Loegler Victor, Runge Jan-Niklas, Eberlein Chris, Peltier Émilien, Harrouard Jules, Miot-Sertier Cécile, Albertin Warren, Friedrich Anne, Schacherer Joseph
Université de Strasbourg, CNRS GMGM UMR 7156, Strasbourg, France.
Université de Bordeaux, UMR 1366 Œnologie, ISVV, INRAE, Bordeaux INP, Bordeaux Sciences Agro, Villenave d'Ornon, France.
Nat Commun. 2025 Jul 1;16(1):5500. doi: 10.1038/s41467-025-60706-4.
Genomic architecture changes can significantly influence genome evolution and phenotypic variation within a species. Polyploidization events are thought to be one of the important catalysts for adaptation, speciation and tumorigenesis. However, little is known about the overall impact of such events on the phenotypic landscape at a population level. Here, we completely sequenced and phenotyped a large population of 1060 Brettanomyces bruxellensis yeast isolates, punctuated by multiple independent polyploidization events, notably allopolyploidization, giving rise to a highly structured population related to various anthropized ecological niches. A subgenome-aware population analysis revealed differential genome evolution between the primary and acquired genomes, with the latter showing a higher degree of conservation between isolates. Distinct phenotypic signatures were identified across major populations, with allopolyploid isolates showing an enrichment of extreme phenotypes. Genome-wide association analysis consistently revealed the substantial influence of the acquired genome of allopolyploids, with associated variants exhibiting significantly larger effect sizes than those from the primary genome. Overall, our study illustrates the profound and species-wide impact of polyploidization events on genome evolution and phenotypic diversity. It also provides a useful resource to explore the impact of allopolyploidy on adaptation.
基因组结构变化可显著影响一个物种内的基因组进化和表型变异。多倍体化事件被认为是适应、物种形成和肿瘤发生的重要催化剂之一。然而，关于此类事件在种群水平上对表型格局的总体影响，人们所知甚少。在此，我们对1060株布鲁塞尔酒香酵母分离株组成的大群体进行了全基因组测序和表型分析，这些分离株存在多个独立的多倍体化事件，尤其是异源多倍体化，形成了一个与各种人为生态位相关的高度结构化群体。一项亚基因组群体分析揭示了初级基因组和获得性基因组之间的差异基因组进化，后者在分离株之间表现出更高程度的保守性。在主要群体中鉴定出了不同的表型特征，异源多倍体分离株表现出极端表型的富集。全基因组关联分析一致揭示了异源多倍体获得性基因组的重大影响，相关变异的效应大小显著大于初级基因组中的变异。总体而言，我们的研究阐明了多倍体化事件对基因组进化和表型多样性的深远及全物种影响。它还为探索异源多倍体对适应的影响提供了有用的资源。
