Macroevolutionary diversity of traits and genomes in the model yeast genus Saccharomyces

Abstract

Species is the fundamental unit to quantify biodiversity. In recent years, the model yeast Saccharomyces cerevisiae has seen an increased number of studies related to its geographical distribution, population structure, and phenotypic diversity. However, seven additional species from the same genus have been less thoroughly studied, which has limited our understanding of the macroevolutionary leading to the diversification of this genus over the last 20 million years. Here, we report the geographies, hosts, substrates, and phylogenetic relationships for approximately 1,800 Saccharomyces strains, covering the complete genus with unprecedented breadth and depth. We generated and analyzed complete genome sequences of 163 strains and phenotyped 128 phylogenetically diverse strains. This dataset provides insights about genetic and phenotypic diversity within and between species and populations, quantifies reticulation and incomplete lineage sorting, and demonstrates how gene flow and selection have affected traits, such as galactose metabolism. These findings elevate the genus Saccharomyces as a model to understand biodiversity and evolution in microbial eukaryotes.

Beyond Saccharomyces pastorianus for modern lager brews: Exploring non-cerevisiae Saccharomyces hybrids with heterotic maltotriose consumption and novel aroma profile

“…Our HTS identified so far uncharacterized S. mikatae Mtt + wild strains as well as the recently reported Mtt + S. mikatae LSYS65-1 strain (Peris et al, 2022). Parallel studies conducted by other authors demonstrated that the two S. jurei strains TUM 629 and D5095 T are also able to utilize wort maltotriose to a certain extent (Giannakou et al, 2021;Hutzler et al, 2021) and that some S. mikatae strains are able to grow on this sugar (Peris et al, 2022).…”

“…Our finding that S. mikatae strains exhibit growth on maltotriose as the sole carbon source provides an example of the high intraspecies phenotypic diversity uncovered recently for the species despite its low genetic diversity (Peris et al, 2022). However, only a limited number of strains have been tested so far for wort fermentability.…”

“…Therefore, synthetic medium with maltotriose (SM + Mtt) and a different maltotriose batch with a higher purity were used in a next step to test the best performers in a single array including two S. jurei strains (Supplementary strain CBS 12357 T (Mtt − ) was set to 1 and the performances of all other strains were shown as fold-change in comparison (Supplementary Figure S2B). The top-performing strains included four non-cerevisiae Saccharomyces strains-the S. jurei D5095 T and S. mikatae LSYS65-1 strains which were recently reported as Mtt + in parallel studies (Giannakou et al, 2021;Peris et al, 2022) and two S. mikatae strains not described yet in literature for the phenotype tested-NBRC 11002 and NBRC 10997 (Supplementary Figure S2).…”

An adaptive interaction between cell type and metabolism drives ploidy evolution in a wild yeast

“…Indeed, there is clade-specific variation within S. cerevisiae as to whether the MAL1 locus is occupied by the generalist AGT1 or a gene encoding a high-specificity maltose transporter [153], suggesting that domestication may have shaped the genetic architecture of α-glucoside metabolism in this model eukaryote [154]. Supporting this notion, AGT1 homologs can be readily detected in publicly available Saccharomyces genomes, while growth on maltotriose—a sugar transported by AGT1 but not most other maltose transporters—is extremely rare [62]. A notable exception is Saccharomyces jurei, the first wild Saccharomyces reported to grow on maltotriose, which contains a clear homolog of AGT1 that requires extensive starvation or depletion of fermentable carbon sources for its induction [155].…”

“…A focal ecological and industrial trait in this wild species is the ability to consume and metabolize the α-glucoside maltose, which is the most abundant sugar in the wort used to brew beer [60,61]. This trait is nearly ubiquitous among isolates of Saccharomyces eubayanus and its sister species Saccharomyces uvarum [62], but it has been lost [63] or severely curtailed [64] in the Holarctic subpopulation of S. eubayanus [51]. Paradoxically, members of this group contain functional structural maltose metabolism genes, and their inability to use this sugar as a carbon source may be due to cis- or trans-regulatory evolution resulting in altered expression of structural metabolism genes.…”