{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,17]],"date-time":"2026-08-17T23:21:05Z","timestamp":1787008865505,"version":"build-2736575974"},"reference-count":93,"publisher":"Oxford University Press (OUP)","issue":"9","license":[{"start":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T00:00:00Z","timestamp":1567641600000},"content-version":"vor","delay-in-days":4,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000925","name":"National Health and Medical Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000925","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000923","name":"Australian Research Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000923","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100001782","name":"University of Melbourne","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100001782","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000054","name":"National Cancer Institute","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100000054","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["R01CA164719"],"award-info":[{"award-number":["R01CA164719"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000831","name":"Natural History Museum","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000831","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2019,9,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Background<\/jats:title>\n                    <jats:p>Schistosoma haematobium causes urogenital schistosomiasis, a neglected tropical disease affecting &amp;gt;100 million people worldwide. Chronic infection with this parasitic trematode can lead to urogenital conditions including female genital schistosomiasis and bladder cancer. At the molecular level, little is known about this blood fluke and the pathogenesis of the disease that it causes. To support molecular studies of this carcinogenic worm, we reported a draft genome for S. haematobium in 2012. Although a useful resource, its utility has been somewhat limited by its fragmentation.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Findings<\/jats:title>\n                    <jats:p>Here, we systematically enhanced the draft genome of S. haematobium using a single-molecule and long-range DNA-sequencing approach. We achieved a major improvement in the accuracy and contiguity of the genome assembly, making it superior or comparable to assemblies for other schistosome species. We transferred curated gene models to this assembly and, using enhanced gene annotation pipelines, inferred a gene set with as many or more complete gene models as those of other well-studied schistosomes. Using conserved, single-copy orthologs, we assessed the phylogenetic position of S. haematobium in relation to other parasitic flatworms for which draft genomes were available.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>We report a substantially enhanced genomic resource that represents a solid foundation for molecular research on S. haematobium and is poised to better underpin population and functional genomic investigations and to accelerate the search for new disease interventions.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/gigascience\/giz108","type":"journal-article","created":{"date-parts":[[2019,9,5]],"date-time":"2019-09-05T06:54:58Z","timestamp":1567666498000},"source":"Crossref","is-referenced-by-count":44,"title":["High-quality\n                    <i>Schistosoma haematobium<\/i>\n                    genome achieved by single-molecule and long-range sequencing"],"prefix":"10.1093","volume":"8","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9432-9816","authenticated-orcid":false,"given":"Andreas J","family":"Stroehlein","sequence":"first","affiliation":[{"name":"Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne , Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9957-4674","authenticated-orcid":false,"given":"Pasi K","family":"Korhonen","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne , Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Teik Min","family":"Chong","sequence":"additional","affiliation":[{"name":"Institute of Biological Sciences, Faculty of Science, University of Malaya , 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan Lue","family":"Lim","sequence":"additional","affiliation":[{"name":"Institute of Biological Sciences, Faculty of Science, University of Malaya , 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1883-1115","authenticated-orcid":false,"given":"Kok