Draft Genome Sequence of a Primate Isolate of Kazachstania pintolopesii

Kazachstania pintolopesii is an opportunistic mammalian pathobiont from the K. telluris species complex. No draft genomes of this species are currently available. Here, we report the first draft genome sequence of a primate isolate of K. pintolopesii (NCYC 4417).

Kazachstania pintolopesii is an ascomycetous yeast and relative of K. bovina, K. heterogenica, K. slooffiae and K. telluris [1]. Collectively, these species constitute the K. telluris complex, a phylogenetically distinct group of thermotolerant yeasts able to grow at 37°C and above [1,2]. They are widely distributed [1], but are found predominantly in the gastrointestinal (GI) tracts and nasal passages of birds and mammals [1][2][3]. Rodents are the principal hosts for K. pintolopesii [1,2,4] with a recent study extending its host range to include cynomolgus macaques [5]. These fungi are also considered pathobionts causing infections in rodents, primates, and less frequently in humans [2,6,7]. K. pintolopesii is in addition to being a gut commensal also associated with fatal infections in laboratory mice [2], and with ankylosing spondylitis in cynomolgus macaques [8]. Draft genomes for three members of the complex have been published [9][10][11], but despite its potential significance as a pathobiont no K. pintolopesii genomes have been published to date.
Here, we have combined short-and long-read sequencing to obtain the genome sequence of K. pintolopesii NCYC 4417, a faeces-derived isolate from a captive adult macaque. A faecal homogenate was prepared in sterile phosphate-buffered saline (PBS) and cultured onto Sabouraud dextrose (SD) agar plates containing penicillin (25 U/mL) and streptomycin (25 U/mL) at 37°C. Species identity, from single colonies, was determined by PCR amplification and Sanger sequencing of the ribosomal DNA internal transcribed spacer 1 (ITS1) region of the ribosomal DNA locus using primers ITS1F [12] and ITS2 [13]. The ITS1 sequence of strain NCYC 4417 (GenBank accession number PRJEB63679) is 99.7% identical to that of the K. pintolopesii type strain CBS 2985 (GenBank accession number NR_155233).
For short-and long-read sequencing, total genomic DNA was extracted from a stationary phase SD culture using a MasterPure Yeast DNA Purification Kit (Cambio, Cambridge, UK). Short-read Illumina sequencing was performed using a modified 20-fold dilution of DNA Prep (Flex) reagent and run on a NextSeq 500 sequencer, producing 9,108,736 paired-end 150-bp reads (* 186 9 coverage). Nanopore sequencing was performed using a MinION sequencer (Oxford Nanopore Technologies, ONT), ligation sequencing kit SQK-LSK109 (ONT) and flow cell FLO-MIN106 R9.4.1 (ONT). This produced a total of 437,446 reads with an average read length of 4,069 bases (* 127 9 coverage).
Author Contributions All authors contributed to the study conception and design. Material preparation, data collection and analysis were performed by SAJ, AP, CP, AT, DB, RH, SH, SGPF and SRC. The first draft of the manuscript was written by SAJ and SRC, and all authors commented on previous versions of the manuscript. All authors read and approved the final manuscript.
Funding This research was funded in part by a Biotechnology and Biological Sciences Research Council (BBSRC) awarded Core Capability Grant BB/CCG1860/1, project grant BB/ N000250/1, and Institute Strategic Programme Grant Gut Microbes and Health (BB/R012490/1) and its constituent projects BBS/E/F/000PR10353, BBS/E/F/000PR10355.
Data availability This whole-genome shotgun project has been deposited at DDJB/ENA/Genbank (Biosample Number SAMEA112953918, BioProject Number PRJEB61520, and Assembly Accession Number GCA_950065675.1). The version described in this paper is version 1. The raw reads were deposited at SRA (Accession Numbers ERR11267923 and ERR11267961).This article was written according to MycopathologiaGENOMES checklist requirements [22].

Declarations
Conflict of interest The authors have no relevant financial or non-financial interests to disclose.
Ethics Approval This article does not include human participants, or any procedures carried out on animals.

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