Insights Into the Genome Structure of Natural Hybrid Zygosaccharomyces sp. Yeasts Isolated From Miso

There is currently much interest in the Zygosaccharomyces sp. used to produce fermented foods. Here we have used sequencing and PCR to explore differences in the genomic structures of various haploid and allodiploid Zygosaccharomyces sp. strains isolated from miso. In haploid strains, internal transcribed spacer (ITS) sequences had high identity with the ITS sequences of the type strain Z. rouxii CBS732 (92%-100%). In allodiploid strains, some ITS sequences showed high identity (92%-100%), while others showed relatively low identity (69%-83%) with CBS732. By sequencing multiple ITS regions, it might be possible to predict whether a yeast strain is haploid or allodiploid. We also explored the mating-type like loci (MTLs) of these strains. Allodiploid natural hybrid strains commonly had a P-subgenome sequence inserted in the right arm of the active MAT locus, but the length of the insert differed by strain. A 36-kbp P-subgenome sequence was also inserted into the left arm region of the surrounding MTL in the miso strain MG101. It is likely that loss of heterozygosity occurs around MTLs with homologous sequences. Last, we sequenced the whole genome of yeast strain NBRC1877, which was isolated from Japanese miso 60 years ago. The draft sequence identified chromosomes with a different structure from those of Z. rouxii CBS732. Further comparisons revealed that these chromosomes exist in other Zygosaccharomyces sp. allodiploid yeast strains and may have been formed by reciprocal translocation between tRNA genes during the process of evolution.