Population genomics of domestic and wild yeasts

David M Carter ,Douda Bensasson,Austin Burt,Sarah Sims,Alexander Van Oudenaarden,Leopold Parts,Vassiliki Koufopanou,Richard Durbin,Anders Blomberg,Gianni Liti,Elizabeth Bailes,Ian Goodhead,Michael A Quail ,Alan M Moses ,Casey M Bergman ,Stephen A James ,Michael O’kelly ,Matthew C Jones ,Isheng Jason Tsai ,David B H Barton ,Robert P Davey ,Ian N Roberts ,Frances J.d Smith ,Edward J Louis

doi:10.1038/npre.2008.1988.1

Abstract

AbstractThe natural genetics of an organism is determined by the distribution of sequences of its genome. Here we present one- to four-fold, with some deeper, coverage of the genome sequences of over seventy isolates of the domesticated baker's yeast, Saccharomyces cerevisiae, and its closest relative, the wild S. paradoxus, which has never been associated with human activity. These were collected from numerous geographic locations and sources (including wild, clinical, baking, wine, laboratory and food spoilage). These sequences provide an unprecedented view of the population structure, natural (and artificial) selection and genome evolution in these species. Variation in gene content, SNPs, indels, copy numbers and transposable elements provide insights into the evolution of different lineages. Phenotypic variation broadly correlates with global genome-wide phylogenetic relationships however there is no correlation with source. S. paradoxus populations are well delineated along geographic boundaries while the variation among worldwide S. cerevisiae isolates show less differentiation and is comparable to a single S. paradoxus population. Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae shows a few well defined geographically isolated lineages and many different mosaics of these lineages, supporting the notion that human influence provided the opportunity for outbreeding and production of new combinations of pre-existing variation.

Highlights

The S. cerevisiae population structure is more complex
Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for crossbreeding and production of new combinations of pre-existing variation
Much of the unplaced material is subtelomeric. This is in contrast to a genome-wide analysis of copy number based on the numbers of reads of each strain aligning to each gene in the reference sequence, which showed very little significant copy number variation (CNV) outside the rDNA region

Summary

Introduction

The S. cerevisiae population structure is more complex. There are five lineages that exhibit the same phylogenetic relationship across their entire genomes, which we consider to be ‘clean’ non-mosaic lineages (Fig. 1C). Rather than one or two domestication events leading to the extant baker's yeasts, the population structure of S. cerevisiae consists of a few well-defined geographically isolated lineages and many different mosaics of these lineages, supporting the idea that human influence provided the opportunity for crossbreeding and production of new combinations of pre-existing variation. We report nearly complete genome sequences of S. cerevisiae and S. paradoxus from a large variety of sources and locations (Table S1 and S2).

Results

Conclusion