Draft Genome Sequence of the Sophorolipid-Producing Yeast Pseudohyphozyma bogoriensis ATCC 18809

ABSTRACT

Pseudohyphozyma bogoriensis is gaining attention as a microbial source of high-value sophorolipids. We report here on its genomic sequence, which will improve our understanding of its metabolic pathways and allow the development of genome manipulation systems. PacBio sequencing was performed, yielding a 26-Mbp genome with 57% GC content and encoding 7,847 predicted proteins.

ANNOUNCEMENT

Pseudohyphozyma bogoriensis, with the homotypic synonyms Rhodotorula bogoriensis and Vanrijia bogoriensis (1, 2) and the basionym Candida bogoriensis (3), is an aerobic yeast in the family Chrysozymaceae, subphylum Pucciniomycotina, and phylum Basidiomycota. P. bogoriensis produces a structurally unique sophorolipid composed of 13-hydroxydocosanoic acid (4–8), with increasing industrial applications (5, 9). These molecules have antimicrobial properties and have been suggested as anti-inflammation and anticancer compounds (10–14). Achieving substantial improvements through genetic manipulations necessitates an understanding of the gene content. To define the yeast metabolic capabilities, a draft genome sequence was generated.

P. bogoriensis ATCC 18809, acquired from the American Type Culture Collection, was isolated from the surface of a Randia malleifera leaf (15). The culture was maintained on yeast and malt (0.3% yeast extract, 0.3% malt extract, 0.5% peptone, and 1% glucose) agar plates; individual colonies were inoculated into liquid medium and then incubated for 48 h at 25°C on a rotary shaker at 225 rpm. Prior to genomic DNA (gDNA) extraction, the freshly harvested cells were subjected to enzymatic digestion with Zymolyase (Zymo; E1005-A), according to the manufacturer’s instructions. DNA was extracted using the YeaStar kit (Zymo; D2002), and the quality and quantity were initially assessed using the DS-11 spectrophotometer (DeNovix Inc., Wilmington, DE).

The genome was sequenced and assembled using the Pacific Biosciences Sequel System (PacBio, Menlo Park, CA) at the Genomics Core Facility of Drexel University (Philadelphia, PA). The PacBio 10-kb library preparation protocol was applied without Covaris g-TUBE shearing. Size selection of the gDNA was performed using the Blue Pippin kit (Sage Science, Beverly, MA), followed by DNA damage repair using PacBio reagents. The gDNA was then converted into a SMRTbell library using the SMRTbell template prep kit version 1.0-SPv3 Sequel, according to the manufacturer’s instructions. For quality assessment, the size distribution of the library was determined using an Agilent Bioanalyzer 12000 chip (Agilent Technologies Inc., Santa Clara, CA). The size-selected library was sequenced on the PacBio Sequel 1 platform using single-molecule real-time (SMRT) cell technology (4 cells). Read quality control was performed using the SMRTLink version 5.1.0 workflow. There were 2,383,328 subread sequences, with 180× genome coverage, and the N₅₀ read value was 6,803 bp. The postfiltered reads were used for genome assembly using Hierarchical Genome Assembly (HGAP) version 4 software (PacBio). Default parameters were used for all tools except where otherwise noted. The final assembly resulted in 304 contigs, with an overall GC content of 57.01%. The average contig N₅₀ read value was 159,754 bp, and the maximum size was 672,149 bp. The total assembly length was 26,004,456 bp, and the mitochondrial genome identified from the assembly totaled 145,115 bp. The yeast genome contained 7,847 predicted protein-encoding genes, annotated using Augustus version 3.3.1 (16) with Cryptococcus neoformans as the model in Funannotate version 1.5.3 (17). The mitochondrial genome had 37 protein-encoding genes, annotated using FGENESH with C. neoformans as the model and mold/mitochondrial genetic code (18). A total of 176 tRNA genes (108 nuclear and 68 mitochondrial) were identified using tRNAscan version 2.0 (19).

P. bogoriensis is a promising platform for commercial biosurfactant production. Recently, a sophorolipid gene cluster was reported for Starmerella bombicola (7, 9). We report here on the assembly and annotation of P. bogoriensis genomes, which should provide functional genomics tools for efficient genome manipulation.

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/ENA/GenBank under the accession number JALBUQ000000000. The version described in this paper is version JALBUQ010000000; the BioSample accession number is SAMN26542470, and the BioProject accession number is PRJNA814273. The raw data can be found in the Sequence Read Archive under the accession number SRR20187078.