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

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Protocol publication

[…] Saccharomycopsis is the sole genus of the family Saccharomycopsidaceae (). One member of this genus, the starch-degrading yeast S. fibuligera, is known for its contributions to rice wine fermentation (). The role of S. fibuligera as an enzyme producer also spurred interest in using this yeast for bioethanol production (). Recently, whole-genome sequencing studies revealed that the genome of S. fibuligera encompasses seven chromosomes with about 18 Mb (). 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 (). S. fermentans (formerly classified as Arthroascus fermentans) was isolated in 1994 from the soil of a Taiwanese orchard and was shown to ferment glucose (references and and references therein). Saccharomycopsis species are natural auxotrophs for organic sulfur (). In S. fibuligera, the absence of genes involved in sulfate assimilation has been observed ().The usefulness of non-S. cerevisiae yeasts in fermentation and biotechnology depends on detailed characterization of the microbial genomes. Thus, additional draft genome sequences are required to not only provide species-specific markers for identification but also initiate pathway analyses and enable targeted strain improvements. Furthermore, a deeper understanding of the molecular biology of Saccharomycopsis species—specifically of their predacious behavior—is warranted. To this end, we recently established the draft genome of another predacious Saccharomycopsis yeast, S. fodiens strain CBS 8332 (). We confirmed that, just like S. fibuligera, S. fodiens also lacks the genes in the sulfate assimilation pathway.Here, we report the draft genome sequence of S. fermentans, obtained using Illumina MiSeq paired-end read sequencing. S. fermentans was grown in complex medium (1% [wt/vol] yeast extract-peptone-dextrose [YPD], 2% [wt/vol] peptone, and 2% [wt/vol] dextrose) at 30°C with constant shaking. DNA extraction and sequencing were performed at LGC Genomics (Berlin, Germany). Two paired-end libraries were sequenced, producing 10,363,062 raw reads. These were quality trimmed, resulting in 4,807,796 high-quality reads with the short fragment library and 4,521,208 high-quality reads with an 8-kb mate pair library. These were assembled using Bowtie2 version 2.1.0. The initial assembly generated 160 contigs with a total content of 14,266,439 bp and a contig N50 of 265,725 bp. The contigs were then further assembled into 33 scaffolds harboring 14,461,413 bp, with an N50 of 2,146,288 bp. The longest scaffold contains 3,513,907 bp, with 13 scaffolds larger than 20 kb. The overall GC content is 35.1%.For a draft annotation of the nuclear genome, open reading frames (ORFs) with a size of >300 nt were predicted and compared using blastx to translated proteins in the Saccharomyces cerevisiae genome. In all, 5,917 nonoverlapping ORFs were detected in S. fermentans, and of those, 3,882 genes produced hits with S. cerevisiae. An additional blast search against other organisms in the nonredundant database at NCBI (https://blast.ncbi.nlm.nih.gov/Blast.cgi) generated a further 263 hits (E values, <10−10). We could also verify the absence of genes required for sulfate assimilation in S. fermentans. Additionally, we identified 149 tRNA genes in the S. fermentans genome using tRNAscan-SE (). […]

Pipeline specifications

Software tools Bowtie2, BLASTX, tRNAscan-SE
Applications Genome annotation, WGS analysis
Organisms Fungi, Saccharomyces cerevisiae