In a Nature Genetics paper, scientists used SMRT Sequencing to detect and compare structural variations in several yeast strains in order to understand evolutionary genome dynamics. They found different rates of evolution among domesticated and wild strains, and suggest that “the influence of human activities” could explain this.
“Contrasting evolutionary genome dynamics between domesticated and wild yeasts” comes from lead author Jia-Xing Yue, senior author Gianni Liti, and collaborators at the Université Côte d’Azur, the Wellcome Trust Sanger Institute, and other institutes. Choosing long reads to facilitate accurate detection of structural variants, they used PacBio sequencing and generated “end-to-end genome assemblies for 12 strains representing major subpopulations of the partially domesticated yeast Saccharomyces cerevisiae and its wild relative Saccharomyces paradoxus,” the scientists report. “The raw PacBio de novo assemblies of both nuclear and mitochondrial genomes showed compelling completeness and accuracy, with most chromosomes assembled into single contigs, and highly complex regions accurately assembled.”
According to the team, the final 12 assemblies provided “unprecedented resolution” for analyzing subtelomeric regions, which yielded a detailed look at evolutionary genome dynamics. “In chromosomal cores, S. paradoxus shows faster accumulation of balanced rearrangements (inversions, reciprocal translocations and transpositions), whereas S. cerevisiae accumulates unbalanced rearrangements (novel insertions, deletions and duplications) more rapidly,” the scientists write. “In subtelomeres, both species show extensive interchromosomal reshuffling, with a higher tempo in S. cerevisiae.” The accelerated evolution in baker’s yeast is likely to be at least partly a function of human activity and the human-associated environments to which the organisms have been exposed, they add.
The authors note that this study is an indicator of the utility of SMRT Sequencing for population genomics. Ultimately, they say, their results offer an intriguing new explanation for “why S. cerevisiae, but not its wild relative, is one of our most biotechnologically important organisms.”
July 11, 2017 | General