Genome sequences of two isolates of the yeast Candida zeylanoides: UCD849 from soil in Ireland, and AWD from an African wild dog

Candida zeylanoides is a species in the Kurtzmaniella clade of the budding yeast family Debaryomycetaceae (1). Strains have previously been isolated from sources including human (skin, throat, sputum, feces), animals (dog skin, dolphin skin), sea water, meats (salami, sausages, chilled beef), and plants (red clover) (1). It can be an opportunistic pathogen (2), and it has some biotechnological potential (3, 4).

C. zeylanoides UCD849 was isolated (Table 1) as part of an undergraduate research module (5). Soil material was passaged twice at room temperature in 9 mL liquid yeast extract-peptone-dextrose (YPD) containing chloramphenicol (30 µg/mL) and ampicillin (100 µg/mL) and cultured on YPD plates. The species was identified by PCR and Sanger sequencing of the ribosomal DNA internal transcribed spacer (ITS) and D1/D2 regions (accession numbers OR541107 and OR541115). Sequence identity was 100% (569/569 bp) in the ITS, and 99% (570/573 bp) in the D1/D2 region, to the type strain of C. zeylanoides (accession numbers KY102539 and NG_060834). DNA for genome sequencing was isolated from liquid YPD cultures grown at 30°C. For short-read sequencing, DNA was isolated by phenol/chloroform extraction. Illumina library construction (300-cycle v1.5 kit) and sequencing was done by Novogene (UK) Company Ltd. using a NovaSeq 6000 instrument with S4 flowcell and yielded 7.4 million read pairs (2 × 150 bp). Low-quality reads and adapter sequences were removed using Skewer (v0.2.2) (6). For long-read sequencing, DNA was extracted using a Biosearch Technology Masterpure yeast DNA purification kit (MPY80010). Oxford Nanopore (ONT) sequencing was done by combining two runs on a MinION MK1C instrument with flowcells FLO-MIN112 (R10.4) and FLO-MIN114 (R10.4.1) and barcoding kit SQK-NBD112-24. Raw data were basecalled (fast model) and demultiplexed using Guppy integrated in MinKNOW (v21.11) (ONT). NanoFilt (v2.3.0) (7) retained 63,110 reads with quality ≥7 and length ≥1,000 bp (reads N50 = 18,323 bp), which were then assembled using Canu (v2.0.0) (8), followed by five rounds of error correction using NextPolish (v1.4.1) with the Illumina reads (9). Default parameters were used for all software. Two gaps were closed manually: one in the rDNA array, and one that we closed using a 98 bp section of a contig from a de novo SPAdes (10) Illumina assembly. There is a single rDNA array located internally on chromosome 3 (accession number CP134677).

After isolation (Table 1) C. zeylanoides strain AWD was plated onto Sabouraud dextrose agar (Hardy Diagnostics) and incubated at 30°C for 48 h under aerobic conditions. Species identification was done using a MALDI Biotyper Sirius CA System (Bruker Daltonics) as outlined (13). For genomic DNA sequencing, C. zeylanoides AWD was grown aerobically at 30°C for 48 h on Trypticase soy agar (Hardy Diagnostics) and sent to SeqCenter (www.seqcenter.com). A ZymoBIOMICS DNA kit (Zymo Research) was used to isolate genomic DNA. Libraries were prepared using an Illumina DNA Prep kit (catalog 20060059) following the manufacturer’s recommendations, with custom IDT 10 bp unique dual indices. DNA was sequenced on an Illumina NextSeq 2000 instrument, which produced 17.9 million read pairs (2 × 151 bp). BCL Convert v4.0.3 (Illumina) was used for demultiplexing, adapter trimming, and quality control. The genome was assembled using Unicycler v0.5.0 (14).

For the genome assembly statistics of both strains see Table 1. Both isolates are available on request.

This work was supported by undergraduate teaching resources from University College Dublin and by the European Research Council (789341).

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.