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

Abstract

BackgroundGenomic 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.ResultsWe 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.ConclusionsThe 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 materialThe online version of this article (doi:10.1186/s13068-016-0653-4) contains supplementary material, which is available to authorized users.

Draft Genome Sequence of Saccharomycopsis fodiens CBS 8332, a Necrotrophic Mycoparasite with Biocontrol Potential

“…BLASTX searches against the nonredundant database at NCBI ( https://blast.ncbi.nlm.nih.gov/Blast.cgi ) generated a further 373 hits. As was observed for S. fibuligera , also S. fodiens lacks genes required for sulfate uptake and assimilation ( 8 ). Running tRNAscan on the scaffolds identified 162 tRNA genes ( 12 ).…”

“…Subsequently, S. fibuligera genes encoding these enzymes were used in heterologous hosts, such as Saccharomyces cerevisiae and Yarrowia lipolytica ( 3 – 7 ). This interest in using S. fibuligera also spurred genome sequencing of this yeast ( 8 ).…”

Draft Genome Sequence of Saccharomycopsis fermentans CBS 7830, a Predacious Yeast Belonging to the Saccharomycetales

“…The role of S. fibuligera as an enzyme producer also spurred interest in using this yeast for bioethanol production ( 3 ). Recently, whole-genome sequencing studies revealed that the genome of S. fibuligera encompasses seven chromosomes with about 18 Mb ( 4 ). Other members of the genus Saccharomycopsis , including S. fermentans , have been described as predacious yeasts that generate penetration pegs with which they kill other fungal cells utilizing prey cell content ( 5 ).…”

“…Saccharomycopsis species are natural auxotrophs for organic sulfur ( 8 ). In S. fibuligera , the absence of genes involved in sulfate assimilation has been observed ( 4 ).…”

The reported point centromeres of Scheffersomyces stipitis are retrotransposon long terminal repeats

“…In the yeasts Ogataea polymorpha (Hanson, Byrne, & Wolfe, ; Ravin et al, ), Debaryomyces hansenii (Lynch, Logue, Butler, & Wolfe, ; Marie‐Nelly et al, ), and Saccharomycopsis fubuligera (Choo et al, ), as well as Scheffersomyces stipitis as discussed below, centromeric regions contain clusters of retrotransposons related to S . cerevisiae Ty5.…”