Gan","family":"Chan","sequence":"additional","affiliation":[{"name":"Institute of Biological Sciences, Faculty of Science, University of Malaya , 50603 Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0930-9314","authenticated-orcid":false,"given":"Bonnie","family":"Webster","sequence":"additional","affiliation":[{"name":"Parasites and Vectors Division, The Natural History Museum , Cromwell Rd, South Kensington, London SW7 5BD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1999-1716","authenticated-orcid":false,"given":"David","family":"Rollinson","sequence":"additional","affiliation":[{"name":"Parasites and Vectors Division, The Natural History Museum , Cromwell Rd, South Kensington, London SW7 5BD, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-1765-0002","authenticated-orcid":false,"given":"Paul J","family":"Brindley","sequence":"additional","affiliation":[{"name":"School of Medicine & Health Sciences, Department of Microbiology, Immunology & Tropical Medicine, George Washington University , 2300 Eye Street, NW, Suite 502, Washington, DC 20037, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4423-1690","authenticated-orcid":false,"given":"Robin B","family":"Gasser","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne , Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8756-229X","authenticated-orcid":false,"given":"Neil D","family":"Young","sequence":"additional","affiliation":[{"name":"Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Veterinary and Agricultural Sciences, The University of Melbourne , Corner Flemington Road and Park Drive, Parkville, VIC 3010, Australia"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2019,9,5]]},"reference":[{"key":"2024111714225360500_bib1","doi-asserted-by":"crossref","first-page":"411","DOI":"10.1016\/S1473-3099(06)70521-7","article-title":"Schistosomiasis and water resources development: systematic review, meta-analysis, and estimates of people at risk","volume":"6","author":"Steinmann","year":"2006","journal-title":"Lancet Infect Dis"},{"key":"2024111714225360500_bib2","doi-asserted-by":"crossref","first-page":"1106","DOI":"10.1016\/S0140-6736(06)69440-3","article-title":"Human schistosomiasis","volume":"368","author":"Gryseels","year":"2006","journal-title":"Lancet"},{"key":"2024111714225360500_bib3","doi-asserted-by":"crossref","first-page":"333","DOI":"10.1016\/S0046-8177(86)80456-7","article-title":"The pathobiology of Schistosoma haematobium infection in humans","volume":"17","author":"Smith","year":"1986","journal-title":"Hum Pathol"},{"key":"2024111714225360500_bib4","doi-asserted-by":"crossref","first-page":"656","DOI":"10.1111\/j.1365-3024.2009.01157.x","article-title":"Schistosomiasis and liver fibrosis","volume":"31","author":"Andrade","year":"2009","journal-title":"Parasite Immunol"},{"key":"2024111714225360500_bib5","doi-asserted-by":"crossref","first-page":"1060","DOI":"10.4269\/ajtmh.2011.11-0135","article-title":"HIV target cells in Schistosoma haematobium-infected female genital mucosa","volume":"85","author":"Jourdan","year":"2011","journal-title":"Am J Trop Med Hyg"},{"key":"2024111714225360500_bib6","doi-asserted-by":"crossref","first-page":"246","DOI":"10.1016\/j.pt.2015.03.005","article-title":"The role of estrogens and estrogen receptor signaling pathways in cancer and infertility: the case of schistosomes","volume":"31","author":"Botelho","year":"2015","journal-title":"Trends Parasitol"},{"key":"2024111714225360500_bib7","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1097\/01.idc.0000269904.90155.ce","article-title":"Association between schistosomiasis and cancer: a review","volume":"15","author":"Palumbo","year":"2007","journal-title":"Infect Dis Clin Pract"},{"key":"2024111714225360500_bib8","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1186\/s13071-016-1799-4","article-title":"Schistosomiasis vaccines: where do we stand?","volume":"9","author":"Tebeje","year":"2016","journal-title":"Parasit Vectors"},{"key":"2024111714225360500_bib9","doi-asserted-by":"crossref","first-page":"1825","DOI":"10.1017\/S0031182009000493","article-title":"Praziquantel: its use in control of schistosomiasis in sub-Saharan Africa and current research needs","volume":"136","author":"Doenhoff","year":"2009","journal-title":"Parasitology"},{"key":"2024111714225360500_bib10","doi-asserted-by":"crossref","first-page":"423","DOI":"10.1016\/j.actatropica.2012.04.013","article-title":"Time