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However, its production is constrained by the poor performance of industrial microbes in hydrolysates that are generated during biomass pretreatment.\n                    <jats:italic>Scheffersomyces stipitis<\/jats:italic>\n                    is a native xylose fermenting yeast and a promising platform for 2G bioethanol production, and adaptive evolution under hydrolysate stress has yielded strains with enhanced performance. However, the chromosomal basis of this adaptation is unknown. Here, we demonstrate that chromosome scale structural variation, rather than point mutations, underlies the improved phenotype of the evolved strains. By integrating long- and short-read genome sequencing, we identify two major chromosomal rearrangements in the top performing isolate: a reciprocal translocation between chromosomes 1 and 2 that disrupts the NUDIX hydrolase gene\n                    <jats:italic>YSA1<\/jats:italic>\n                    , and the formation of a mitotically stable 175\u00a0kb minichromosome derived from chromosome 5. Functional analyses show that disruption of\n                    <jats:italic>YSA1<\/jats:italic>\n                    enhances xylose utilisation and ethanol yield, while the minichromosome contributes to improved performance in hydrolysate conditions. These findings provide direct evidence that balanced rearrangements and minichromosome formation can be selected during prolonged stress and can generate adaptive phenotypes. Taken together, our study establishes genome reorganisation as a key driver of adaptation in\n                    <jats:italic>S. stipitis<\/jats:italic>\n                    .\n                  <\/jats:p>","DOI":"10.1007\/s10577-026-09813-6","type":"journal-article","created":{"date-parts":[[2026,9,2]],"date-time":"2026-09-02T04:39:44Z","timestamp":1788323984000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Structural genome variation drives adaptation of the xylose-fermenting yeast Scheffersomyces stipitis to lignocellulosic hydrolysates"],"prefix":"10.1007","volume":"34","author":[{"given":"Samuel","family":"Vega-Est\u00e9vez","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Armitage","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bruce S.","family":"Dien","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Patricia J.","family":"Slininger","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-1704-3168","authenticated-orcid":false,"given":"Alessia","family":"Buscaino","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2026,9,2]]},"reference":[{"key":"9813_CR1","doi-asserted-by":"publisher","first-page":"1515","DOI":"10.1007\/s10529-008-9728-z","volume":"30","author":"FK Agbogbo","year":"2008","unstructured":"Agbogbo FK, Coward-Kelly G (2008) Cellulosic ethanol production using the naturally occurring xylose-fermenting yeast, Pichia stipitis. 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