Saccharomycopsis fibuligera Raw sequence reads

Background: Saccharomycopsis fibuligera is found worldwide as a major amylolytic yeast in indigenous fermentation and has long historical grounds in biotechnological applications. It is also one of chalk molds on dark bread popular in Europe.Results: We performed whole-genome (WG) sequencing and de novo assembly of S. fibuligera KJJ81 and KPH12, two isolates from wheat-based Nuruk, a culture starter for a traditional Korean rice wine. Quite intriguingly, WG assembly of S. fibuligera KJJ81, estimated to be ~38 Mb in length, revealed a hybrid between the KPH12 genome of ~19 Mb and another unidentified genome showing 88.1% nucleotide identity to the KPH12 genome. Two subgenomes of KJJ81 are highly conserved, except a large deletion of ribosomal DNA cluster and one reciprocal translocation, indicating a very recent hybridization event. Their phylogeny inference based on genome information shows an early divergence before the separation of CTG and the Saccharomycetaceae clades in the subphylum Saccharomycotina. Transcriptome profiles based on RNA-seq analysis suggested marginal Crabtree effect at high glucose and activation of sulfur metabolism toward methionine biosynthesis at sulfur limitation in this yeast. Notably, lack of sulfate assimilation genes reflects a unique phenotype of Saccharomycopsis clades as natural sulfur auxotrophs. Extended gene families were identified particularly for amylases, ß-glucosidase, and acidic proteases, supporting major roles of S. fibuligera in digesting fermentation mash. Moreover, comparative genome analysis of S. fibuligera ATCC36309, an isolate from chalky rye bread in Germany, indicated that ATCC36309 shares a common progenitor with KPH12 with 98.0 % genome sequence identity and suggested that the interchromosomal translocation between chromosomes 3 and 5 had occurred in the KPH12 genome before generating the KJJ81 hybrid genome.Conclusion: S. fibuligera has drawn increasing attention due to its unique physiological characters useful for various biotechnological applications. The high-quality reference genome of S. fibuligera presented in this study will facilitate the discovery of new genes and the omics study of metabolism with industrial potential. Moreover, as the first genome in the genus Saccharomycopsis, the genomic features of S. fibuligera and its hybrid isolate would provide in-depth insights into fungal genome dynamics as evolutionary adaptation.