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Background  Genomic studies on fungal species with hydrolytic activity have gained increased attention due to their great biotechnological potential for biomass-based biofuel production. The amylolytic yeast  Saccharomycopsis fibuligera  has served as a good source of enzymes and genes involved in saccharification. Despite its long history of use in food fermentation and bioethanol production, very little is known about the basic physiology and genomic features of  S. fibuligera .    Results  We performed whole-genome (WG) de novo sequencing and complete assembly of  S. fibuligera  KJJ81 and KPH12, two isolates from wheat-based  Nuruk  in Korea. Intriguingly, the KJJ81 genome (~38 Mb) was revealed as a hybrid between the KPH12 genome (~18 Mb) and another unidentified genome sharing 88.1% nucleotide identity with the KPH12 genome. The seven chromosome pairs of KJJ81 subgenomes exhibit highly conserved synteny, indicating a very recent hybridization event. The phylogeny inferred from WG comparisons showed an early divergence of  S. fibuligera  before the separation of the CTG and  Saccharomycetaceae  clades in the subphylum  Saccharomycotina . Reconstructed carbon and sulfur metabolic pathways, coupled with RNA-Seq analysis, suggested a marginal Crabtree effect under high glucose and activation of sulfur metabolism toward methionine biosynthesis under sulfur limitation in this yeast. Notably, the lack of sulfate assimilation genes in the  S. fibuligera  genome reflects a unique phenotype for  Saccharomycopsis  clades as natural sulfur auxotrophs. Extended gene families, including novel genes involved in saccharification and proteolysis, were identified. Moreover, comparative genome analysis of  S. fibuligera  ATCC 36309, an isolate from chalky rye bread in Germany, revealed that an interchromosomal translocation occurred in the KPH12 genome before the generation of the KJJ81 hybrid genome.    Conclusions  The completely sequenced  S. fibuligera  genome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference of  S. fibuligera  in the degradation of fermentation mash. The gene inventory facilitates the discovery of new genes applicable to the production of novel valuable enzymes and chemicals. Moreover, as the first gapless genome assembly in the genus  Saccharomycopsis  including members with desirable traits for bioconversion, the unique genomic features of  S. fibuligera  and its hybrid will provide in-depth insights into fungal genome dynamics as evolutionary adaptation.    Electronic supplementary material  The online version of this article (doi:10.1186/s13068-016-0653-4) contains supplementary material, which is available to authorized users.

biotechnology for biofuels

Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeast Saccharomycopsis fibuligera and its interspecies hybrid