{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,18]],"date-time":"2026-03-18T00:58:49Z","timestamp":1773795529226,"version":"3.50.1"},"reference-count":90,"publisher":"Oxford University Press (OUP)","issue":"6","license":[{"start":{"date-parts":[[2020,7,25]],"date-time":"2020-07-25T00:00:00Z","timestamp":1595635200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/academic.oup.com\/journals\/pages\/open_access\/funder_policies\/chorus\/standard_publication_model"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2020,9,26]]},"abstract":"<jats:title>ABSTRACT<\/jats:title><jats:p>In recent years, \u2018multi-omic\u2019 sciences have affected all aspects of fundamental and applied biological research. Yeast taxonomists, though somewhat timidly, have begun to incorporate complete genomic sequences into the description of novel taxa, taking advantage of these powerful data to calculate more reliable genetic distances, construct more robust phylogenies, correlate genotype with phenotype and even reveal cryptic sexual behaviors. However, the use of genomic data in formal yeast species descriptions is far from widespread. The present review examines published examples of genome-based species descriptions of yeasts, highlights relevant bioinformatic approaches, provides recommendations for new users and discusses some of the challenges facing the genome-based systematics of yeasts.<\/jats:p>","DOI":"10.1093\/femsyr\/foaa042","type":"journal-article","created":{"date-parts":[[2020,7,23]],"date-time":"2020-07-23T19:13:56Z","timestamp":1595531636000},"source":"Crossref","is-referenced-by-count":57,"title":["Towards yeast taxogenomics: lessons from novel species descriptions based on complete genome sequences"],"prefix":"10.1093","volume":"20","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9687-6186","authenticated-orcid":false,"given":"D","family":"Libkind","sequence":"first","affiliation":[{"name":"Centro de Referencia en Levaduras y Tecnolog\u00eda Cervecera (CRELTEC), Instituto Andino Patag\u00f3nico de Tecnolog\u00edas Biol\u00f3gicas y Geoambientales (IPATEC) \u2013 CONICET \/ Universidad Nacional del Comahue, Bariloche, Argentina"}]},{"given":"N","family":"\u010cade\u017e","sequence":"additional","affiliation":[{"name":"Biotechnical Faculty, University of Ljubljana, Jamnikarjeva 101, 1000 Ljubljana, Slovenia"}]},{"given":"D A","family":"Opulente","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA"},{"name":"DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA"}]},{"given":"Q K","family":"Langdon","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Wisconsin Energy Institute, J. F. Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA"}]},{"given":"C A","family":"Rosa","sequence":"additional","affiliation":[{"name":"Departamento de Microbiologia, ICB, C.P. 486, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270\u2013901, Brazil"}]},{"given":"J P","family":"Sampaio","sequence":"additional","affiliation":[{"name":"UCIBIO, Departamento de Ci\u00eancias da Vida, Faculdade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal"}]},{"given":"P","family":"Gon\u00e7alves","sequence":"additional","affiliation":[{"name":"UCIBIO, Departamento de Ci\u00eancias da Vida, Faculdade de Ci\u00eancias e Tecnologia, Universidade Nova de Lisboa, 2829-516 Caparica, Portugal"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5088-7461","authenticated-orcid":false,"given":"C T","family":"Hittinger","sequence":"additional","affiliation":[{"name":"Laboratory of Genetics, Wisconsin Energy Institute, J. 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Crow Institute for the Study of Evolution, Center for Genomic Science Innovation, University of Wisconsin-Madison, Madison, WI, USA"},{"name":"DOE Great Lakes Bioenergy Research Center, University of Wisconsin-Madison, Madison, WI, USA"}]},{"given":"M A","family":"Lachance","sequence":"additional","affiliation":[{"name":"Department of Biology, University of Western Ontario, London N6A 5B7, Ontario, Canada"}]}],"member":"286","published-online":{"date-parts":[[2020,7,25]]},"reference":[{"key":"2021070900070334800_bib1","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/ncomms5044","article-title":"A gondwanan imprint on the global diversity and domestication of the wine and cider yeast Saccharomyces uvarum","volume":"5","author":"Almeida","year":"2014","journal-title":"Nature Comm"},{"key":"2021070900070334800_bib2","doi-asserted-by":"crossref","first-page":"117","DOI":"10.4056\/sigs.531120","article-title":"Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison","volume":"2","author":"Auch","year":"2010","journal-title":"Stand Genomic Sci"},{"key":"2021070900070334800_bib3","doi-asserted-by":"crossref","first-page":"1141","DOI":"10.1002\/yea.1154","article-title":"A history of research on yeasts 8: taxonomy","volume":"21","author":"Barnett","year":"2004","journal-title":"Yeast"},{"key":"2021070900070334800_bib4","doi-asserted-by":"crossref","first-page":"901","DOI":"10.1186\/s12864-016-3244-7","article-title":"Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma","volume":"17","author":"Bellora","year":"2016","journal-title":"BMC Genomics"},{"key":"2021070900070334800_bib5","doi-asserted-by":"crossref","first-page":"7067","DOI":"10.1073\/pnas.1701658114","article-title":"Evolutionary strata on young mating-type chromosomes despite the lack of sexual antagonism","volume":"114","author":"Branco","year":"2017","journal-title":"Proc Natl Acad Sci USA"},{"key":"2021070900070334800_bib7","doi-asserted-by":"crossref","first-page":"461","DOI":"10.1099\/ijsem.0.002516","article-title":"Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes","volume":"68","author":"Chun","year":"2018","journal-title":"Int J Syst Evol Microbiol"},{"key":"2021070900070334800_bib8","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1099\/ijs.0.054171-0","article-title":"Integrating genomics into the taxonomy and systematics of the bacteria and archaea","volume":"64","author":"Chun","year":"2014","journal-title":"Int J Syst Evol Microbiol"},{"key":"2021070900070334800_bib9","doi-asserted-by":"crossref","first-page":"249","DOI":"10.1186\/1471-2148-11-249","article-title":"Evidence for maintenance of sex determinants but not of sexual stages in red yeasts, a group of early diverged basidiomycetes","volume":"11","author":"Coelho","year":"2011","journal-title":"BMC Evol Biol"},{"key":"2021070900070334800_bib10","doi-asserted-by":"crossref","first-page":"352","DOI":"10.1016\/j.csbj.2015.04.005","article-title":"Homology-independent metrics for comparative genomics","volume":"13","author":"Coutinho","year":"2015","journal-title":"Comput Struct Biotechnol J"},{"key":"2021070900070334800_bib6","doi-asserted-by":"crossref","first-page":"e0210792","DOI":"10.1371\/journal.pone.0210792","article-title":"Genomic content of a novel yeast species Hanseniaspora gamundiae sp. nov. from fungal stromata (Cyttaria) associated with a unique fermented beverage in Andean Patagonia, Argentina. 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