Many interspecific chromosomal introgressions are highly prevalent in Holarctic Saccharomyces uvarum strains found in human‐related fermentations

Abstract

In the last two decades, the extensive genome sequencing of strains belonging to the Saccharomyces genus has revealed the complex reticulated evolution of this group. Among the various evolutionary mechanisms described, the introgression of large chromosomal regions resulting from interspecific hybridization has recently shed light on Saccharomyces uvarum species. In this work we provide the de novo assembled genomes of four S. uvarum strains presenting more than 712 kb of introgressed loci inherited from both Saccharomyces eubayanus and Saccharomyces kudriavzevii species. In order to study the prevalence of such introgressions in a large population, we designed multiplexed PCR markers able to survey the inheritance of eight chromosomal regions. Our data confirm that introgressions are widely disseminated in Holarctic S. uvarum populations and are more frequently found in strains isolated from human-related fermentations. According to the origin of the strains (nature or cider-or wine-related processes), some loci are over-represented, suggesting their positive selection by human activity. Except for one locus located on chromosome 7, the introgressions present a low level of heterozygozity similar to that observed for nine neutral markers (microsatellites). Finally, most of the loci tested showed an expected Mendelian segregation after meiosis and can recombine with their chromosomal counterpart in S. uvarum.

Bioprospecting for brewers: Exploiting natural diversity for naturally diverse beers

“…In this context, several natural Saccharomyces hybrids have been isolated from industrial settings, such as wineries and beer fermentation tanks, demonstrating that hybrid selection based on greater fitness under fermentation conditions has already occurred. The best example is S. pastorianus ( S. cerevisiae × S. eubayanus ) and reviewed elsewhere (Gibson & Liti, ); however, many other interspecies hybrids have also been recovered (Albertin et al, ; Gonzalez, Barrio, & Querol, ; Krogerus, Preiss, & Gibson, ; Peris et al, ). For example, S. cerevisiae × Saccharomyces kudriavzevii hybrid strains were recovered in brewing environments (Gonzalez et al, ; Peris et al, ).…”

“…However, wild Saccharomyces strains with introgressions from other species do occur (Albertin et al, ; Almeida et al, ; Peter et al, )—some examples are found in S. cerevisiae with introgressions from other species including the closely related species S. paradoxus (Duan et al, ; Peter et al, ). Still, most isolates exhibiting horizontal gene transfers are generally associated with human activities: such as those found in S. uvarum , where introgressions from S. eubayanus and S. kudriavzevii were described (Albertin et al, ). These antecedents suggest that hybrids are fitter solely when associated with fermentation environments but do not persist in the wild.…”

TheSSU1checkup, a rapid tool for detecting chromosomal rearrangements of theSaccharomyces cerevisiaechromosome XVI. An ecological and technological study on wine yeast

“…The following PCR program allows the amplification of all the expected fragments from the rearranged and the wild type VIII, XV and XVI chromosomes: initial denaturation at 95 °C for 15 min, followed by 35 cycles of 94 °C for 30 s, 55 °C for 90 s, 72 °C for 90 s, ending with a hold at 60 °C for 30 min. DNA templates for PCR were extracted in 96-well microplates using the previously described LiAc-SDS protocol (Chernova et al, 2018). Before analysis, PCR products were diluted 60 times in ddH 2 O and 1 μL of this solution was mixed with 0.2 μL of the internal size standard GenScanTM 1200 LIZ ® (Applied Biosystems, France) and 9.8 μL of highly deionized Hi-DiTM formamide (Applied Biosystems, France).…”

A study of phenotypic plasticity ofSaccharomyces cerevisiaein natural grape juices shed light on allelic variation under balanced selection

“…The DNA of S. cerevisiae strains was quickly extracted in 96-well microplate format using a customized LiAc-SDS protocol (Albertin et al 2017). Fifteen polymorphic microsatellite loci SCAAT3 ( C3, C5, SCYOR267C, C8, C11, SCAAT2, YKL172, SCAAT6, C9, C4, SCAAT5, SCAAT1, C6, YPL009, YKL172W ) were used for estimating the genetic relationships within 96 commercial starters and the four monosporic parental strains (GN, SB, M2, F15) used in this work (S3 Table).…”