{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,24]],"date-time":"2026-09-24T19:35:38Z","timestamp":1790278538581,"version":"4.1.0"},"reference-count":101,"publisher":"Oxford University Press (OUP)","issue":"7","license":[{"start":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T00:00:00Z","timestamp":1595203200000},"content-version":"vor","delay-in-days":19,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["U54HG003079"],"award-info":[{"award-number":["U54HG003079"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004396","name":"Thailand Research Fund","doi-asserted-by":"publisher","award":["DPG6280002"],"award-info":[{"award-number":["DPG6280002"]}],"id":[{"id":"10.13039\/501100004396","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,7,1]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>Paragonimus spp. (lung flukes) are among the most injurious foodborne helminths, infecting ~23 million people and subjecting ~292 million to infection risk. Paragonimiasis is acquired from infected undercooked crustaceans and primarily affects the lungs but often causes lesions elsewhere including the brain. The disease is easily mistaken for tuberculosis owing to similar pulmonary symptoms, and accordingly, diagnostics are in demand.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>We assembled, annotated, and compared draft genomes of 4 prevalent and distinct Paragonimus species: Paragonimus miyazakii, Paragonimus westermani, Paragonimus kellicotti, and Paragonimus heterotremus. Genomes ranged from 697 to 923 Mb, included 12,072\u201312,853 genes, and were 71.6\u201390.1% complete according to BUSCO. Orthologous group analysis spanning 21 species (lung, liver, and blood flukes, additional platyhelminths, and hosts) provided insights into lung fluke biology. We identified 256 lung fluke\u2013specific and conserved orthologous groups with consistent transcriptional adult-stage Paragonimus expression profiles and enriched for iron acquisition, immune modulation, and other parasite functions. Previously identified Paragonimus diagnostic antigens were matched to genes, providing an opportunity to optimize and ensure pan-Paragonimus reactivity for diagnostic assays.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>This report provides advances in molecular understanding of Paragonimus and underpins future studies into the biology, evolution, and pathogenesis of Paragonimus and related foodborne flukes. We anticipate that these novel genomic and transcriptomic resources will be invaluable for future lung fluke research.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/gigascience\/giaa073","type":"journal-article","created":{"date-parts":[[2020,7,20]],"date-time":"2020-07-20T10:06:48Z","timestamp":1595239608000},"source":"Crossref","is-referenced-by-count":26,"title":["Comparative genomics and transcriptomics of 4 <i>Paragonimus<\/i> species provide insights into lung fluke parasitism and pathogenesis"],"prefix":"10.1093","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-6820-446X","authenticated-orcid":false,"given":"Bruce A","family":"Rosa","sequence":"first","affiliation":[{"name":"Department of Internal Medicine, Washington University School of Medicine , 660 S Euclid Ave, St. Louis, MO 63110,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Young-Jun","family":"Choi","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Washington University School of Medicine , 660 S Euclid Ave, St. Louis, MO 63110,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Samantha N","family":"McNulty","sequence":"additional","affiliation":[{"name":"The McDonnell Genome Institute at Washington University, School of Medicine , 4444 Forest Park Ave, St. Louis, MO 63108,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hyeim","family":"Jung","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Washington University School of Medicine , 660 S Euclid Ave, St. Louis, MO 63110,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"John","family":"Martin","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Washington University School of Medicine , 660 S Euclid Ave, St. Louis, MO 63110,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Takeshi","family":"Agatsuma","sequence":"additional","affiliation":[{"name":"Department of Environmental Health Sciences, Kochi Medical School , Kohasu, Oko-cho 185-1, Nankoku, Kochi, 783-8505,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hiromu","family":"Sugiyama","sequence":"additional","affiliation":[{"name":"Laboratory of Helminthology, Department of Parasitology, National Institute of Infectious Diseases , 1-23-1 Toyama, Shinjuku-ku, Tokyo 162-8640,","place":["Japan"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Thanh Hoa","family":"Le","sequence":"additional","affiliation":[{"name":"Department of Immunology, Institute of Biotechnology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cay Giay, Ha Noi 10307,","place":["Vietnam"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pham Ngoc","family":"Doanh","sequence":"additional","affiliation":[{"name":"Institute of Ecology and Biological Resources, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cay Giay, Ha Noi 10307,","place":["Vietnam"]},{"name":"Graduate University of Science and Technology, Vietnam Academy of Science and Technology , 18 Hoang Quoc Viet, Cay Giay, Ha Noi 10307,","place":["Vietnam"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wanchai","family":"Maleewong","sequence":"additional","affiliation":[{"name":"Research and Diagnostic Center for Emerging Infectious Diseases, Khon Kaen University , 123 Moo 16 Mittraphap Rd., Nai-Muang, Muang District, Khon Kaen 40002,","place":["Thailand"]},{"name":"Department of Parasitology, Faculty of Medicine, Khon Kaen University , 123 Moo 16 Mittraphap Rd., Nai-Muang, Muang District, Khon Kaen 40002,","place":["Thailand"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David","family":"Blair","sequence":"additional","affiliation":[{"name":"College of Marine and Environmental Sciences, James Cook University , 1 James Cook Drive, Townsville, Queensland 4811,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Paul J","family":"Brindley","sequence":"additional","affiliation":[{"name":"Departments of Microbiology, Immunology and Tropical Medicine, and Research Center for Neglected Diseases of Poverty, and Pathology School of Medicine & Health Sciences, George Washington University , Ross Hall 2300 Eye Street, NW, Washington, DC 20037,","place":["USA"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peter U","family":"Fischer","sequence":"additional","affiliation":[{"name":"Department of Internal Medicine, Washington University School of Medicine , 660 S Euclid Ave, St. Louis, MO 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