Draft Genome Sequences of the Highly Halotolerant Strain Zygosaccharomyces rouxii ATCC 42981 and the Novel Allodiploid Strain Zygosaccharomyces sapae ATB301T Obtained Using the MinION Platform

Here, we report draft genome sequences of the halotolerant and allodiploid strains Zygosaccharomyces rouxii ATCC 42981 and Zygosaccharomyces sapae ABT301T. Illumina and Oxford Nanopore MinION sequencing revealed genome sizes of 20.9 and 24.7 Mb, respectively.

T he halotolerant yeasts of the genus Zygosaccharomyces find relevant applications in food spoilage and fermentation (1). They exhibit high diversity in response to high solute concentrations, tendency to hybridization, and ectopic recombination at the mating type loci, leading to ploidy and karyotype variation (2,3). Zygosaccharomyces rouxii ATCC 42981 is an allodiploid strain isolated from Japanese miso, which grows at NaCl and dextrose concentrations up to 3.0 M and 70% (wt/vol), respectively (4). Zygosaccharomyces sapae represents a novel species, first described in high-sugar traditional balsamic vinegar (TBV), for which ABT301 (ϭ CBS 12607 T ϭ MUCL 54092 T ϭ UMCC 152 T ) is the type strain (5). ABT301 T is a sugar-resistant and slow-growing strain more sensitive to salt than is ATCC 42981. Under standard conditions, ATCC 42981 produces more glycerol than does ABT301 T and better retains it in the cell under conditions of salt stress (6). ATCC 42981 is thought to have arisen from hybridization between two divergent parents (3,5,(7)(8)(9), while no evidence about the origin of strain ABT301 T is available. Here, we present the draft genome sequences of ATCC 42981 and ABT301 T .
Single-colony isolates were obtained from the Unimore Microbial Culture Collection (UMCC) of the University of Modena and Reggio Emilia in Italy. ABT301 T was isolated from a TBV sample in May to June 2004 (10). DNA was extracted by using the phenolchloroform-isoamyl alcohol method (11) after cell wall enzymatic lysis with 300 U lyticase (Sigma, St. Louis, MO) and subjected to short-read and long-read sequencing by using the MiSeq (Illumina) and MinION (ONT) platforms. Illumina libraries were prepared with an average insert size of ϳ600 bp and sequenced in paired-end mode on a MiSeq instrument using a v3 600-cycle chemistry kit. In total, 2,234,027 and 3,452,971 short paired-end reads were generated for ATCC 42981 and ABT301 T , respectively.
Comparison with haploid CBS 732 T showed that the ATCC 42981 and ABT301 T assembled genomes had a 2.14 and 2.53 times larger assembly size and contained a 2.11 and 2.46 times higher number of protein-coding genes, respectively (Table 1). For both genomes we dissected three haplotypes, and one of them was identical to that of CBS 732 T (identity cutoff, 0.92). The data suggest a recursive hybridization model (21). The reported assemblies will decipher how hybridization, followed by functional genome stabilization, may offer a rapid adaptation strategy to salt stress environments in yeasts.
Data availability. The BioProject has been deposited in GenBank under number PRJEB26771. All sequencing reads of Z. rouxii ATCC 42981 and Z. sapae ABT301 T have been deposited at EMBL/GenBank under the accession numbers UEMZ01000001 to UEMZ01000033 and UEGL01000001 to UEGL01000052, respectively.

ACKNOWLEDGMENTS
This work was partially supported by the Italian Ministry of Education, University and Research (MIUR), within the framework of the Italian National Grant for Fundamental Research (FFABR 2017). L.P.P. is funded by the National Science Centre (Poland) Polonez-1 framework from the European Union's Horizon 2020 research and innovation program under the Marie Skłodowska-Curie grant agreement number 665778.
We acknowledge Paolo Giudici for his helpful advice and discussions and Luciana De Vero, Ph.D., for maintaining the UMCC strains.
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.