Tsouris, A. | Search bioRxiv

bioRxiv2020

nPhase: An accurate and contiguous phasing method for polyploids

While genome sequencing and assembly are now routine, we still do not have a full and precise picture of polyploid genomes. Phasing these genomes, i.e. deducing haplotypes from genomic data, remains a challenge. Despite numerous attempts, no existing polyploid phasing method provides accurate and contiguous haplotype predictions. To address this need, we developed nPhase, a ploidy agnostic pipeline and algorithm that leverage the accuracy of short reads and the length of long reads to solve reference alignment-based phasing for samples of unspecified ploidy (https://github.com/nPhasePipeline/nPhase). nPhase was validated on virtually constructed polyploid genomes of the model species Saccharomyces cerevisiae, generated by combining sequencing data of homozygous isolates. nPhase obtained on average >95% accuracy and a contiguous 1.25 haplotigs per haplotype to cover >90% of each chromosome (heterozygosity rate [≥]0.5%). This new phasing method opens the door to explore polyploid genomes through applications such as population genomics and hybrid studies.

genomics↗

bioRxiv2020

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

Ale brewing yeast are the result of admixture between diverse strains of Saccharomyces cerevisiae, 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.

evolutionary biology↗