法国索邦大学Gilles Fischer、Joseph Schacherer和蔚蓝海岸大学Gianni Liti研究团队合作在研究中取得进展。他们利用142株菌株端粒到端粒的组装揭示了酿酒酵母基因组结构景观。相关论文发表在2023年7月31日出版的《自然-遗传学》杂志上。

研究人员重塑了酿酒酵母参考组装小组（ScRAP），包含142种代表该物种系统发育和生态多样性的参考基因组。ScRAP包含几种杂合二倍体和多倍体分离株的相相单倍体组装。研究人员发现了约4，800个非冗余SV，它们提供了基因组多样性的广泛图谱，包括端粒长度和转座元件动态。研究揭示了复杂非整倍体的出现频率，其中大染色体经历了大片段缺失和易位。

研究人员发现SVs可以影响断点附近的基因表达，并对基因库进化做出了实质性贡献。研究还发现染色体末端存在水平区域插入并可以产生新的端粒。总体而言，ScRAP证明了泛基因组在理解种群规模基因组进化方面的益处。

据介绍，泛基因组为在序列多态性和结构变异（SV）水平对物种遗传多样性准确表征提供了途径。

附：英文原文

Title: Telomere-to-telomere assemblies of 142 strains characterize the genome structural landscape in Saccharomyces cerevisiae

Author: ODonnell, Samuel, Yue, Jia-Xing, Saada, Omar Abou, Agier, Nicolas, Caradec, Claudia, Cokelaer, Thomas, De Chiara, Matteo, Delmas, Stphane, Dutreux, Fabien, Fournier, To, Friedrich, Anne, Kornobis, Etienne, Li, Jing, Miao, Zepu, Tattini, Lorenzo, Schacherer, Joseph, Liti, Gianni, Fischer, Gilles

Issue&Volume: 2023-07-31

Abstract: Pangenomes provide access to an accurate representation of the genetic diversity of species, both in terms of sequence polymorphisms and structural variants (SVs). Here we generated the Saccharomyces cerevisiae Reference Assembly Panel (ScRAP) comprising reference-quality genomes for 142 strains representing the species’ phylogenetic and ecological diversity. The ScRAP includes phased haplotype assemblies for several heterozygous diploid and polyploid isolates. We identified circa (ca.) 4,800 nonredundant SVs that provide a broad view of the genomic diversity, including the dynamics of telomere length and transposable elements. We uncovered frequent cases of complex aneuploidies where large chromosomes underwent large deletions and translocations. We found that SVs can impact gene expression near the breakpoints and substantially contribute to gene repertoire evolution. We also discovered that horizontally acquired regions insert at chromosome ends and can generate new telomeres. Overall, the ScRAP demonstrates the benefit of a pangenome in understanding genome evolution at population scale.

DOI: 10.1038/s41588-023-01459-y

Source: https://www.nature.com/articles/s41588-023-01459-y