title: Whole-genome de novo sequencing, combined with RNA-Seq analysis, reveals unique genome and physiological features of the amylolytic yeastSaccharomycopsis fibuligeraand its interspecies hybrid.
abstract: 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 yeastSaccharomycopsis fibuligerahas 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 ofS. fibuligera.
  
  
  RESULTS
  We performed whole-genome (WG) de novo sequencing and complete assembly ofS. fibuligeraKJJ81 and KPH12, two isolates from wheat-basedNurukin 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 ofS. fibuligerabefore the separation of the CTG andSaccharomycetaceaeclades in the subphylumSaccharomycotina. 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 theS. fibuligeragenome reflects a unique phenotype forSaccharomycopsisclades as natural sulfur auxotrophs. Extended gene families, including novel genes involved in saccharification and proteolysis, were identified. Moreover, comparative genome analysis ofS. fibuligeraATCC 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 sequencedS. fibuligeragenome with high-quality annotation and RNA-Seq analysis establishes an important foundation for functional inference ofS. fibuligerain 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 genusSaccharomycopsisincluding members with desirable traits for bioconversion, the unique genomic features ofS. fibuligeraand its hybrid will provide in-depth insights into fungal genome dynamics as evolutionary adaptation.
authors.affiliation: Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea.
authors.forename: Jin Ho
authors.initials: JH
authors.lastname: Choo
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea.
authors.forename: Chang Pyo
authors.initials: CP
authors.lastname: Hong
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea.
authors.forename: Jae Yun
authors.initials: JY
authors.lastname: Lim
authors.affiliation: School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea.
authors.forename: Jeong-Ah
authors.initials: JA
authors.lastname: Seo
authors.affiliation: Department of Food Science and Engineering, Ewha Womans University, Seoul, 03760 South Korea.
authors.forename: Young-Suk
authors.initials: YS
authors.lastname: Kim
authors.affiliation: Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea.
authors.forename: Dong Wook
authors.initials: DW
authors.lastname: Lee
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea.
authors.forename: Sin-Gi
authors.initials: SG
authors.lastname: Park
authors.affiliation: Theragen Bio Institute, TheragenEtex, Suwon, 16229 South Korea.
authors.forename: Gir Won
authors.initials: GW
authors.lastname: Lee
authors.affiliation: School of Systems Biomedical Science, Soongsil University, Seoul, 06978 South Korea.
authors.forename: Emily
authors.initials: E
authors.lastname: Carroll
authors.affiliation: Department of Agricultural Biotechnology, Seoul National University, Seoul, 08826 South Korea.
authors.forename: Yin-Won
authors.initials: YW
authors.lastname: Lee
authors.affiliation: Department of Life Science, Chung-Ang University, Seoul, 06974 South Korea.
authors.forename: Hyun Ah
authors.initials: HA
authors.lastname: Kang
keywords: Amylolytic yeasts; Genome; Hybrid; RNA-Seq; Saccharomycopsis fibuligera