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Saccharomyces bayanus  is a yeast species described as one of the two parents of the hybrid brewing yeast  S. pastorianus . Strains CBS380 T  and NBRC1948 have been retained successively as pure-line representatives of  S. bayanus.  In the present study, sequence analyses confirmed and upgraded our previous finding:  S. bayanus  type strain CBS380 T  harbours a mosaic genome. The genome of strain NBRC1948 was also revealed to be mosaic. Both genomes were characterized by amplification and sequencing of different markers, including genes involved in maltotriose utilization or genes detected by array-CGH mapping. Sequence comparisons with public  Saccharomyces  spp. nucleotide sequences revealed that the CBS380 T  and NBRC1948 genomes are composed of: a predominant non- cerevisiae  genetic background belonging to  S. uvarum,  a second unidentified species provisionally named  S. lagerae,  and several introgressed  S. cerevisiae  fragments. The largest  cerevisiae -introgressed DNA common to both genomes totals 70kb in length and is distributed in three contigs, cA, cB and cC. These vary in terms of length and presence of  MAL31  or  MTY1  (maltotriose-transporter gene). In NBRC1948, two additional  cerevisiae -contigs, cD and cE, totaling 12kb in length, as well as several smaller  cerevisiae  fragments were identified. All of these contigs were partially detected in the genomes of  S. pastorianus  lager strains CBS1503 ( S. monacensis ) and CBS1513 ( S. carlsbergensis ) explaining the noticeable common ability of  S. bayanus  and  S. pastorianus  to metabolize maltotriose. NBRC1948 was shown to be inter-fertile with  S. uvarum  CBS7001. The cross involving these two strains produced F1 segregants resembling the strains CBS380 T  or NRRLY-1551. This demonstrates that these  S. bayanus  strains were the offspring of a cross between  S. uvarum  and a strain similar to NBRC1948 .  Phylogenies established with selected  cerevisiae  and non- cerevisiae  genes allowed us to decipher the complex hybridisation events linking  S. lagerae / S. uvarum / S. cerevisiae  with their hybrid species,  S. bayanus/pastorianus.

Deciphering the Hybridisation History Leading to the Lager Lineage Based on the Mosaic Genomes of Saccharomyces bayanus Strains NBRC1948 and CBS380T