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Nature Research, Nature Genetics, 3(47), p. 235-241, 2015

DOI: 10.1038/ng.3215

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The genomic and phenotypic diversity of Schizosaccharomyces pombe

This paper is made freely available by the publisher.
This paper is made freely available by the publisher.

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Abstract

Although the standard laboratory strain of S. pombe has been extensively studied, genetic variation and phenotypic diversity have been analyzed only in preliminary ways 1–3. Remarkably little is known about the evolutionary history or ecology of this model organism. It was first described in East African millet beer in 1893, and the standard laboratory strain was isolated from French wine in 1924 (ref. 4). Natural isolates have also been collected from vineyards in Sicily and cachaça (a sugarcane spirit) in Brazil and have been found to contribute to the microbial ecology of kombucha (fermented tea) 1,5,6. The diverse origins of these natural isolates (Fig. 1a and Supplementary Table 1) suggest that this yeast species is now widely distributed. To further describe S. pombe, we analyzed the genetic and phenotypic variation in natural isolates. Because the natural environment is not known, we collected all isolates available from the major stock centers and those given to us by microbial ecologists (Supplementary Table 1). These 161 strains had been collected over the last 100 years, in over 20 countries across the globe, primarily from cultivated fruit or various fermentations. Notably, the strains of known origin had been associated with human activities, providing little information about the natural environment of the species. RESULTS Variation and population structure We sequenced the genome of all strains to at least 18-fold coverage , with a median of 76-fold coverage. To facilitate the detection of genetic variants, we mapped reads to the reference genome 7. Mapping was comprehensive and accurate owing to the small, non-repetitive