Draft Genome Sequence of a Basidiomycetous Yeast, Ustilago shanxiensis CBS 10075, Which Produces Mannosylerythritol Lipids.

The basidiomycetous yeast Ustilago shanxiensis CBS 10075, which was isolated from a wilting leaf in China, produces mannosylerythritol lipid (MEL) biosurfactants. Here, we report the draft genome sequence of U. shanxiensis CBS 10075, which was 21.7 Mbp in size, with a GC content of 52.55%, comprising 65 scaffolds.

ANNOUNCEMENT

Ustilago shanxiensis CBS 10075 (renamed from Pseudozyma shanxiensis CBS 10075) is a basidiomycetous yeast that was isolated from a withered leaf of Quercus mongolica Fisch in China (1). Yeast strains of the genus Pseudozyma typically produce functional glycolipids, such as mannosylerythritol lipids (MELs). U. shanxiensis CBS 10075 produces MEL-C compounds as a mixture of 4-O-[(2′,4′-di-O-acetyl-3′-O-alka(e)noyl)-β-d-mannopyranosyl]-d-erythritol and 4-O-[(4′-O-acetyl-3′-O-alka(e)noyl-2′-O-butanoyl)-β-d-mannopyranosyl]-d-erythritol. The MELs produced by U. shanxiensis CBS 10075 are more hydrophilic than those typically produced by yeasts such as Moesziomyces antarcticus (renamed from Pseudozyma antarctica) (2).

U. shanxiensis CBS 10075 was grown at 25°C for 48 h in 30 ml of YM medium at 250 rpm. The total genomic DNA was obtained by phenol-chloroform extraction followed by isopropanol precipitation. The paired-end DNA library (insert size, ∼500 bp) of the U. shanxiensis genome was prepared using a NEBNext Ultra DNA library preparation kit for Illumina (New England BioLabs, Ipswich, MA, USA), and sequencing was performed using the MiSeq platform (Illumina, San Diego, CA, USA). Sequencing data comprising a total of 10,427,528 paired-end reads were generated; each read was 250 bp in length. A mate-paired library (insert size, ∼3,200 bp) was then prepared using a Nextera mate pair sample preparation kit (Illumina), generating 9,469,570 mate-paired reads. The quality of paired-end and mate-paired reads was checked by FastQC version 0.11.2. Genome sequence assembly using the ALLPATHS-LG version R46449 assembler (3) provided 65 scaffolds (N50, 770,995 bp; scaffold L50, 8) composed of 271 contigs generated from the paired-end and mate-paired reads, with 81× and 64.5× sequence coverage, respectively. The U. shanxiensis CBS 10075 draft genome size was 21.7 Mbp (GC content, 52.55%). The length of the longest scaffold was 2,733 kbp. Five MEL biosynthesis genes were predicted using AUGUSTUS version 2.5.5 (4) and annotated using NCBI BLAST version 2.2.29 with RefSeq version 65 (5, 6). Default parameters were used except where otherwise noted.

The CBS 10075 genome sequence contained a conserved MEL biosynthesis gene cluster comprising five genes in scaffold 6, namely, UshEMT1 (an erythritol-mannosyl-transferase), UshMAC1 and UshMAC2 (acyl-coenzyme A [CoA]-dependent acyltransferases), UshMAT1 (an acetyltransferase), and UshMMF1 (a putative MEL transporter). This cluster of MEL biosynthesis genes was first reported in Ustilago maydis (7), and the evolutionary relationships among other MEL-producing organisms has since been investigated by comparing the amino acid sequences of enzymes in the MEL biosynthetic pathway (8). Recently, Ustilago hordei UM4857-4 was found to possess a cluster of MEL biosynthesis genes (9) that showed the greatest identity to U. shanxiensis CBS 10075 in this study (UshEMT1, 87.7%; UshMAC1, 80.8%; UshMAC2, 87.3%; UshMAT1, 57.0%; UshMMF1, 87.1%). The genome sequence of U. shanxiensis CBS 10075 will improve our understanding of the molecular mechanisms driving MEL production and will enable the development of MELs tailored for a range of industries.

Data availability.

The nucleic acid sequence of the U. shanxiensis CBS 10075 genome has been deposited in DDBJ/EMBL/GenBank under accession numbers BPMX01000001 to BPMX01000065. The DDBJ Sequence Read Archive (DRA) accession number is DRR306489. The protein identification numbers are as follows: UshMAC2, GIZ99647; UshEMT1, GIZ99648; UshMAC1, GIZ99649; UshMMF1, GIZ99650; and UshMAT1, GIZ99651.