Åsa Pérez-Bercoff, Tonia L. Russell, Paul V. Attfield, Philip J.L. Bell & Richard J. Edwards. http://f1000research.com/posters/4-1025.
We have a unique opportunity to study how new biological pathways have evolved to produce a yeast with a novel metabolic activity. Thirty-seven Saccharomyces cerevisiae strains were grown as a mixed population, and adapted on a specific media for 1463 days, undergoing sexual mating every two months. As a pilot study, three of the ancestral strains from the starting population, including two diploids, were selected for new PacBio RSII long-read single molecule real time (SMRT) sequencing at the Ramaciotti Centre for Genomics. High quality complete genomes were assembled de novo using the hierarchical genome-assembly process (HGAP3) using only PacBio non-hybrid long-read SMRT sequencing data, and corrected using Quiver. In addition, we have shotgun metagenomic Illumina data from a population exhibiting early adaptation to growth on the selective media. We are developing methods to map these short-read data onto several high quality ancestral genomes in order to estimate the relative contribution of each ancestor’s genetic variation to the evolved population, and identify possible sites of recombination. In addition, metagenomic data is being mapped against the official S. cerevisiae reference strain S288c to conduct variant calling to identify single nucleotide polymorphisms (SNPs) that are not present in any of our ancestral or reference genomes. These will be compared to the publicly available “100 yeast genomes”, and partitioned into natural variation and candidates for novel mutations. By doing these comparisons we hope to elucidate how the population has evolved to acquire its novel characteristics.