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To improve knowledge about <jats:italic>Saccharomycodeacea<\/jats:italic> our group determined whole-genome sequences of <jats:italic>Hanseniaspora guilliermondii<\/jats:italic> (UTAD222) and <jats:italic>S. ludwigii<\/jats:italic> (UTAD17), two members of this family. While in the case of <jats:italic>H. guilliermondii<\/jats:italic> the genomic information elucidated crucial aspects concerning the physiology of this species in the context of wine fermentation, the draft sequence obtained for <jats:italic>S. ludwigii<\/jats:italic> was distributed by more than 1000 contigs complicating extraction of biologically relevant information. In this work we describe the results obtained upon resequencing of <jats:italic>S. ludwigii<\/jats:italic> UTAD17 genome using PacBio as well as the insights gathered from the exploration of the annotation performed over the assembled genome.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>Resequencing of <jats:italic>S. ludwigii<\/jats:italic> UTAD17 genome with PacBio resulted in 20 contigs totaling 13\u2009Mb of assembled DNA and corresponding to 95% of the DNA harbored by this strain. Annotation of the assembled UTAD17 genome predicts 4644 protein-encoding genes. Comparative analysis of the predicted <jats:italic>S. ludwigii<\/jats:italic> ORFeome with those encoded by other <jats:italic>Saccharomycodeacea<\/jats:italic> led to the identification of 213 proteins only found in this species. Among these were six enzymes required for catabolism of N-acetylglucosamine, four cell wall \u03b2-mannosyltransferases, several flocculins and three acetoin reductases. Different from its sister <jats:italic>Hanseniaspora<\/jats:italic> species, neoglucogenesis, glyoxylate cycle and thiamine biosynthetic pathways are functional in <jats:italic>S. ludwigii<\/jats:italic>. Four efflux pumps similar to the Ssu1 sulfite exporter, as well as robust orthologues for 65% of the <jats:italic>S. cerevisiae<\/jats:italic> SO<jats:sub>2<\/jats:sub>-tolerance genes, were identified in <jats:italic>S. ludwigii<\/jats:italic> genome.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This work provides the first genome-wide picture of a <jats:italic>S. ludwigii<\/jats:italic> strain representing a step forward for a better understanding of the physiology and genetics of this species and of the <jats:italic>Saccharomycodeacea<\/jats:italic> family. The release of this genomic sequence and of the information extracted from it can contribute to guide the design of better wine preservation strategies to counteract spoilage prompted by <jats:italic>S. ludwigii<\/jats:italic>. It will also accelerate the exploration of this species as a cell factory, specially in production of fermented beverages where the use of Non-<jats:italic>Saccharomyces<\/jats:italic> species (including spoilage species) is booming.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12864-021-07438-z","type":"journal-article","created":{"date-parts":[[2021,2,23]],"date-time":"2021-02-23T13:03:23Z","timestamp":1614085403000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Genome sequencing, annotation and exploration of the SO2-tolerant non-conventional yeast Saccharomycodes ludwigii"],"prefix":"10.1186","volume":"22","author":[{"given":"Maria J.","family":"Tavares","sequence":"first","affiliation":[]},{"given":"Ulrich","family":"G\u00fcldener","sequence":"additional","affiliation":[]},{"given":"Ana","family":"Mendes-Ferreira","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7556-0385","authenticated-orcid":false,"given":"Nuno P.","family":"Mira","sequence":"additional","affiliation":[]}],"member":"297","published-online":{"date-parts":[[2021,2,23]]},"reference":[{"key":"7438_CR1","first-page":"747","volume-title":"The yeasts","author":"K Boundy-Mills","year":"1904","unstructured":"Boundy-Mills K, Stratford M, Miller MW. 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