Draft genome sequence of potentially dikaryotic black fungus Aureobasidium melanogenum isolated from aircraft

ABSTRACT

The Ascomycota yeast Aureobasidium melanogenum strain W12 was isolated from an aircraft polymer-coated surface. The genome size is 53,160,883 bp with a G + C content of 50.13%. The genome contains fatty acid transporters, cutinases, hydroxylases, and lipases potentially used for survival on polymer coatings on aircraft.

ANNOUNCEMENT

Here, we describe the draft genome sequence for the yeast, Aureobasidium melanogenum strain W12 (formerly Aureobasidium pullulans var. melanogenum), isolated from the polymer-coated surface of an aircraft. This microorganism was sequenced to understand the taxonomy and enzymatic function underlying biodegradation and bioremediation on polymer coatings (1).

Aureobasidium melanogenum strain W12 cells were isolated from samples collected inside of an aircraft (2) via sterile swab. Cultures were recovered from glycerol freezer stocks by streaking onto potato dextrose agar (PDA). An isolated colony was re-suspended in tryptic soy broth (TSB) and grown overnight at 27°C on a rotary wheel. A 1 mL aliquot of overnight culture was harvested, and the pellet was used for DNA extractions. Genomic DNA was extracted using the Qiagen Power Microbiome kit according to the manufacturer’s instructions and the DNA was quantified using the Qubit dsDNA assay (Life Technologies). Sequencing libraries were prepared using the Nextera DNA Flex Library preparation kit following the manufacturer’s instructions (Illumina, San Diego, CA) and sequenced using 150 bp paired-end sequencing on an Illumina NextSeq 550.

Sequence data-processing steps used default parameters unless otherwise specified. Sequencing yielded 51,597,569 raw PE reads which were trimmed using Trimmomatic (ver. 0.39) (3) and quality-filtered using FastQC (ver. 0.11.9) (4). The PE reads were assembled using SPAdes (ver. 3.15.2) (5), yielding an average coverage of 291×, 967 contigs, 50.13% G + C content, N50 of 124,772 bp, L50 of 129, and genome size of 53,160,883 bp calculated by QUAST (ver. 5.0.2) (6). Genome completeness was estimated at 97.9% using BUSCO (ver. 5.2.1) (7) with the Dothideomycetes reference database (dothideomycetes_odb10); however 90.8% of orthologs were duplicated. Microscopy imagining suggests (Fig. 1) that this strain is a dikaryon, which would account for the larger genome size compared to other Aureobasidium species and the large number of duplicated orthologs. We masked the assembled genome using RepeatMasker with the Dfam database (ver. 3.3) (8). We compared the internal transcribed spacer (ITS), actin, and β-tubulin sequences to the NCBI reference, A. melanogenum CBS 110374. All reference sequences were >99% identical to those of CBS 110374. Note that 18S and 28S rRNA genes have only partial sequences for the reference CBS 110374. We also compared the average nucleotide identity to CBS 110374 (9) using FastANI (v0.1.13) (10) for an ANI score of 89.1.

Fig 1.

Confocal microscopy images of Aureobasidium melanogenum W12 (A) with cell walls stained with calcofluor white and nuclei stained with DAPI and (B) nuclei stained with DAPI. Cytosol is faintly fluorescent due to nonspecific binding of DAPI. Colors inverted for publication.

This strain of A. melanogenum is a putative dikaryon. Following the BUSCO result that indicated a large amount of ortholog duplication, we investigated the cells further. We stained nuclei of cells with DAPI (ThermoFisher) following kit protocol and imaged them with confocal microscopy (Zeiss LSM880 Inverted Laser Scanning Confocal Microscope), which showed two nuclei in several cells (Fig. 1).

DATA AVAILABILITY

The raw sequencing reads and draft genome with annotation have been deposited in GenBank under BioProject accession number PRJNA811524. The Short Read Archive (SRA) database accession number for raw sequencing reads is SRR25036557. The draft annotated genome assembly accession number is JAULBJ000000000.