Draft Genome Sequence of the Yeast Pseudozyma antarctica Type Strain JCM10317, a Producer of the Glycolipid Biosurfactants, Mannosylerythritol Lipids.

The basidiomycetous yeast Pseudozyma antarctica is known as a producer of industrial enzymes and the extracellular glycolipids, mannosylerythritol lipids. Here, we report the draft genome sequence of the type strain JCM10317. The draft genome assembly has a size of 18.1 Mb and a G+C content of 60.9%, and it consists of 197 scaffolds.

GENOME ANNOUNCEMENT

Pseudozyma antarctica is a basidiomycetous yeast belonging to the class Ustilaginomycetes, which includes the plant pathogen, Ustilago maydis (1, 2). The species is known to produce attractive enzymes, which are used in a wide range of industrial fields (3, 4). In recent years, the type strain has also received considerable attention as a producer of the glycolipid biosurfactants known as mannosylerythritol lipids (MELs) (5). The type strain of P. antarctica is thus a promising organism for the industrial production of several attractive materials; however, little about this strain is known. Here, we report the draft genome sequence of P. antarctica JCM10317 (CBS 214.83), the type strain isolated from lake sediment at Antarctica, formerly Sporobolomyces antarctica (2).

The paired-end DNA library (insert size: ~500 bp) was prepared using a NEBNext Ultra DNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA), and sequencing was performed using the Illumina platform (MiSeq). Sequence data totaling 11,086,474 paired-end reads, each 250 bp in length, were generated. Additionally, a mate-paired library (insert size: ~3200 bp) was prepared using a Nextera Mate Pair Sample Prep Kit (Illumina, San Diego, CA, USA), and sequencing resulted in 10,198,878 mate-paired reads. The Allpaths-LG assembler (6) was used to generate 276 contigs with 65.5× and 69.2× genome coverage from the paired-end and mate paired libraries, respectively. The contigs derived from the two libraries were assembled into 197 scaffolds. Accordingly, the draft genome size of strain JCM10317 was 18.1 Mb (G+C content: 60.9%). The length of the longest scaffold was 2,397 kb, and the N50 length was 701,213 kb with eight scaffolds.

Using the database of U. maydis UM521 (MIPS U. maydis Database, http://mips.helmholtz-muenchen.de/genre/proj/ustilago) as references, 6,845 protein-coding genes were automatically predicted using the AUGUSTUS program (7), and 5,901 (86.2%) and 5,877 (85.9%) of the genes were found to be homologous to proteins in the P. antarctica T-34 (accession no. DF196767 to DF196793) (8) and RefSeq protein database (9) of the National Center for Biotechnology Information (BLASTp e-value: 1e−10; aligned region: ≥70% of the reference sequence; sequence identity: ≥25%), respectively. In addition, 57.8% of the genes were also tentatively assigned protein function(s) based on EuKaryotic Orthologous Groups (KOG) classification by searching against the eggNOG database (10).

The gene responsible for lipase B (CALB), which is a major industrial enzyme, was located on scaffold 7. The five genes encoding erythritol/mannose transferase (emt1), acyl transferase (mac1 and mac2), putative transporter (mmf1), and acetyl transferase (mat1), which are responsible for MEL biosynthesis, were conserved on scaffold 31 as a gene cluster identical to those of the other MEL producers, P. antarctica T-34 (11), and shared 94.8%, 91.1%, 86.8%, 93.4%, and 92.4% identity. The genome data of the P. antarctica JCM10317 will facilitate understanding of its genomic characteristics and lead to further utilization of the species in a range of industries.

Nucleotide sequence accession numbers.

The nucleotide sequence of the P. antarctica JCM10317 genome has been deposited in DDBJ/EMBL/GenBank under the accession numbers BBIZ01000001 to BBIZ01000276 (as WGS entries) and DF830068 to DF830264 (as 197 entries).