The genome sequence of the highly acetic acid-tolerant Zygosaccharomyces bailii-derived interspecies hybrid strain ISA1307, isolated from a sparkling wine plant

Abstract

In this work, it is described the sequencing and annotation of the genome of the yeast strain ISA1307, isolated from a sparkling wine continuous production plant. This strain, formerly considered of the Zygosaccharomyces bailii species, has been used to study Z. bailii physiology, in particular, its extreme tolerance to acetic acid stress at low pH. The analysis of the genome sequence described in this work indicates that strain ISA1307 is an interspecies hybrid between Z. bailii and a closely related species. The genome sequence of ISA1307 is distributed through 154 scaffolds and has a size of around 21.2 Mb, corresponding to 96% of the genome size estimated by flow cytometry. Annotation of ISA1307 genome includes 4385 duplicated genes (∼ 90% of the total number of predicted genes) and 1155 predicted single-copy genes. The functional categories including a higher number of genes are 'Metabolism and generation of energy', 'Protein folding, modification and targeting' and 'Biogenesis of cellular components'. The knowledge of the genome sequence of the ISA1307 strain is expected to contribute to accelerate systems-level understanding of stress resistance mechanisms in Z. bailii and to inspire and guide novel biotechnological applications of this yeast species/strain in fermentation processes, given its high resilience to acidic stress. The availability of the ISA1307 genome sequence also paves the way to a better understanding of the genetic mechanisms underlying the generation and selection of more robust hybrid yeast strains in the stressful environment of wine fermentations.

Keywords: Zygosaccharomyces bailii; genome sequencing and annotation; hybrid yeast strains; weak acid food preservatives tolerance; wine yeast strains.

Figure 1.

Estimation of genome size and karyotyping of the ISA1307 strain. (A) Representative cell cycle analysis histogram of S. cerevisiae BY4741 or BY4743 (in black) and ISA1307 (in grey). ISA1307 and S. cerevisiae cells were cultivated in YPD growth medium until stationary phase and then labelled with SYBR Green I to stain genomic DNA. Mean fluorescent intensities (MFI) of G₀/G₁ peaks of the cell cycle histogram were estimated by flow cytometry. The MFI values obtained for the two S. cerevisiae strains were used to build a calibration curve that was used to calculate the size of the genome of the ISA1307 strain (12.16 Mb for the size of the genome of the haploid strain S. cerevisiae BY4741). (B) Karyotype of the reference strain Z. bailii ATCC58445 (lane 2) and of the ISA1307 strain (lane 3). Total genomic DNA of both yeast species cultivated in YPD growth medium until stationary phase was separated by PFGE. The size of ISA1307 high-molecular-weight chromosomes was estimated based on the high-molecular-weight standard [Hansenula wingei (Bio-Rad)—lane 1], while the size of low-molecular-weight chromosomes was estimated using S. cerevisiae chromosomes' size (not shown).

Figure 2.

Multigenome alignment of genomic regions of S. cerevisiae S288c, Z. rouxii CBS732, Z. bailii CLIB213T and the interspecies hybrid strain ISA1307. In this picture are shown aligments of Z. bailii CLIB213^T, S. cerevisiae S288c, Z. rouxii CBS732 and the hybrid strain ISA1307 centered in different genomic regions. Each coloured square represents a different scaffold found in the genomes of Z. bailii CLIB213^T or of ISA1307 or represents a chromsomes of S. cerevisiae S288c or Z. rouxii CBS732. Conserved synteny blocks are shown in shaded boxes. This image was obtained using the multigenome alignment GBrowse_syn (http://mips.helmholtz-muenchen.de/gbrowse2/cgi-bin/gbrowse_syn/zbailii).

Figure 3.

Functional classes of genes predicted to be encoded by the genome of the ISA1307 strain. The genes predicted by the annotation of the genome of the ISA1307 strain (detailed in Section 2) were clustered according to their biological function using the FunCatDB. The number of genes included in each functional category is indicated.

Figure 4.

Frequency of putative domains in the ISA1307 predicted proteome. The proteins predicted to be encoded by the ISA1307 genome were searched for putative conserved domains using InterProScan and domains found present in >50 predicted proteins were selected and are highlighted.