Allodiploid Zygosaccharomyces genomes sequencing assists in deciphering the genetic basis of hybrid sterility

In Saccharomyces cerevisiae diploid MATα/MATa cells, a1-α2 heterodimer encoded by mating-type (MAT) genes is the master sensor of diploidy, promoting the meiosis under starvation, and the repression of haploid-specific genes (h-sgs), such as HO gene, under standard growth conditions. However, how other biotech yeasts govern life cycle remains poorly understood. Halotolerant Zygosaccharomyces rouxii yeasts have applications in food spoilage and fermentation, and exhibit ploidy and karyotype variation, tendency to hybridization, and high diversity in osmostress response. Here, the allodiploid Z. rouxii ATCC42981 serves as a model to investigate how transcriptional network incompatibility affects hybrid sterility. To extend the Zygosaccharomyces genomic knowledge, we sequenced ATCC42981 and Z. sapae ABT301T genomes. We obtained high-quality assemblies (33-45 scaffolds) by combining heterozygosity reduction and assisting the assembling process with Z. rouxii CBS732T reference chromosomes. Both strains are hybrids derived from one lineage that is over 99% identical to CBS732T and another one not yet identified and ~14% diverging from Z. rouxii type-strain. Interestingly, ATCC42981 and ABT301T differ from one another for the second parent. ATCC42981 kept all reference chromosomes, while ABT301T probably lost one. Both genomes harbor chromosomes from the second parental species, suggesting that unexpectedly no reduction of one of the parental karyotypes occurred after hybridization to resolve genome incompatibility.In ATCC42981 genome, MATa1 and MATα2 genes are from two different parents (Z. rouxii and Z. sapae, respectively). The different evolutionary history of a1 and α2 subunits could generate negative epistasis accounting for ATCC42981 inability to repress HO gene and to regulate the main meiosis inducer IME4 gene. To prove this, Z. sapae MATα was disrupted by a loxP–kanMX–loxP cassette. Surprisingly, we found that the deletion mutants still actively transcribed MATα, expressed HO and were unable to sporulate by autodiploidization. Besides, MATα removal did not rescue the ability of ATCC42981 to make conjugated asci in mixture with Z. rouxii mating testers. Overall, this work suggests that 1) HO expression does not assure mating-type switching; 2) with 1 copy of MAT disrupted, ATCC42981 does not behave as a haploid; 3) MATα deletion induces HMLα loci de-silencing or, alternatively, reveals the incomplete silencing of donor cassettes in the wild type strain.