{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T03:28:01Z","timestamp":1776742081142,"version":"3.51.2"},"reference-count":19,"publisher":"Oxford University Press (OUP)","license":[{"start":{"date-parts":[[2021,11,13]],"date-time":"2021-11-13T00:00:00Z","timestamp":1636761600000},"content-version":"vor","delay-in-days":316,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100006445","name":"Uniwersytet Warszawski","doi-asserted-by":"publisher","award":["BOB-661-54\/20"],"award-info":[{"award-number":["BOB-661-54\/20"]}],"id":[{"id":"10.13039\/501100006445","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,11,13]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>The genus Prototheca houses unicellular, achlorophyllous, yeast-like algae, widely distributed in the environment. Protothecae are the only known plants that have repeatedly been reported to infect vertebrates, including humans. Although rare, protothecosis can be clinically demanding, with an unpredictable and treatment-resistant behavior. Accurate identification of Prototheca species relies upon DNA sequence-based typing of the mitochondrially encoded CYTB gene. However, no bioinformatic tool for the processing and analyzing of protothecal sequence data exists. Moreover, currently available sequence databases suffer from a limited number of records and lack of or flawed sequence annotations, making Prototheca identification challenging and often inconclusive. This report introduces the Prototheca-ID, a user-friendly, web-based application providing fast and reliable speciation of Prototheca isolates. In addition, the application offers the users the possibility of depositing their sequences and associated metadata in a fully open Prototheca-ID database, developed to enhance research integrity and quality in the field of Protothecae and protothecosis.<\/jats:p>\n               <jats:p>Database URL: The Prototheca-ID application is available at https:\/\/prototheca-id.org<\/jats:p>","DOI":"10.1093\/database\/baab073","type":"journal-article","created":{"date-parts":[[2021,11,9]],"date-time":"2021-11-09T12:11:18Z","timestamp":1636459878000},"source":"Crossref","is-referenced-by-count":13,"title":["Prototheca-ID: a web-based application for molecular identification of Prototheca species"],"prefix":"10.1093","volume":"2021","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5593-9432","authenticated-orcid":false,"given":"Miko\u0142aj","family":"Dziurzy\u0144ski","sequence":"first","affiliation":[{"name":"Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, Warsaw 02-096, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5621-7124","authenticated-orcid":false,"given":"Przemyslaw","family":"Decewicz","sequence":"additional","affiliation":[{"name":"Department of Environmental Microbiology and Biotechnology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, Warsaw 02-096, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6927-514X","authenticated-orcid":false,"given":"Mateusz","family":"Iskra","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, Warsaw 02-096, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7560-2100","authenticated-orcid":false,"given":"Zofia","family":"Baku\u0142a","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, Warsaw 02-096, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9553-5742","authenticated-orcid":false,"given":"Tomasz","family":"Jagielski","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Institute of Microbiology, Faculty of Biology, University of Warsaw, I. Miecznikowa 1, Warsaw 02-096, Poland"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2021,11,13]]},"reference":[{"key":"2022021504135183800_R1","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1016\/j.mycmed.2007.08.003","article-title":"Protothecosis. A pseudofungal infection","volume":"17","author":"Jagielski","year":"2007","journal-title":"J. Mycol. Med."},{"key":"2022021504135183800_R2","doi-asserted-by":"crossref","first-page":"143","DOI":"10.1007\/s11046-020-00508-y","article-title":"Protothecosis in dogs and cats - new research directions","volume":"186","author":"Masuda","year":"2021","journal-title":"Mycopathologia"},{"key":"2022021504135183800_R3","doi-asserted-by":"crossref","first-page":"556","DOI":"10.1111\/1751-7915.13394","article-title":"Prevalence of Prototheca spp. on dairy farms in Poland - a cross-country study","volume":"12","author":"Jagielski","year":"2019","journal-title":"Microb. Biotechnol."},{"key":"2022021504135183800_R4","doi-asserted-by":"crossref","first-page":"997","DOI":"10.1016\/j.vetmic.2012.11.003","article-title":"First outbreak of bovine mastitis caused by Prototheca blaschkeae","volume":"162","author":"Ricchi","year":"2013","journal-title":"Vet. Microbiol."},{"key":"2022021504135183800_R5","doi-asserted-by":"crossref","first-page":"1941","DOI":"10.1128\/JCM.00323-08","article-title":"Bovine mastitis associated with Prototheca blaschkeae","volume":"46","author":"Marques","year":"2008","journal-title":"J. Clin. Microbiol."},{"key":"2022021504135183800_R6","doi-asserted-by":"crossref","first-page":"4625","DOI":"10.3168\/jds.2010-3178","article-title":"Molecular characterization of Prototheca strains isolated from Italian dairy herds","volume":"93","author":"Ricchi","year":"2010","journal-title":"J. Dairy Sci."},{"key":"2022021504135183800_R7","doi-asserted-by":"crossref","first-page":"S188","DOI":"10.1093\/mmy\/myx162","article-title":"Medical phycology 2017","volume":"56","author":"Todd","year":"2018","journal-title":"Med. Mycol."},{"key":"2022021504135183800_R8","doi-asserted-by":"crossref","first-page":"230","DOI":"10.1128\/CMR.00032-06","article-title":"Human protothecosis","volume":"20","author":"Lass-Fl\u00f6rl","year":"2007","journal-title":"Clin. Microbiol. Rev."},{"key":"2022021504135183800_R9","doi-asserted-by":"crossref","DOI":"10.1128\/JCM.00584-18","article-title":"CYTB as a new genetic marker for differentiation of Prototheca species","volume":"56","author":"Jagielski","year":"2018","journal-title":"J. Clin. Microbiol."},{"key":"2022021504135183800_R10","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pone.0081223","article-title":"Ribosomal internal transcribed spacer of Prototheca wickerhamii has characteristic structure useful for identification and genotyping","volume":"8","author":"Hirose","year":"2013","journal-title":"PLoS One"},{"key":"2022021504135183800_R11","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1093\/mmy\/myx039","article-title":"Molecular characterization of Prototheca strains isolated in China revealed the first cases of protothecosis associated with Prototheca zopfii genotype 1","volume":"56","author":"Hirose","year":"2018","journal-title":"Med. 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