Investigating the evolution of complex, novel traits using whole genome sequencing and molecular palaeontology

Åsa Pérez-Bercoff, Psyche Arcenal, Anna Sophia Grobler, Philip J. L. Bell, Paul V. Attfield and Richard J. Edwards.

Åsa presented the latest updates from our ARC Linkage Project with Microbiogen Pty Ltd at the Sydney Bioinformatics Research Symposium 2018. She will be giving an expanded version of the talk at the Genetics Society of AustralAsia 2018 conference in Canberra (1-4 July), if you missed it.

Abstract

Understanding how new biochemical pathways evolve in a sexually reproducing population is a complex and largely unanswered question. We are using PacBio whole-genome sequencing and deep population resequencing to explore the evolution of a novel biochemical pathway in yeast over several thousand generations. Growth of wild Saccharomyces cerevisiae strains on the pentose sugar xylose is barely perceptible. A mass-mated starting population was evolved under selection on Xylose Minimal Media with forced sexual mating every two months for four years, producing a population that can grow on and utilise xylose as its sole carbon source.

We are now using a novel “molecular palaeontology” approach to trace the evolutionary process and identify functionally significant loci under selection. Populations at seven key time points during their evolution have been sequenced using Illumina short-read sequencing. In addition, all the parental strains from the founding population have been subject to PacBio de novo whole-genome sequencing and assembly. By constructing reliable whole genomes of the ancestors of our populations, we can the trace evolution of these populations over time. We can therefore track the trajectory of allele frequencies through time, identifying the contributions of different founding strains and novel mutations. We are using these data to estimate the proportions and regions of the genome that have evolved neutrally, under purifying selection, or adaptively in response to xylose selection. Our unique array of both extant and past, but not extinct, populations allow us to test popular models of molecular evolution.