"Wick RR, Judd LM, Holt KE. Performance of neural network basecalling tools for Oxford nanopore sequencing. Genome Biol. 2019;20:129.","journal-title":"Genome Biol"},{"key":"4484_CR47","doi-asserted-by":"publisher","first-page":"e0226234","DOI":"10.1371\/journal.pone.0226234","volume":"15","author":"A Scheunert","year":"2020","unstructured":"Scheunert A, Dorfner M, Lingl T, Oberprieler C. Can we use it? On the utility of de novo and reference-based assembly of nanopore data for plant plastome sequencing. PLoS ONE. 2020;15:e0226234.","journal-title":"PLoS ONE"},{"key":"4484_CR48","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1186\/s13059-018-1462-9","volume":"19","author":"FJ Rang","year":"2018","unstructured":"Rang FJ, Kloosterman WP, de Ridder J. From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy. Genome Biol. 2018;19:90.","journal-title":"Genome Biol"},{"key":"4484_CR49","doi-asserted-by":"publisher","first-page":"2137","DOI":"10.1002\/elps.201300174","volume":"34","author":"CR O\u2019Donnell","year":"2013","unstructured":"O\u2019Donnell CR, Wang H, Dunbar WB. Error analysis of idealized nanopore sequencing. Electrophoresis. 2013;34:2137\u201344.","journal-title":"Electrophoresis"},{"key":"4484_CR50","doi-asserted-by":"publisher","first-page":"8","DOI":"10.1016\/j.vetpar.2009.12.032","volume":"169","author":"U Parkar","year":"2010","unstructured":"Parkar U, Traub RJ, Vitali S, Elliot A, Levecke B, Robertson I, et al. Molecular characterization of Blastocystis isolates from zoo animals and their animal-keepers. Vet Parasitol. 2010;169:8\u201317.","journal-title":"Vet Parasitol"},{"key":"4484_CR51","doi-asserted-by":"publisher","first-page":"314","DOI":"10.1016\/j.ijppaw.2019.11.003","volume":"10","author":"J Li","year":"2019","unstructured":"Li J, Karim MR, Li D, Rahaman Sumon SMM, Siddiki SHMF, Rume FI, et al. Molecular characterization of Blastocystis sp. in captive wildlife in Bangladesh National Zoo: non-human primates with high prevalence and zoonotic significance. Int J Parasitol Parasites Wildl. 2019;10:314\u201320.","journal-title":"Int J Parasitol Parasites Wildl"},{"key":"4484_CR52","doi-asserted-by":"publisher","first-page":"575","DOI":"10.1007\/s00436-018-6149-3","volume":"118","author":"JG Maloney","year":"2019","unstructured":"Maloney JG, Lombard JE, Shivley CB, Urie NJ, Santin M. Zoonotic and genetically diverse subtypes of Blastocystis in US pre-weaned dairy heifer calves. Parasitol Res. 2019;118:575\u201382.","journal-title":"Parasitol Res"}],"container-title":["Parasites &amp; Vectors"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13071-020-04484-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/article\/10.1186\/s13071-020-04484-6\/fulltext.html","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/link.springer.com\/content\/pdf\/10.1186\/s13071-020-04484-6.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2021,9,29]],"date-time":"2021-09-29T10:17:42Z","timestamp":1632910662000},"score":1,"resource":{"primary":{"URL":"https:\/\/parasitesandvectors.biomedcentral.com\/articles\/10.1186\/s13071-020-04484-6"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,11,25]]},"references-count":52,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2020,12]]}},"alternative-id":["4484"],"URL":"https:\/\/doi.org\/10.1186\/s13071-020-04484-6","relation":{},"ISSN":["1756-3305"],"issn-type":[{"value":"1756-3305","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,11,25]]},"assertion":[{"value":"19 August 2020","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"12 November 2020","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"25 November 2020","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"Not applicable.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Ethics approval and consent to participate"}},{"value":"Not applicable.","order":2,"name":"Ethics","group":{"name":"EthicsHeading","label":"Consent for publication"}},{"value":"The authors declare that they have no competing interests.","order":3,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"595"}}