The fission yeast Schizosaccharomyces pombe has been widely used to study eukaryotic cell biology, but almost all of this work has used derivatives of a single strain. We have studied 81 independent natural isolates and 3 designated laboratory strains of Schizosaccharomyces pombe. Schizosaccharomyces pombe varies significantly in size but shows only limited variation in proliferation in different environments compared with Saccharomyces cerevisiae. Nucleotide diversity, π, at a near neutral site, the central core of the centromere of chromosome II is approximately 0.7%. Approximately 20% of the isolates showed karyotypic rearrangements as detected by pulsed field gel electrophoresis and filter hybridization analysis. One translocation, found in 6 different isolates, including the type strain, has a geographically widespread distribution and a unique haplotype and may be a marker of an incipient speciation event. All of the other translocations are unique. Exploitation of this karyotypic diversity may cast new light on both the biology of telomeres and centromeres and on isolating mechanisms in single-celled eukaryotes.

Kinetochores in multicellular eukaryotes are usually associated with heterochromatin. Whether this heterochromatin simply promotes the cohesion necessary for accurate chromosome segregation at cell division or whether it also has a role in kinetochore assembly is unclear. Schizosaccharomyces pombe is an important experimental system for investigating centromere function, but all of the previous work with this species has exploited a single strain or its derivatives. The laboratory strain and most other S. pombe strains contain three chromosomes, but one recently discovered strain, CBS 2777, contains four. We show that the genome of CBS 2777 is related to that of the laboratory strain by a complex chromosome rearrangement. As a result, two of the kinetochores in CBS 2777 contain the central core sequences present in the laboratory strain centromeres, but lack adjacent heterochromatin. The closest block of heterochromatin to these rearranged kinetochores is ∼100 kb away at new telomeres. Despite lacking large amounts of adjacent heterochromatin, the rearranged kinetochores bind CENP-A Cnp1 and CENP-C Cnp3 in similar quantities and with similar specificities as those of the laboratory strain. The simplest interpretation of this result is that constitutive kinetochore assembly and heterochromatin formation occur autonomously.yeast | microbial diversity | epigenesis T he fission yeast Schizosaccharomyces pombe is a key system for the experimental study of centromere function. To date, all of this work has involved the strain 968h 90 and its derivatives 972h − and 975h + , each of which contains three chromosomes. Each of these chromosomes contains a kinetochore embedded in heterochromatin (1) and resembles the centromeres of many metazoan organisms; consequently they have been intensively studied. These studies have demonstrated that heterochromatin is necessary for the formation of new kinetochores (2-4), but that once formed, kintetochores (5) can be maintained on a circular plasmid in the absence of heterochromatin. In evolution, novel centromeres form on regions of chromosomes lacking heterochromatin but subsequently acquire it (6, 7), an order of events at odds with the conclusions of published studies of S. pombe. Thus, the relationship between heterochromatin and kinetochore assembly in S. pombe requires investigation using new approaches.A study of 88 independent natural isolates of S. pombe showed that this fission yeast is karyotypically variable, and that one Japanese strain, CBS 2777, contains four chromosomes (8). In the present study, we determined the genome sequence and organization of CBS 2777 and found that it is related to the karyotype of the laboratory strains by a complex rearrangement. We show that two of the centromeres in CBS 2777 lack flanking heterochromatic repeated sequences. This DNA is not detectably associated with siRNA and does not show any detectable enrichment of Rad21 (cohesin) binding. Despite these differences in flanking DNA, the rearranged centromeres in CBS 2777 bind the cons...