Genomic stability and adaptation of beer brewing yeasts during serial repitching in the brewery

Abstract

<jats:title>Abstract</jats:title><jats:p>Ale brewing yeast are the result of admixture between diverse strains of <jats:italic>Saccharomyces cerevisiae</jats:italic>, resulting in a heterozygous tetraploid that has since undergone numerous genomic rearrangements. As a result, comparisons between the genomes of modern related ale brewing strains show both extensive aneuploidy and mitotic recombination that has resulted in a loss of intragenomic diversity. Similar patterns of intraspecific admixture and subsequent selection for one haplotype have been seen in many domesticated crops, potentially reflecting a general pattern of domestication syndrome between these systems. We set out to explore the evolution of the ale brewing yeast, to understand both polyploid evolution and the process of domestication in the ecologically relevant environment of the brewery. Utilizing a common brewery practice known as ‘repitching’, in which yeasts are reused over multiple beer fermentations, we generated population time courses from multiple breweries utilizing similar strains of ale yeast. Applying whole-genome sequencing to the time courses, we have found that the same structural variations in the form of aneuploidy and mitotic recombination of particular chromosomes reproducibly rise to detectable frequency during adaptation to brewing conditions across multiple related strains in different breweries. Our results demonstrate that domestication of ale strains is an ongoing process and will likely continue to occur as modern brewing practices develop.</jats:p>

Macrosynteny analysis between Lentinula edodes and Lentinula novae-zelandiae reveals signals of domestication in Lentinula edodes

“…Research on fungal genome structure in response to domestication suggests large macrosyntenic rearrangements can occur frequently and rapidly within populations and can even lead to diversification of lineages 7 – 9 , 11 , 13 , 31 , 41 . For example, research in brewer’s yeast has shown that chromosomes can fragment and subsequently be misrepaired by being fused together at telomere regions, resulting in new chromosomes with embedded telomeric sequences within them 11 , 13 , 41 .…”

“…This has allowed for the production of genome assemblies with high levels of contiguity, something previously difficult and expensive to attain with second generation short-read sequencing technologies. These highly contiguous genomes allow for exploration of a number of areas that were previously intractable, such as: large-scale genome structure analysis, known as macrosynteny 30 ; and longitudinal studies investigating how genome structure changes over time 31 . Large-scale genome synteny analysis is difficult to undertake with fragmented genomes, with previous efforts focused on specific loci and the ordering of the genes; this is known as microsynteny 32 – 35 .…”

<strong>SMARTdenov</strong><strong>o: A <em>de novo</em> Assembler Using Long Noisy Reads</strong>

“…SMARTdenovo has been available since 2015 on github, but its performance not only remains comparable with current assemblers, and but also has several advantages as described. Furthermore, given its excellent performance for use on corrected long sequence reads, it continues to be widely used in for genome assembly projects today [33][34][35][36][37][38][39][40][41][42].…”

SMARTdenovo: a de novo assembler using long noisy reads

“…Furthermore, given its excellent performance for use on corrected long sequence reads, it continues to be widely used in for genome assembly projects today [34][35][36][37][38][39][40][41][42][43].…”