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. 2022 Jun 13;11(7):e00224-22. doi: 10.1128/mra.00224-22

Draft Genome Sequences of Five Cystobasidium ongulense Strains Isolated from Areas near Syowa Station, East Antarctica

Masaharu Tsuji a,✉, Jun-ichi Ishihara b, Yasuhiro Gotoh c, Tetsuya Hayashi c, Hiroki Takahashi b
Editor: Jason E Stajichd
PMCID: PMC9302155  PMID: 35695498

ABSTRACT

Cystobasidium ongulense has been reported from East Ongul Island near Syowa Station, East Antarctica, as a new basidiomycetous yeast species. This species has cold active lipases and cellulases that are active even at subzero temperatures. We report draft genome sequences of five Cystobasidium ongulense strains isolated from East Antarctica.

ANNOUNCEMENT

Cystobasidium ongulense was isolated from East Ongul Island, East Antarctica, and reported as a new species of basidiomycete yeast (1). Since this yeast can grow in a wide range of temperatures, from −3°C to 30°C, the genomic information of this yeast is expected to be valuable as a new genetic resource (2).

This study analyzed the whole-genome sequences of two strains (9A-2 = JCM 31527 and 9A-5 = JCM 31528) isolated from East Ongul Island and three strains (051-20-1, 056-1-20Y-3, and 056-20-8) isolated from Inhovde, near Syowa Station.

Each strain was cultured in yeast extract-peptone-dextrose (YPD) liquid medium (Difco) at 15°C for 5 days. The cells from cultures were collected by centrifugation at 3,500 × g for 5 min at 4°C. The cell pellets were washed with sterile distilled water and precipitated by centrifugation again. The cell pellets were dried using a vacuum freeze dryer. The lyophilized cells were powdered in a mortar and used for genome extraction. The genomic DNA of five Cystobasidium ongulense strains was extracted and purified using a NucleoBond AXG100 column with a Nucleo buffer set III (TaKaRa Bio) according to the manufacturer’s protocol. The concentration and purification of the genomic DNA were determined using a NanoDrop spectrophotometer (Thermo Scientific) and the Qubit double-stranded DNA (dsDNA) broad-range (BR) assay kit (Thermo Scientific). Then, the genomic DNA was digested using the microTUBE (Covaris), and the genomic library was constructed using the Illumina TruSeq DNA PCR-free library preparation kit (Illumina). The quality of the library was confirmed using the Quant-iT PicoGreen dsDNA assay kit, and the library size was checked using the Agilent 2200 TapeStation system (Agilent Technologies, Inc.). The paired-end sequence reaction was performed on a HiSeq 2500 instrument (Illumina). Adapters and low-quality bases were trimmed using fastp ver. 0.12.4 (3). Assembly of the nuclear genomes was conducted using VelvetOptimiser ver. 2.2.6 (4). The completeness of the assemblies was assessed using BUSCO ver. 5.2.2 (5) with the database basidiomycota_odb10 (the number of the marker is 1764). After the identification of repeat sequences using RepeatModeler ver. 2.0.1 and RepeatMasker ver. 4.1.2 (6), annotation was performed using the BRAKER2 ver. 2.1.6 (7–11) automated annotation pipeline using the fungi protein data set from OrthoDB ver. 10 (12). BRAKER2 ab initio gene predictions were carried out using AUGUSTUS ver. 3.4.0 (10) and GeneMark-EP+ ver. 4.64 (13). The resulting BRAKER2 gtf file was parsed using TSEBRA (14) and AGAT ver. 0.8.0 (15). Finally, functional annotation was performed using InterProScan ver. 5 (16), Phobius ver. 1.01 (17), antiSMASH ver. 6.0 (18), and EggNog mapper ver. 2.1.3 (19) against the eggNOG database ver. 5.0.1 (20) using diamond ver. 2.0.9 (21).

A summary of the genomic analysis results of the five C. ongulense strains is shown in Table 1. Briefly, the genome size ranged from 19.9 Mb to 20.1 Mb, the GC content ranged from 49.1 to 49.2%, and the BUSCO score was 92.4 to 92.7%. Consequently, the number of protein coding genes predicted ranged from 7,183 to 7,250.

TABLE 1.

Assembly summary for draft genomic data of five Cystobasidium ongulense strains

Data for strain:
Characteristic 9A-2 (=JCM 31527) 9A-5 (=JCM 31528) 051-20-1 056-1-20Y-3 056-20-8
Sampling site East Ongule Island East Ongule Island Inhovde Inhovde Inhovde
No. of reads 8,304,954,096 6,269,707,240 7,317,973,400 7,758.637,304 7,164,512,704
No. of scaffolds 69 67 120 73 81
Total length (Mb) 19.9 19.9 20.1 20.0 20.0
Coverage (×) 392 297 337 361 330
GC content (%) 49.2 49.2 49.2 49.1 49.1
Scaffold N50 value (kb) 2,125 2,126 1,057 1,432 1,222
No. of proteins 7,190 7,183 7,243 7,227 7,250
BUSCO score (%) 92.6 92.6 92.7 92.6 92.4
GenBank accession no. BQUO00000000.1 BQUP00000000.1 BQUQ00000000.1 BQUR00000000.1 BQUS00000000.1
SRA accession no. DRR118811, DRR118812 DRR118813, DRR118814 DRR118815, DRR118816 DRR118817, DRR118818 DRR118819, DRR118820
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We believe that the genomic information of C. ongulense will help us understand how Antarctic fungi adapt to the extreme environment.

Data availability.

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under BioProject accession number PRJDB6568 with accession numbers BQUO00000000.1 (9A-2), BQUP00000000.1 (9A-5), BQUQ00000000.1 (051-20-1), BQUR00000000.1 (056-1-20Y-3), and BQUS00000000.1 (056-20-8). The raw reads are available under SRA accession numbers DRR118811, DRR118812 (9A-2), DRR118813, DRR118814 (9A-5), DRR118815, DRR118816 (051-20-1), DRR118817, DRR118818 (056-1-20Y-3), and DRR118819, DRR118820 (056-20-8).

ACKNOWLEDGMENTS

This work was supported by National Institute of Polar Research (NIPR) research project KP-309, general collaboration project number 2-29. This work was also supported by a JSPS Grant-in-Aid for Young Scientists (A) (number 16H06211), JSPS KAKENHI grant number 16H06279 (PAGS), and Institution for Fermentation, Osaka, general research grant number G-2022-1-007.

Contributor Information

Masaharu Tsuji, Email: spindletuber@gmail.com.

Jason E. Stajich, University of California, Riverside

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Associated Data

This section collects any data citations, data availability statements, or supplementary materials included in this article.

Data Availability Statement

This whole-genome shotgun project has been deposited at DDBJ/EMBL/GenBank under BioProject accession number PRJDB6568 with accession numbers BQUO00000000.1 (9A-2), BQUP00000000.1 (9A-5), BQUQ00000000.1 (051-20-1), BQUR00000000.1 (056-1-20Y-3), and BQUS00000000.1 (056-20-8). The raw reads are available under SRA accession numbers DRR118811, DRR118812 (9A-2), DRR118813, DRR118814 (9A-5), DRR118815, DRR118816 (051-20-1), DRR118817, DRR118818 (056-1-20Y-3), and DRR118819, DRR118820 (056-20-8).

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