to set the agenda for schistosomiasis elimination","volume":"128","author":"Rollinson","year":"2013","journal-title":"Acta Trop"},{"key":"2024111714225360500_bib11","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1017\/S0031182009990552","article-title":"A wake up call for urinary schistosomiasis: reconciling research effort with public health importance","volume":"136","author":"Rollinson","year":"2009","journal-title":"Parasitology"},{"key":"2024111714225360500_bib12","article-title":"Sustaining the drive to overcome the global impact of neglected tropical diseases","volume-title":"Second WHO Report on Neglected Tropical Diseases","author":"World Health Organization","year":"2013"},{"key":"2024111714225360500_bib13","doi-asserted-by":"crossref","first-page":"e267","DOI":"10.1371\/journal.pntd.0000267","article-title":"The NIH-NIAID schistosomiasis resource center","volume":"2","author":"Lewis","year":"2008","journal-title":"PLoS Negl Trop Dis"},{"key":"2024111714225360500_bib14","doi-asserted-by":"crossref","first-page":"221","DOI":"10.1038\/ng.1065","article-title":"Whole-genome sequence of Schistosoma haematobium","volume":"44","author":"Young","year":"2012","journal-title":"Nat Genet"},{"key":"2024111714225360500_bib15","doi-asserted-by":"crossref","first-page":"e31164","DOI":"10.1371\/journal.pone.0031164","article-title":"Insights into SCP\/TAPS proteins of liver flukes based on large-scale bioinformatic analyses of sequence datasets","volume":"7","author":"Cantacessi","year":"2012","journal-title":"PLoS One"},{"key":"2024111714225360500_bib16","doi-asserted-by":"crossref","first-page":"2893","DOI":"10.1038\/srep02893","article-title":"A genome-wide analysis of annexins from parasitic organisms and their vectors","volume":"3","author":"Cantacessi","year":"2013","journal-title":"Sci Rep"},{"key":"2024111714225360500_bib17","doi-asserted-by":"crossref","first-page":"D728","DOI":"10.1093\/nar\/gks1087","article-title":"SchistoDB: an updated genome resource for the three key schistosomes of humans","volume":"41","author":"Zerlotini","year":"2013","journal-title":"Nucleic Acids Res"},{"key":"2024111714225360500_bib18","doi-asserted-by":"crossref","first-page":"242","DOI":"10.1186\/1756-3305-7-242","article-title":"Identification of G protein-coupled receptors in Schistosoma haematobium and S. mansoni by comparative genomics","volume":"7","author":"Campos","year":"2014","journal-title":"Parasit Vectors"},{"key":"2024111714225360500_bib19","doi-asserted-by":"crossref","first-page":"17759","DOI":"10.1038\/srep17759","article-title":"Defining the Schistosoma haematobium kinome enables the prediction of essential kinases as anti-schistosome drug targets","volume":"5","author":"Stroehlein","year":"2015","journal-title":"Sci Rep"},{"key":"2024111714225360500_bib20","doi-asserted-by":"crossref","first-page":"e1002605","DOI":"10.1371\/journal.ppat.1002605","article-title":"A novel mouse model of Schistosoma haematobium egg-induced immunopathology","volume":"8","author":"Fu","year":"2012","journal-title":"PLoS Pathog"},{"key":"2024111714225360500_bib21","doi-asserted-by":"crossref","first-page":"e1348","DOI":"10.1371\/journal.pntd.0001348","article-title":"Genetic manipulation of Schistosoma haematobium, the neglected schistosome","volume":"5","author":"Rinaldi","year":"2011","journal-title":"PLoS Negl Trop Dis"},{"key":"2024111714225360500_bib22","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1016\/j.ijpara.2012.10.023","article-title":"Tumour-like phenotypes in urothelial cells after exposure to antigens from eggs of Schistosoma haematobium: an oestrogen-DNA adducts mediated pathway?","volume":"43","author":"Botelho","year":"2013","journal-title":"Int J Parasitol"},{"key":"2024111714225360500_bib23","doi-asserted-by":"crossref","first-page":"861","DOI":"10.1093\/infdis\/jiu527","article-title":"New research tools for urogenital schistosomiasis","volume":"211","author":"Rinaldi","year":"2015","journal-title":"J Infect Dis"},{"key":"2024111714225360500_bib24","doi-asserted-by":"crossref","first-page":"405","DOI":"10.1186\/gb-2013-14-6-405","article-title":"The advantages of SMRT sequencing","volume":"14","author":"Roberts","year":"2013","journal-title":"Genome Biol"},{"key":"2024111714225360500_bib25","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1016\/j.biotechadv.2016.03.001","article-title":"Making sense of genomes of parasitic worms: tackling bioinformatic