Complex Ancestries of Lager-Brewing Hybrids Were Shaped by Standing Variation in the Wild Yeast Saccharomyces eubayanus

Abstract

Lager-style beers constitute the vast majority of the beer market, and yet, the genetic origin of the yeast strains that brew them has been shrouded in mystery and controversy. Unlike ale-style beers, which are generally brewed with Saccharomyces cerevisiae, lagers are brewed at colder temperatures with allopolyploid hybrids of Saccharomyces eubayanus x S. cerevisiae. Since the discovery of S. eubayanus in 2011, additional strains have been isolated from South America, North America, Australasia, and Asia, but only interspecies hybrids have been isolated in Europe. Here, using genome sequence data, we examine the relationships of these wild S. eubayanus strains to each other and to domesticated lager strains. Our results support the existence of a relatively low-diversity (π = 0.00197) lineage of S. eubayanus whose distribution stretches across the Holarctic ecozone and includes wild isolates from Tibet, new wild isolates from North America, and the S. eubayanus parents of lager yeasts. This Holarctic lineage is closely related to a population with higher diversity (π = 0.00275) that has been found primarily in South America but includes some widely distributed isolates. A second diverse South American population (π = 0.00354) and two early-diverging Asian subspecies are more distantly related. We further show that no single wild strain from the Holarctic lineage is the sole closest relative of lager yeasts. Instead, different parts of the genome portray different phylogenetic signals and ancestry, likely due to outcrossing and incomplete lineage sorting. Indeed, standing genetic variation within this wild Holarctic lineage of S. eubayanus is responsible for genetic variation still segregating among modern lager-brewing hybrids. We conclude that the relationships among wild strains of S. eubayanus and their domesticated hybrids reflect complex biogeographical and genetic processes.

Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

“…The Kr values between S. eubayanus and S. uvarum (0.073) obtained here are in agreement with previous findings and are similar to those of the most divergent P. rhodozyma strains. However, recent reports showed large intraspecific diversity (as high as 1 %) within both Saccharomyces species [26–28], so Kr values are prone to vary considerably, depending on the lineages used for comparison. The only Basidiomycota cases we could retrieve for comparison was that of the sister species Cryptococcus gattii and C. neoformans , which have Kr values 2-fold higher than P. rhodozyma (0.14); similarly, two varieties of C. neoformans (var.…”

Novel brewing yeast hybrids: creation and application

“…This seems to be due to a lack of maltotriose transporters (Hebly et al 2015; Baker et al 2015). However, so far, only one Patagonian isolate, the S. eubayanus type strain CBS12357, has been characterized in terms of maltotriose utilization (Gibson et al 2013; Hebly et al 2015) and newly found strains, e.g., Northern Hemisphere isolates from China and North America (Bing et al 2014; Peris et al 2016) and the New Zealand isolate (Gayevskiy and Goddard 2016) remain to be characterized. The two subgroups of the lager yeasts, Saaz and Frohberg, also differ in their sugar utilization characteristics.…”

“…Since the original isolation of S. eubayanus in South America, there have been a number of isolations elsewhere, including from North America (Peris et al 2014, 2016), East Asia (Bing et al 2014), and New Zealand (Gayevskiy and Goddard 2015) but, interestingly, not as yet from Europe. Recent sequence analysis suggests that there may be a Northern Hemisphere, or “Holarctic,” group of related strains with a wide geographical distribution, comprised (so far) of certain strains found in Tibet and in North America (Peris et al 2016).…”

“…Recent sequence analysis suggests that there may be a Northern Hemisphere, or “Holarctic,” group of related strains with a wide geographical distribution, comprised (so far) of certain strains found in Tibet and in North America (Peris et al 2016). Furthermore, it appears that it is a combination of the standing variation found among the Tibetan and North American strains that most closely matches the S. eubayanus parent of lager yeast (Peris et al 2016). It therefore cannot be concluded with any certainty that the parental S. eubayanus strain came directly from Asia as suggested by the “Silk Road” hypothesis (Bing et al 2014).…”

“…Moreover, these new hybrid strains can be generated without the use of targeted genetic modification, the use of which in the brewing industry still remains limited as a result of regulations and public opinion (Twardowski and Malyska 2015). In addition to their immediate industrial applications, these new yeast hybrids may also help to elucidate the evolutionary history of industrial hybrid yeast strains, which still remains a subject of debate (Baker et al 2015; Okuno et al 2016; Peris et al 2016). …”