In Saccharomyces cerevisiae the MSH4-MSH5, MLH1-MLH3, and MUS81-MMS4 complexes act to promote crossing over during meiosis. MSH4-MSH5, but not MUS81-MMS4, promotes crossovers that display interference. A role for MLH1-MLH3 in crossover control is less clear partly because mlh1⌬ mutants retain crossover interference yet display a decrease in crossing over that is only slightly less severe than that seen in msh4⌬ and msh5⌬ mutants. We analyzed the effects of msh5⌬, mlh1⌬, and mms4⌬ single, double, and triple mutants on meiotic crossing over at four consecutive genetic intervals on chromosome XV using newly developed computer software. mlh1⌬ mms4⌬ double mutants displayed the largest decrease in crossing over (13-to 15-fold) of all mutant combinations, yet these strains displayed relatively high spore viability (42%). In contrast, msh5⌬ mms4⌬ and msh5⌬ mms4⌬ mlh1⌬ mutants displayed smaller decreases in crossing over (4-to 6-fold); however, spore viability (18-19%) was lower in these strains than in mlh1⌬ mms4⌬ strains. These data suggest that meiotic crossing over can occur in yeast through three distinct crossover pathways. In one pathway, MUS81-MMS4 promotes interference-independent crossing over; in a second pathway, both MSH4-MSH5 and MLH1-MLH3 promote interference-dependent crossovers. A third pathway, which appears to be repressed by MSH4-MSH5, yields deleterious crossovers. I N most eukaryotic organisms the correct segregation in both reciprocal exchanges, termed crossovers (CO), and of chromosomes at the first meiotic division requires nonreciprocal exchanges, termed noncrossovers (NCO). reciprocal exchange between homologs. The physicalThe classical double-strand break repair (DSBR) model manifestations of these crossover events, chiasmata, proproposes that these events result from alternative resoluvide the contacts between homologous chromosomes tions of a common Holliday junction intermediate (rethat are necessary for segregation ( Jones 1987). This viewed in Pâques and Haber 1999). Recent studies, cohesion or "chiasma binder" function ensures the genhowever, have suggested that COs and NCOs are proeration of a bipolar spindle in which tension is genercessed via separate pathways. In support of this idea, ated at the kinetochores (Maguire 1974

Bioethanol is a biofuel produced mainly from the fermentation of carbohydrates derived from agricultural feedstocks by the yeast Saccharomyces cerevisiae. One of the most widely adopted strains is PE-2, a heterothallic diploid naturally adapted to the sugar cane fermentation process used in Brazil. Here we report the molecular genetic analysis of a PE-2 derived diploid (JAY270), and the complete genome sequence of a haploid derivative (JAY291). The JAY270 genome is highly heterozygous (;2 SNPs/kb) and has several structural polymorphisms between homologous chromosomes. These chromosomal rearrangements are confined to the peripheral regions of the chromosomes, with breakpoints within repetitive DNA sequences. Despite its complex karyotype, this diploid, when sporulated, had a high frequency of viable spores. Hybrid diploids formed by outcrossing with the laboratory strain S288c also displayed good spore viability. Thus, the rearrangements that exist near the ends of chromosomes do not impair meiosis, as they do not span regions that contain essential genes. This observation is consistent with a model in which the peripheral regions of chromosomes represent plastic domains of the genome that are free to recombine ectopically and experiment with alternative structures. We also explored features of the JAY270 and JAY291 genomes that help explain their high adaptation to industrial environments, exhibiting desirable phenotypes such as high ethanol and cell mass production and high temperature and oxidative stress tolerance. The genomic manipulation of such strains could enable the creation of a new generation of industrial organisms, ideally suited for use as delivery vehicles for future bioenergy technologies.

Ionizing radiation is an established source of chromosome aberrations (CAs). Although double-strand breaks (DSBs) are implicated in radiation-induced and other CAs, the underlying mechanisms are poorly understood. Here, we show that, although the vast majority of randomly induced DSBs in G 2 diploid yeast cells are repaired efficiently through homologous recombination (HR) between sister chromatids or homologous chromosomes, Ϸ2% of all DSBs give rise to CAs. Complete molecular analysis of the genome revealed that nearly all of the CAs resulted from HR between nonallelic repetitive elements, primarily Ty retrotransposons. Nonhomologous end-joining (NHEJ) accounted for few, if any, of the CAs. We conclude that only those DSBs that fall at the 3-5% of the genome composed of repetitive DNA elements are efficient at generating rearrangements with dispersed small repeats across the genome, whereas DSBs in unique sequences are confined to recombinational repair between the large regions of homology contained in sister chromatids or homologous chromosomes. Because repeatassociated DSBs can efficiently lead to CAs and reshape the genome, they could be a rich source of evolutionary change.ectopic recombination ͉ gamma radiation ͉ genome rearrangements ͉ nonallelic homologous recombination ͉ retrotransposon