SMBE2016: Investigating the evolution of new biochemical pathways in baker’s yeast Saccharomyces cerevisiae

Well done to Åsa for her oral presentation at SMBE2016 (#204):

Investigating the evolution of new biochemical pathways in baker’s yeast Saccharomyces cerevisiae

Åsa Pérez-Bercoff, Tonia L. Russell, Philip J. L. Bell, Paul V. Attfield & Richard J. Edwards

Abstract

Understanding how new biochemical pathways evolve in a sexually reproducing population is a complex and largely unanswered question. We have successfully evolved a novel biochemical pathway in yeast using a sex based population approach.

For over 30 years, wild type Saccharomyces has been widely reported to not grow on xylose at all, but we discovered that most strains can grow, albeit at almost undetectable rates. A mass mated starting population of Saccharomyces cerevisiae strains was evolved under selection on Xylose Minimal Media (XMM) with forced sexual mating every ~two months for 1463 days. This produced a population that could grow on xylose as a sole carbon source. Initial studies show the xylose growth trait is quantitative and presumably governed by many genes. To investigate the evolution of the xylose phenotype, a xylose utilising strain MBG11a was isolated. MBG11a was sequenced with PacBio RSII long read sequencing at the Ramaciotti Centre for Genomics. A high quality complete genome was assembled de novo using the hierarchical genome-assembly process (HGAP3) using only PacBio non-hybrid long-read SMRT sequencing data, corrected using Quiver, and compared to the genome of the S. cerevisiae S288C reference genome.

Approximately 98.5% of the MBG11a genome could be aligned to S288C at 99.5% sequence identity, with over 15,000 non-synonymous and 200 nonsense SNP differences. We have crossed MBG11a with a reference wild type yeast strain (X2180 gal2, Xyl-) and are testing offspring on different minimal media in an attempt to identify MBG11a variants responsible for the novel growth phenotype.

Understanding what has occurred in the evolving yeast population, and how the yeast genome adapted under the selection pressures is of broad interest as it allows experimental analysis of how novel complex biological functions can evolve in an organism.