Chromosome-level Subgenome-awarede novoAssembly ofSaccharomyces bayanusProvides Insight into Genome Divergence after Hybridization

Abstract

AbstractInterspecies hybridization is prevalent in various eukaryotic lineages and plays important roles in phenotypic diversification, adaption, and speciation. To better understand the changes that occurred in the different subgenomes of a hybrid species and how they facilitated adaptation, we completed chromosome-levelde novoassemblies of all 16 pairs chromosomes for a recently formed hybrid yeast,Saccharomyces bayanusstrain CBS380 (IFO11022), using Nanopore MinION long-read sequencing. Characterization ofS. bayanussubgenomes and comparative analysis with the genomes of its parent species,S. uvarumandS. eubayanus,provide several new insights into understanding genome evolution after a relatively recent hybridization. For instance, multiple recombination events between the two subgenomes have been observed in each chromosome, followed by loss of heterozygosity (LOH) in most chromosomes in nine chromosome pairs. In addition to maintaining nearly all gene content and synteny from its parental genomes,S. bayanushas acquired many genes from other yeast species, primarily through the introgression ofS. cerevisiae, such as those involved in the maltose metabolism. In addition, the patterns of recombination and LOH suggest an allotetraploid origin ofS. bayanus. The gene acquisition and rapid LOH in the hybrid genome probably facilitated its adaption to maltose brewing environments and mitigated the maladaptive effect of hybridization.