Interspecies hybridization is prevalent in various eukaryotic lineages and plays important roles in phenotypic diversification, adaptation, and speciation. To better understand the changes that occurred in the different subgenomes of a hybrid species and how they facilitate adaptation, we have completed chromosome-level de novo assemblies of all chromosomes for a recently formed hybrid yeast, Saccharomyces bayanus strain CBS380, using Oxford Nanopore Technologies' MinION long-read sequencing. We characterize the S. bayanus genome and compare it with its parent species, Saccharomyces uvarum and Saccharomyces eubayanus, and other S. bayanus genomes to better understand genome evolution after a relatively recent hybridization event. We observe multiple recombination events between the subgenomes in each chromosome, followed by loss of heterozygosity (LOH) in nine chromosome pairs. In addition to maintaining nearly all gene content and synteny from its parental genomes, S. bayanus has acquired many genes from other yeast species, primarily through the introgression of Saccharomyces cerevisiae, such as those involved in the maltose metabolism. Finally, the patterns of recombination and LOH suggest an allotetraploid origin of S. bayanus. The gene acquisition and rapid LOH in the hybrid genome probably facilitated its adaptation to maltose brewing environments and mitigated the maladaptive effect of hybridization. This paper describes the first in-depth study using long-read sequencing technology of an S. bayanus hybrid genome, which may serve as an excellent reference for future studies of this important yeast and other yeast strains.

中文翻译：

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染色体水平的亚基因组感知从头组装提供了对杂交后巴亚酵母菌基因组分化的见解


种间杂交在各种真核生物谱系中普遍存在，并在表型多样化、适应和物种形成中起重要作用。为了更好地了解杂交物种的不同亚基因组中发生的变化以及它们如何促进适应，我们使用 Oxford Nanopore Technologies 的 MinION 长读长测序完成了最近形成的杂交酵母 Saccharomyces bayanus 菌株 CBS380 的所有染色体的染色体水平从头组装。我们表征了 S. bayanus 基因组，并将其与其亲本物种 Saccharomyces uvarum 和 Saccharomyces eubayanus 以及其他 S. bayanus 基因组进行比较，以更好地了解相对较新的杂交事件后的基因组进化。我们观察到每条染色体中亚基因组之间的多个重组事件，然后是 9 对染色体中的杂合性缺失 （LOH）。除了保持其亲本基因组中几乎所有的基因含量和同线外，S. bayanus 还从其他酵母物种获得了许多基因，主要是通过酿酒酵母的渗入，例如参与麦芽糖代谢的那些。最后，重组和 LOH 的模式表明 S. bayanus 的同种异体四倍体起源。杂交基因组中的基因获取和快速 LOH 可能促进了其对麦芽糖酿造环境的适应，并减轻了杂交的适应不良效应。本文描述了首次使用长读长测序技术对 S. bayanus 杂交基因组进行深入研究，这可能为未来研究这种重要酵母和其他酵母菌株提供极好的参考。