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Recent advances in genomics approaches have provided a suitable framework to understand these phenotypes, which ultimately depend on genetically encoded determinants. In this work, we review how the study of genome sequences has been key to ascertain the bases of virulence and drug resistance traits. We focus on the contribution of comparative genomics, population genomics and directed evolution studies. In addition, we discuss how different types of genomic mutations (small or structural variants) contribute to intraspecific differences in virulence or drug resistance. Finally, we review current challenges in the field and anticipate future directions to solve them. In summary, this work provides a short overview of how genomics can be used to understand virulence and drug resistance in fungal pathogens.<\/jats:p>","DOI":"10.1042\/bst20211123","type":"journal-article","created":{"date-parts":[[2022,6,17]],"date-time":"2022-06-17T12:23:42Z","timestamp":1655468622000},"page":"1259-1268","update-policy":"https:\/\/doi.org\/10.1042\/crossmark_policy","source":"Crossref","is-referenced-by-count":32,"title":["Using genomics to understand the mechanisms of virulence and drug resistance in fungal pathogens"],"prefix":"10.1042","volume":"50","author":[{"given":"Miquel \u00c0ngel","family":"Schikora-Tamarit","sequence":"first","affiliation":[{"name":"1Barcelona Supercomputing Centre (BSC-CNS), Pla\u00e7a Eusebi G\u00fcell, 1-3, 08034 Barcelona, Spain"},{"name":"2Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Toni","family":"Gabald\u00f3n","sequence":"additional","affiliation":[{"name":"1Barcelona Supercomputing Centre (BSC-CNS), Pla\u00e7a Eusebi G\u00fcell, 1-3, 08034 Barcelona, Spain"},{"name":"2Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac 10, 08028 Barcelona, Spain"},{"name":"3Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain"},{"name":"4Centro de Investigaci\u00f3n Biom\u00e9dica En Red de Enfermedades Infecciosas, Barcelona, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"288","published-online":{"date-parts":[[2022,6,17]]},"reference":[{"key":"2022062915334629900_BST-2021-1123CC1","doi-asserted-by":"publisher","first-page":"57","DOI":"10.3390\/jof3040057","article-title":"Global and multi-national prevalence of fungal diseases-estimate precision","volume":"3","year":"2017","journal-title":"J. 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