斯特拉斯堡大学Joseph Schacherer团队宣布他们的研究开发出了从基因型到表型与1086近端粒到端粒酵母基因组。相关论文于2025年10月15日发表在《自然》杂志上。

在这里，研究团队提出了广泛的基因组和表型抗性的酵母酿酒酵母基于近端粒到端粒组装的1086天然分离。利用这些高邻接的组件，该团队生成了一个高度完整的全物种结构变异图谱，基于基因的泛基因组和图形泛基因组。通过整合整个物种捕获的全谱遗传变异，研究组对8391个分子和有机体特征进行了全基因组关联研究。与仅基于单核苷酸多态性的分析相比，结构变异和小插入-删除突变的包含将遗传力估计平均提高了14.3%。与其他变异类型相比，结构变异更频繁地与性状相关，并表现出更大的多效性。值得注意的是，分子和有机体性状的遗传结构明显不同。总之，这项工作提供了一个独特的数据集，阐明了不同形式的遗传变异如何形成表型多样性，并为其他真核生物系统的整合、基因组规模研究奠定了基础。

据介绍，揭示在自然种群中观察到的显着表型多样性的遗传基础仍然是生物学的核心挑战。尽管取得了重大进展，但还没有一个物种具有真正全面的遗传变异图谱。

附：英文原文

Title: From genotype to phenotype with 1,086 near telomere-to-telomere yeast genomes

Author: Loegler, Victor, Thiele, Pia, Teyssonnire, Elie, Tsouris, Andreas, Brach, Gauthier, Cruaud, Corinne, Payen, Emilie, Engelen, Stefan, Dunham, Maitreya J., Hou, Jing, Friedrich, Anne, Schacherer, Joseph

Issue&Volume: 2025-10-15

Abstract: Unravelling the genetic basis of the remarkable phenotypic diversity observed in natural populations remains a central challenge in biology1,2,3,4. Despite major advances5,6,7,8,9,10,11,12,13,14,15,16,17,18,19, no species has yet been characterized with a truly comprehensive atlas of genetic variation. Here we present an extensive genomic and phenotypic resource for the yeast Saccharomyces cerevisiae based on near telomere-to-telomere assemblies of 1,086 natural isolates. Leveraging these high-contiguity assemblies, we generated a highly complete species-wide structural variant atlas, gene-based pangenome and graph pangenome. By incorporating the full spectrum of genetic variation captured across the species, we conducted genome-wide association studies across 8,391 molecular and organismal traits19,20,21,22. The inclusion of structural variants and small insertion–deletion mutations improved heritability estimates by an average of 14.3% compared with analyses based only on single-nucleotide polymorphisms. Structural variants were more frequently associated with traits and exhibited greater pleiotropy than other variant types. Notably, the genetic architecture of molecular and organismal traits differed markedly. Together, this work provides a unique dataset that illuminates how diverse forms of genetic variation shape phenotypic diversity and lays the groundwork for integrative, genome-scale studies in other eukaryotic systems.

DOI: 10.1038/s41586-025-09637-0

Source: https://www.nature.com/articles/s41586-025-09637-0