challenges","volume":"34","author":"Korhonen","year":"2016","journal-title":"Biotechnol Adv"},{"key":"2024111714225360500_bib26","doi-asserted-by":"crossref","first-page":"758","DOI":"10.1038\/nrg.2016.119","article-title":"The state of play in higher eukaryote gene annotation","volume":"17","author":"Mudge","year":"2016","journal-title":"Nat Rev Genet"},{"key":"2024111714225360500_bib27","doi-asserted-by":"crossref","first-page":"1112","DOI":"10.1101\/gr.100099.109","article-title":"Protein variation in blood-dwelling schistosome worms generated by differential splicing of micro-exon gene transcripts","volume":"20","author":"DeMarco","year":"2010","journal-title":"Genome Res"},{"key":"2024111714225360500_bib28","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1038\/nrg3174","article-title":"A beginner's guide to eukaryotic genome annotation","volume":"13","author":"Yandell","year":"2012","journal-title":"Nat Rev Genet"},{"key":"2024111714225360500_bib29","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 Schistosoma mansoni","volume":"6","author":"Protasio","year":"2012","journal-title":"PLoS Negl Trop Dis"},{"key":"2024111714225360500_bib30","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":"Tsai","year":"2013","journal-title":"Nature"},{"key":"2024111714225360500_bib31","doi-asserted-by":"crossref","first-page":"e54732","DOI":"10.1371\/journal.pone.0054732","article-title":"The carcinogenic liver fluke, Clonorchis sinensis: new assembly, reannotation and analysis of the genome and characterization of tissue transcriptomes","volume":"8","author":"Huang","year":"2013","journal-title":"PLoS One"},{"key":"2024111714225360500_bib32","doi-asserted-by":"crossref","first-page":"133","DOI":"10.1126\/science.1162986","article-title":"Real-time DNA sequencing from single polymerase molecules","volume":"323","author":"Eid","year":"2009","journal-title":"Science"},{"key":"2024111714225360500_bib33","doi-asserted-by":"crossref","first-page":"6808","DOI":"10.1038\/s41598-018-25020-8","article-title":"Improved strategy for the curation and classification of kinases, with broad applicability to other eukaryotic protein groups","volume":"8","author":"Stroehlein","year":"2018","journal-title":"Sci Rep"},{"key":"2024111714225360500_bib34","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1101\/gr.193474.115","article-title":"Chromosome-scale shotgun assembly using an in vitro method for long-range linkage","volume":"26","author":"Putnam","year":"2016","journal-title":"Genome Res"},{"key":"2024111714225360500_bib35","year":"2019"},{"key":"2024111714225360500_bib36","doi-asserted-by":"crossref","first-page":"3506","DOI":"10.1093\/bioinformatics\/btu538","article-title":"LoRDEC: accurate and efficient long read error correction","volume":"30","author":"Salmela","year":"2014","journal-title":"Bioinformatics"},{"key":"2024111714225360500_bib37","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":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"2024111714225360500_bib38","first-page":"1111.5572","article-title":"Faster and more accurate sequence alignment with SNAP","author":"Zaharia","year":"2011","journal-title":"arXiv"},{"key":"2024111714225360500_bib39","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The sequence alignment\/map format and SAMtools","volume":"25","author":"Li","year":"2009","journal-title":"Bioinformatics"},{"key":"2024111714225360500_bib40","year":"2019","journal-title":"Picard tools"},{"key":"2024111714225360500_bib41","doi-asserted-by":"crossref","first-page":"1581","DOI":"10.1101\/gr.133652.111","article-title":"HaploMerger: reconstructing allelic relationships for polymorphic diploid genome assemblies","volume":"22","author":"Huang","year":"2012","journal-title":"Genome Res"},{"key":"2024111714225360500_bib42","doi-asserted-by":"crossref","first-page":"e47768","DOI":"10.1371\/journal.pone.0047768","article-title":"Mind the gap: upgrading genomes with Pacific Biosciences RS long-read sequencing technology","volume":"7","author":"English","year":"2012","journal-title":"PLoS One"},{"key":"2024111714225360500_bib43","doi-asserted-by":"crossref","first-page":"211","DOI":"10.1186\/1471-2105-15-211","article-title":"SSPACE-LongRead: scaffolding bacterial draft genomes using long read sequence information","volume":"15","author":"Boetzer","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"2024111714225360500_bib44"},{"key":"2024111714225360500_bib45","doi-asserted-by":"crossref","first-page":"421","DOI":"10.1186\/1471-2105-10-421","article-title":"BLAST+: