Whole-genome sequencing from the New Zealand Saccharomyces cerevisiae population reveals the genomic impacts of novel microbial range expansion.

Peter Higgins,Matthew R Goddard,Cooper A Grace,Soon A Lee,A Rokas

doi:10.1093/g3journal/jkaa027

Abstract

Saccharomyces cerevisiae is extensively utilized for commercial fermentation, and is also an important biological model; however, its ecology has only recently begun to be understood. Through the use of whole-genome sequencing, the species has been characterized into a number of distinct subpopulations, defined by geographical ranges and industrial uses. Here, the whole-genome sequences of 104 New Zealand (NZ) S. cerevisiae strains, including 52 novel genomes, are analyzed alongside 450 published sequences derived from various global locations. The impact of S. cerevisiae novel range expansion into NZ was investigated and these analyses reveal the positioning of NZ strains as a subgroup to the predominantly European/wine clade. A number of genomic differences with the European group correlate with range expansion into NZ, including 18 highly enriched single-nucleotide polymorphism (SNPs) and novel Ty1/2 insertions. While it is not possible to categorically determine if any genetic differences are due to stochastic process or the operations of natural selection, we suggest that the observation of NZ-specific copy number increases of four sugar transporter genes in the HXT family may reasonably represent an adaptation in the NZ S. cerevisiae subpopulation, and this correlates with the observations of copy number changes during adaptation in small-scale experimental evolution studies.

Highlights

Most plant and animal species have defined geographic ranges which they inhabit
When compared with the 1,011 high quality genomes from Peter et al 2018, the position of New Zealand (NZ) strains in the wider wine clade and global S. cerevisiae phylogeny is shown in Figure 1 and Figure S1
Previous research on NZ S. cerevisiae has disagreed on the position of the NZ S. cerevisiae subgroup within the wine yeast clade (Cromie et al, 2013; Goddard et al, 2010; Gayevskiy et al, 2016)

Summary

Introduction

Most plant and animal species have defined geographic ranges which they inhabit. The invasion of new ranges by species can have major impacts on genetic diversity and population structure (Braga et al, 2019), including admixture, adaptive evolution, and neutral evolution via genetic drift and bottleneck events While some microbes appear to be dispersed ubiquitously, others have restricted distributions, as described by a moderate endemicity model of microbial biogeography (Foissner, 2007). This suggests that, as with macroscopic species, geographic separation has the potential to drive population structure alongside environmental processes (O’Malley, 2008). The factors that constrain or define microbial range are not always clear, and the relative contribution of ecological and geographical factors is still being evaluated (Power et al, 2018; Meyer et al, 2018)

Methods

Results

Conclusion