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Their genetic diversity and evolutionary adaptations remain largely unexplored despite their ecological and oenological significance. This study investigated the phylogenetic relationships, genome structure, selection patterns, and phenotypic diversity of Hanseniaspora species isolated primarily from Australian wine environments, focusing on Hanseniaspora uvarum, the most abundant non-Saccharomyces yeast in wine fermentation. A total of 151 isolates were sequenced, including long-read genomes for representatives of the main phylogenetic clades. Comparative genomics revealed ancestral chromosomal rearrangements between the slow-evolving lineage (SEL) and fast-evolving lineage (FEL) that could have contributed to their evolutionary split, as well as significant loss of genes associated with mRNA splicing, chromatid segregation and signal recognition particle protein targeting in the FEL. Pangenome analysis within H. uvarum identified extensive copy number variation, particularly in genes related to xenobiotic tolerance and nutrient transport. Investigation into the selective landscape following the FEL\/SEL divergence identified diversifying selection in 229 genes in the FEL, with significant enrichment in genes within the lysine biosynthetic pathway. Furthermore, phenotypic screening of 116 isolates revealed substantial intraspecific diversity, with specific species exhibiting enhanced ethanol, osmotic, copper, SO\u2082, and cold tolerance.<\/jats:p>","DOI":"10.1093\/femsyr\/foaf031","type":"journal-article","created":{"date-parts":[[2025,6,10]],"date-time":"2025-06-10T07:37:55Z","timestamp":1749541075000},"source":"Crossref","is-referenced-by-count":17,"title":["Genetic and phenotypic diversity of wine-associated\n                    <i>Hanseniaspora<\/i>\n                    species"],"prefix":"10.1093","volume":"25","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0875-3093","authenticated-orcid":false,"given":"Cristobal A","family":"Onetto","sequence":"first","affiliation":[{"name":"The Australian Wine Research Institute , Glen Osmond, South Australia 5064 ,","place":["Australia"]},{"name":"School of Wine, Food and Agriculture, The University of Adelaide , South Australia 5005 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0227-0189","authenticated-orcid":false,"given":"Chris M","family":"Ward","sequence":"additional","affiliation":[{"name":"The Australian Wine Research Institute , Glen Osmond, South Australia 5064 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4494-5810","authenticated-orcid":false,"given":"Cristian","family":"Varela","sequence":"additional","affiliation":[{"name":"The Australian Wine Research Institute , Glen Osmond, South Australia 5064 ,","place":["Australia"]},{"name":"School of Wine, Food and Agriculture, The University of Adelaide , South Australia 5005 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Hale","sequence":"additional","affiliation":[{"name":"The Australian Wine Research Institute , Glen Osmond, South Australia 5064 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Simon A","family":"Schmidt","sequence":"additional","affiliation":[{"name":"The Australian Wine Research Institute , Glen Osmond, South Australia 5064 ,","place":["Australia"]},{"name":"School of Wine, Food and Agriculture, The University of Adelaide , South Australia 5005 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Anthony R","family":"Borneman","sequence":"additional","affiliation":[{"name":"The Australian Wine Research Institute , Glen Osmond, South Australia 5064 ,","place":["Australia"]},{"name":"School of Wine, Food and Agriculture, The University of Adelaide , South Australia 5005 ,","place":["Australia"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2025,6,11]]},"reference":[{"key":"2025062612073118400_bib1","doi-asserted-by":"publisher","first-page":"W7","DOI":"10.1093\/nar\/gkq291","article-title":"TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations","volume":"38","author":"Abascal","year":"2010","journal-title":"Nucleic Acids Res"},{"key":"2025062612073118400_bib2","doi-asserted-by":"publisher","first-page":"974","DOI":"10.1101\/gr.114876.110","article-title":"CNVnator: an approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing","volume":"21","author":"Abyzov","year":"2011","journal-title":"Genome Res"},{"key":"2025062612073118400_bib3","doi-asserted-by":"publisher","first-page":"79","DOI":"10.1038\/s42003-018-0085-8","article-title":"RAiSD detects positive selection based on multiple signatures of a selective sweep and SNP vectors","volume":"1","author":"Alachiotis","year":"2018","journal-title":"Commun Biol"},{"key":"2025062612073118400_bib4","doi-asserted-by":"publisher","first-page":"1569","DOI":"10.3389\/fmicb.2015.01569","article-title":"Hanseniaspora uvarum from winemaking environments show spatial and temporal genetic clustering","volume":"6","author":"Albertin","year":"2016","journal-title":"Front Microbiol"},{"key":"2025062612073118400_bib5","first-page":"4135","article-title":"GPD1, which encodes glycerol-3-phosphate dehydrogenase, is essential for growth under osmotic stress in Saccharomyces cerevisiae, and its expression is regulated by the high-osmolarity glycerol response pathway","volume":"14","author":"Albertyn","year":"1994","journal-title":"Mol Cel Biol"},{"key":"2025062612073118400_bib6","doi-asserted-by":"publisher","first-page":"109","DOI":"10.3390\/fermentation9020109","article-title":"Aroma profiles of vitis vinifera L. cv. 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