architecture and applications","volume":"10","author":"Camacho","year":"2009","journal-title":"BMC Bioinformatics"},{"key":"2024111714225360500_bib46","doi-asserted-by":"crossref","first-page":"543","DOI":"10.1093\/molbev\/msx319","article-title":"BUSCO applications from quality assessments to gene prediction and phylogenomics","volume":"35","author":"Waterhouse","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2024111714225360500_bib47","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/nature08140","article-title":"Schistosoma japonicum Genome Sequencing and Functional Analysis Consortium. The Schistosoma japonicum genome reveals features of host-parasite interplay","volume":"460","year":"2009","journal-title":"Nature"},{"key":"2024111714225360500_bib48","doi-asserted-by":"crossref","first-page":"e0163962","DOI":"10.1371\/journal.pone.0163962","article-title":"SeqKit: a cross-platform and ultrafast toolkit for FASTA\/Q file manipulation","volume":"11","author":"Shen","year":"2016","journal-title":"PLoS One"},{"key":"2024111714225360500_bib49","doi-asserted-by":"crossref","first-page":"238","DOI":"10.1186\/1471-2105-13-238","article-title":"Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory","volume":"13","author":"Chaisson","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"2024111714225360500_bib50","doi-asserted-by":"crossref","first-page":"W160","DOI":"10.1093\/nar\/gkw257","article-title":"deepTools2: a next generation web server for deep-sequencing data analysis","volume":"44","author":"Ramirez","year":"2016","journal-title":"Nucleic Acids Res"},{"key":"2024111714225360500_bib51","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1093\/bib\/bbs038","article-title":"The UCSC genome browser and associated tools","volume":"14","author":"Kuhn","year":"2013","journal-title":"Brief Bioinform"},{"key":"2024111714225360500_bib52","doi-asserted-by":"crossref","first-page":"e57","DOI":"10.1093\/nar\/gkq1268","article-title":"RATT: Rapid Annotation Transfer Tool","volume":"39","author":"Otto","year":"2011","journal-title":"Nucleic Acids Res"},{"key":"2024111714225360500_bib53","doi-asserted-by":"crossref","first-page":"4.10.1","DOI":"10.1002\/0471250953.bi0410s25","article-title":"Using RepeatMasker to identify repetitive elements in genomic sequences","volume":"25","author":"Tarailo-Graovac","year":"2009","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024111714225360500_bib54","article-title":"Improved pairwise alignment of genomic DNA","author":"Harris","year":"2007"},{"key":"2024111714225360500_bib55","author":"Package recipe 'ucsc-chainnet.'","year":"2019"},{"key":"2024111714225360500_bib56","doi-asserted-by":"crossref","first-page":"491","DOI":"10.1186\/1471-2105-12-491","article-title":"MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects","volume":"12","author":"Holt","year":"2011","journal-title":"BMC Bioinformatics"},{"key":"2024111714225360500_bib57","doi-asserted-by":"crossref","first-page":"R7","DOI":"10.1186\/gb-2008-9-1-r7","article-title":"Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments","volume":"9","author":"Haas","year":"2008","journal-title":"Genome Biol"},{"key":"2024111714225360500_bib58","doi-asserted-by":"crossref","first-page":"1494","DOI":"10.1038\/nprot.2013.084","article-title":"De novo transcript sequence reconstruction from RNA-Seq using the Trinity platform for reference generation and analysis","volume":"8","author":"Haas","year":"2013","journal-title":"Nat Protoc"},{"key":"2024111714225360500_bib59","year":"2019"},{"key":"2024111714225360500_bib60","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/bioinformatics\/btp120","article-title":"TopHat: discovering splice junctions with RNA-Seq","volume":"25","author":"Trapnell","year":"2009","journal-title":"Bioinformatics"},{"key":"2024111714225360500_bib61","doi-asserted-by":"crossref","first-page":"562","DOI":"10.1038\/nprot.2012.016","article-title":"Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks","volume":"7","author":"Trapnell","year":"2012","journal-title":"Nat Protoc"},{"key":"2024111714225360500_bib62","doi-asserted-by":"crossref","first-page":"W465","DOI":"10.1093\/nar\/gki458","article-title":"AUGUSTUS: a web server for gene prediction in eukaryotes that allows user-defined constraints","volume":"33","author":"Stanke","year":"2005","journal-title":"Nucleic Acids