Draft genome sequence of a human isolate of Taiozyma onychis

ABSTRACT

Taiozyma onychis (syn. Wickerhamomyces onychis) is a rare opportunistic human fungal pathogen. Here, we report the draft genome sequence of T. onychis NCYC 4433, a fecal isolate from a 62-year-old female.

ANNOUNCEMENT

Taiozyma onychis (1), formerly Wickerhamomyces onychis (2), is an ascomycetous yeast that has been isolated from both the environment and humans (2–4). Found in the human gut (3), it can also be an opportunistic pathogen, albeit a rare one (2, 4). Here, we combined short- and long-read sequencing to obtain the genome sequence of T. onychis NCYC 4433, a fecal isolate from a 62-year-old female participant of the MOTION Study (5). A fecal homogenate was prepared in sterile phosphate-buffered saline (PBS) and cultured on Sabouraud dextrose (SD) agar plates containing penicillin (25 U/mL) and streptomycin (25 U/mL) and incubated at 30°C. Species identity from single colonies (with identical morphotype) was determined by PCR amplification and Sanger sequencing of the ribosomal DNA internal transcribed spacer (ITS) region (accession number OZ481044.1) using primers ITS1F and ITS4 (6, 7). Sequence identity was 99.45% (542 nt overlap) to the T. onychis type strain NRRL Y-7123^T (KY105910).

Genomic DNA was isolated using a MasterPure Yeast DNA Purification Kit (Cambio) following the manufacturer’s instructions with additional lyticase (100 U) and proteinase K treatment steps from 1.2 mL of a 2-day liquid SD culture grown at 30°C (at 180 rpm). DNA concentration and purity were assessed using a Qubit 4.0 fluorometer (Thermo Fisher Scientific) and a NanoDrop 1000 spectrophotometer (Thermo Fisher Scientific). A short-read library was prepared using a NextSeq 1000/2000 P2 XLEAP-SBS Reagents Kit (300 cycles) (Illumina), with DNA normalized to 5 ng/μL using a 20-fold diluted Illumina DNA Prep Kit protocol (8), barcoded using 10 bp unique dual indexes (UDIs), and sequenced on a NextSeq 2000 instrument. A Nanopore library was prepared from the same gDNA prep without fragmentation or size selection using the SQK-LSK109 1D Ligation Kit (Oxford Nanopore Technologies, ONT) and sequenced on a PromethION instrument (ONT) with a FLO-PRO114M flow cell (ONT). Base calling was performed using Guppy (ONT; v3.6.0) in high-accuracy mode (model dna_r9.4.1_450bps_hac).

Default parameters were used unless otherwise noted. Illumina reads were filtered with fastp v.0.23.2 (9). Nanopore reads were filtered using NanoFilt v.2.3.0 (10), selecting reads with quality ≥10 and length ≥20,000 bp. De novo assembly of the filtered Nanopore reads was performed using Flye v2.9.1 (11) using long reads in ‘ONT regular reads, pre-Guppy5’ mode. The assembly was polished with the Illumina data using three rounds of alignment with BWA-MEM v.0.7.17.1 (12) and Pilon v.1.24 (13) correction. Key sequencing and assembly metrics are shown in Table 1. The assembly includes 10 contigs with a putative telomere repeat sequence (5′- GACACCACACACATCCA-3′)_n identified using Tandem Repeats Finder v.4.09 (14) at one end. Genome completeness was estimated at 95.0% using BUSCO v.5.5.0 (15) with the saccharomycete_odb10 data set. Electrophoretic karyotyping indicates this strain has eight to nine chromosomes similar in size range to Candida albicans SC5314 (Fig. 1) (16).

TABLE 1.

Summary of key sequencing and assembly outputs

Metric	Value
Illumina
Total number of reads	9,679,076
N50 (no. of bases)	150
Total bases (Gb)	1.45673
Genome coveragea	118.4
Oxford Nanopore
Total number of reads	1,059,522
Number of filtered readsb	134,025
N50 (no. of bases)	29,547
Total bases (Gb)	3.95475
Genome coveragea	321.5
Assembled genome
Number of contigs	27
Total genome size (no. of bases)	12,466,078
N50 (no. of bases)	860,330
G + C content (%)	41.15

^a Based on the 12.3 Mb genome of T. onychis NRRL Y-7123^T (GCA_030582435.1).

^b Reads with quality ≥10 and length ≥20,000 bp (filtered using NanoFilt v.2.3.0).

Fig 1.

Karyotype of T. onychis NCYC 4433 (To; lanes 2–4) and C. albicans SC5314 (Ca; lanes 1 and 5; size standard) on an ethidium bromide-stained gel (inverted image). C. albicans chromosome numbers are shown on the left side, while chromosome sizes (in megabases) are shown on the right side. For each strain, yeast cells were embedded in low-melt agarose, and then digested away to intact chromosome-sized DNA that was separated by clamp homogeneous electric field electrophoresis (15).

The NCYC 4433 assembly (GCA_984806805.1) has an average nucleotide identity (17) of 97.66% to the NRRL Y-7123^T assembly (GCA_030582435.1) (18). Augustus v.3.2.3 (19) predicted 5,672 protein-coding genes using the Scheffersomyces stipitis training data set, and 189 tRNA genes were detected using tRNAscan SE 2.0 (20).

DATA AVAILABILITY

This whole-genome shotgun project has been deposited in DDJB/ENA/GenBank (BioProject number PRJEB114437, assembly accession number CFJMSG010000000). The version described in this paper is version 1. The raw reads are available in the NCBI Sequence Read Archive (SRA) under accession numbers ERR17369218 (ONT) and ERR17369219 (Illumina). The predicted protein and tRNA annotation data sets have been deposited in Zenodo (https://doi.org/10.5281/zenodo.21472325).

ETHICS APPROVAL

The biological sample used in this study was obtained from the MOTION study, which received a favorable opinion from an NHS Research Ethics Committee (REC reference: 19/EM/0055; IRAS project ID 241617) and was registered with the Quadram Institute Human Research Governance Committee (HRGC reference: QIB04-2018). Written informed consent was obtained from all study participants for sample collection and their use in research.