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Background  The lager brewing yeast,  S. pastorianus , is a hybrid between  S. cerevisiae  and  S. eubayanus  with extensive chromosome aneuploidy.  S. pastorianus  is subdivided into Group 1 and Group 2 strains, where Group 2 strains have higher copy number and a larger degree of heterozygosity for  S. cerevisiae  chromosomes. As a result, Group 2 strains were hypothesized to have emerged from a hybridization event distinct from Group 1 strains. Current genome assemblies of  S. pastorianus  strains are incomplete and highly fragmented, limiting our ability to investigate their evolutionary history.    Results  To fill this gap, we generated a chromosome-level genome assembly of the  S. pastorianus  strain CBS 1483 from Oxford Nanopore MinION DNA sequencing data and analysed the newly assembled subtelomeric regions and chromosome heterozygosity. To analyse the evolutionary history of  S. pastorianus  strains, we developed Alpaca: a method to compute sequence similarity between genomes without assuming linear evolution. Alpaca revealed high similarities between the  S. cerevisiae  subgenomes of Group 1 and 2 strains, and marked differences from sequenced  S. cerevisiae strains .    Conclusions  Our findings suggest that Group 1 and Group 2 strains originated from a single hybridization involving a heterozygous  S. cerevisiae  strain, followed by different evolutionary trajectories. The clear differences between both groups may originate from a severe population bottleneck caused by the isolation of the first pure cultures. Alpaca provides a computationally inexpensive method to analyse evolutionary relationships while considering non-linear evolution such as horizontal gene transfer and sexual reproduction, providing a complementary viewpoint beyond traditional phylogenetic approaches.

Chromosome level assembly and comparative genome analysis confirm lager-brewing yeasts originated from a single hybridization