Res"},{"key":"2024111714225360500_bib63","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1186\/1471-2105-5-59","article-title":"Gene finding in novel genomes","volume":"5","author":"Korf","year":"2004","journal-title":"BMC Bioinformatics"},{"key":"2024111714225360500_bib64","first-page":"4.6.1","article-title":"Eukaryotic gene prediction using GeneMark.hmm","volume":"35","author":"Borodovsky","year":"2003","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024111714225360500_bib65","doi-asserted-by":"crossref","first-page":"5654","DOI":"10.1093\/nar\/gkg770","article-title":"Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies","volume":"31","author":"Haas","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2024111714225360500_bib66","author":"Pertea","year":"2019"},{"key":"2024111714225360500_bib67","doi-asserted-by":"crossref","first-page":"2178","DOI":"10.1101\/gr.1224503","article-title":"OrthoMCL: identification of ortholog groups for eukaryotic genomes","volume":"13","author":"Li","year":"2003","journal-title":"Genome Res"},{"key":"2024111714225360500_bib68","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1093\/gigascience\/giy018","article-title":"Genome Annotation Generator: a simple tool for generating and correcting WGS annotation tables for NCBI submission","volume":"7","author":"Geib","year":"2018","journal-title":"GigaScience"},{"key":"2024111714225360500_bib69","doi-asserted-by":"crossref","first-page":"65","DOI":"10.1002\/0471223921.ch4","article-title":"Submitting DNA sequences to the databases","volume":"43","author":"Kans","year":"2001","journal-title":"Meth Biochem Anal"},{"key":"2024111714225360500_bib70","doi-asserted-by":"crossref","first-page":"6.10.1","DOI":"10.1002\/0471250953.bi0610s27","article-title":"Using OrthoCluster for the detection of synteny blocks among multiple genomes","volume":"27","author":"Vergara","year":"2009","journal-title":"Curr Protoc Bioinformatics"},{"key":"2024111714225360500_bib71","doi-asserted-by":"crossref","first-page":"1639","DOI":"10.1101\/gr.092759.109","article-title":"Circos: an information aesthetic for comparative genomics","volume":"19","author":"Krzywinski","year":"2009","journal-title":"Genome Res"},{"key":"2024111714225360500_bib72","author":"Inkscape","year":"2019"},{"key":"2024111714225360500_bib73","doi-asserted-by":"crossref","first-page":"e1007513","DOI":"10.1371\/journal.ppat.1007513","article-title":"Whole-genome sequence of the bovine blood fluke Schistosoma bovis supports interspecific hybridization with S. haematobium","volume":"15","author":"Oey","year":"2019","journal-title":"PLoS Pathog"},{"issue":"1","key":"2024111714225360500_bib74","doi-asserted-by":"publisher","DOI":"10.1093\/gigascience\/giy146","article-title":"Whole-genome sequence of the oriental lung fluke Paragonimus westermani","volume":"8","author":"Oey","year":"2019","journal-title":"Gigascience"},{"key":"2024111714225360500_bib75","doi-asserted-by":"crossref","first-page":"D869","DOI":"10.1093\/nar\/gkx998","article-title":"WormBase 2017: molting into a new stage","volume":"46","author":"Lee","year":"2018","journal-title":"Nucleic Acids Res"},{"key":"2024111714225360500_bib76","doi-asserted-by":"crossref","first-page":"1105","DOI":"10.1093\/gbe\/evu078","article-title":"Comparative genomics of flatworms (platyhelminthes) reveals shared genomic features of ecto- and endoparastic neodermata","volume":"6","author":"Hahn","year":"2014","journal-title":"Genome Biol Evol"},{"key":"2024111714225360500_bib77","doi-asserted-by":"crossref","first-page":"263","DOI":"10.1093\/bioinformatics\/btp651","article-title":"AQUA: automated quality improvement for multiple sequence alignments","volume":"26","author":"Muller","year":"2010","journal-title":"Bioinformatics"},{"key":"2024111714225360500_bib78","doi-asserted-by":"crossref","first-page":"1792","DOI":"10.1093\/nar\/gkh340","article-title":"MUSCLE: multiple sequence alignment with high accuracy and high throughput","volume":"32","author":"Edgar","year":"2004","journal-title":"Nucleic Acids Res"},{"key":"2024111714225360500_bib79","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":"Katoh","year":"2013","journal-title":"Mol Biol Evol"},{"key":"2024111714225360500_bib80","doi-asserted-by":"crossref","first-page":"1155","DOI":"10.1093\/bioinformatics\/btg133","article-title":"RASCAL: rapid scanning and correction of multiple sequence