Abstract
The fission yeast Schizosaccharomyces pombe has been widely used as a model eukaryote to study a diverse range of biological processes. However, population genetic studies of this species have been limited to date, and we know very little about the evolutionary processes and selective pressures that are shaping its genome. Here, we sequenced the genomes of 32 worldwide S. pombe strains and examined the pattern of polymorphisms across their genomes. In addition to introns and untranslated regions (UTRs), intergenic regions also exhibited lower levels of nucleotide diversity than synonymous sites, suggesting that a considerable amount of noncoding DNA is under selective constraint and thus likely to be functional. A number of genomic regions showed a reduction of nucleotide diversity probably caused by selective sweeps. We also identified a region close to the end of chromosome 3 where an extremely high level of divergence was observed between 5 of the 32 strains and the remain 27, possibly due to introgression, strong positive selection, or that region being responsible for reproductive isolation. Our study should serve as an important starting point in using a population genomics approach to further elucidate the biology of this important model organism.
Highlights
The eukaryotic genome contains several non-coding regions that are crucial for chromosome maintenance and many other basic cellular processes
With an aim to characterize all such functional non-coding elements that lie between the centromere and telomere, which we termed ‘‘intermeres’’, mainly using model organisms such as the fission yeast Schizosaccharomyces pombe and the budding yeast Saccharomyces cerevisiae, we recently formed an interdisciplinary consortium funded by MEXT (The Ministry of Education, Culture, Sports, Science and Technology, Japan)
The very high coverage allowed us to adopt a stringent cutoff and obtain 9,375,308 sites (,75% of the genome) where the genotypes were confidently assigned for all 32 strains, including 99,381 single nucleotide polymorphisms (SNPs)
Summary
The eukaryotic genome contains several non-coding regions that are crucial for chromosome maintenance and many other basic cellular processes. The fission yeast S. pombe is a unicellular archiascomycete fungus which has been an excellent model species in molecular and cellular biology, for studying cell-cycle control [5], cytokinesis [6], mitosis and meiosis [7], DNA repair and recombination [3], centromere structure [2], and RNAi-mediated heterochromatin assembly [4]. This is largely because S. pombe shares many features with higher eukaryotes that are not present or highly diverged in the budding yeast S. cerevisiae. The 12.5 megabase (Mb) genome of the S. pombe laboratory strain has already been sequenced [8] and compared with three distantly related fission yeast species [9]
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