alignments","volume":"19","author":"Thompson","year":"2003","journal-title":"Bioinformatics"},{"key":"2024111714225360500_bib81","doi-asserted-by":"crossref","first-page":"937","DOI":"10.1006\/jmbi.2001.5187","article-title":"Towards a reliable objective function for multiple sequence alignments","volume":"314","author":"Thompson","year":"2001","journal-title":"J Mol Biol"},{"key":"2024111714225360500_bib82","first-page":"772","article-title":"PartitionFinder 2: new methods for selecting partitioned models of evolution for molecular and morphological phylogenetic analyses","volume":"34","author":"Lanfear","year":"2017","journal-title":"Mol Biol Evol"},{"key":"2024111714225360500_bib83","doi-asserted-by":"crossref","first-page":"456","DOI":"10.1093\/bioinformatics\/bti191","article-title":"RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees","volume":"21","author":"Stamatakis","year":"2005","journal-title":"Bioinformatics"},{"key":"2024111714225360500_bib84","doi-asserted-by":"crossref","first-page":"539","DOI":"10.1093\/sysbio\/sys029","article-title":"MrBayes 3.2: efficient Bayesian phylogenetic inference and model choice across a large model space","volume":"61","author":"Ronquist","year":"2012","journal-title":"Syst Biol"},{"key":"2024111714225360500_bib85","year":"2019"},{"key":"2024111714225360500_bib86","doi-asserted-by":"crossref","first-page":"947","DOI":"10.1016\/j.ijpara.2006.03.005","article-title":"A revision of the interrelationships of Schistosoma including the recently described Schistosoma guineensis","volume":"36","author":"Webster","year":"2006","journal-title":"Int J Parasitol"},{"key":"2024111714225360500_bib87","doi-asserted-by":"crossref","first-page":"586","DOI":"10.1016\/j.molcel.2015.05.004","article-title":"High-throughput sequencing technologies","volume":"58","author":"Reuter","year":"2015","journal-title":"Mol Cell"},{"key":"2024111714225360500_bib88","doi-asserted-by":"crossref","first-page":"62","DOI":"10.3390\/genes10010062","article-title":"A high-quality de novo genome assembly from a single mosquito using PacBio sequencing","volume":"10","author":"Kingan","year":"2019","journal-title":"Genes (Basel)"},{"key":"2024111714225360500_bib89","doi-asserted-by":"crossref","first-page":"e21400","DOI":"10.1371\/journal.pone.0021400","article-title":"Genome assembly has a major impact on gene content: a comparison of annotation in two Bos taurus assemblies","volume":"6","author":"Florea","year":"2011","journal-title":"PLoS One"},{"key":"2024111714225360500_bib90","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1038\/s41587-018-0004-z","article-title":"Errors in long-read assemblies can critically affect protein prediction","volume":"37","author":"Watson","year":"2019","journal-title":"Nat Biotechnol"},{"key":"2024111714225360500_bib91","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1038\/nature08160","article-title":"The genome of the blood fluke Schistosoma mansoni","volume":"460","author":"Berriman","year":"2009","journal-title":"Nature"},{"key":"2024111714225360500_bib92","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/s12864-018-4555-7","article-title":"Improving eukaryotic genome annotation using single molecule mRNA sequencing","volume":"19","author":"Magrini","year":"2018","journal-title":"BMC Genomics"},{"key":"2024111714225360500_bib93","doi-asserted-by":"crossref","unstructured":"Stroehlein AJ, Korhonen PK, Chong TM, et al., Supporting data for \u201cHigh-quality Schistosoma haematobium genome achieved by single-molecule and long-range sequencing.\u201d. GigaScience Database. 2019. 10.5524\/100634.","DOI":"10.1093\/gigascience\/giz108"}],"container-title":["GigaScience"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/8\/9\/giz108\/60714571\/gigascience_8_9_giz108.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/gigascience\/article-pdf\/8\/9\/giz108\/60714571\/gigascience_8_9_giz108.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,11,17]],"date-time":"2024-11-17T09:23:35Z","timestamp":1731835415000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/gigascience\/article\/doi\/10.1093\/gigascience\/giz108\/5560333"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2019,9,1]]},"references-count":93,"journal-issue":{"issue":"9","published-print":{"date-parts":[[2019,9,1]]}},"URL":"https:\/\/doi.org\/10.1093\/gigascience\/giz108","relation":{},"ISSN":["2047-217X"],"issn-type":[{"value":"2047-217X","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2019,9]]},"published":{"date-parts":[[2019,9,1]]},"article-number":"giz108"}}