Rapid identification of Zygosaccharomyces with genus-specific primers

Many interspecies hybrids have been discovered in yeasts, but most of these hybrids are asexual and can replicate only mitotically. Whole-genome duplication has been proposed as a mechanism by which interspecies hybrids can regain fertility, restoring their ability to perform meiosis and sporulate. Here, we show that this process occurred naturally during the evolution of Zygosaccharomyces parabailii, an interspecies hybrid that was formed by mating between 2 parents that differed by 7% in genome sequence and by many interchromosomal rearrangements. Surprisingly, Z. parabailii has a full sexual cycle and is genetically haploid. It goes through mating-type switching and autodiploidization, followed by immediate sporulation. We identified the key evolutionary event that enabled Z. parabailii to regain fertility, which was breakage of 1 of the 2 homeologous copies of the mating-type (MAT) locus in the hybrid, resulting in a chromosomal rearrangement and irreparable damage to 1 MAT locus. This rearrangement was caused by HO endonuclease, which normally functions in mating-type switching. With 1 copy of MAT inactivated, the interspecies hybrid now behaves as a haploid. Our results provide the first demonstration that MAT locus damage is a naturally occurring evolutionary mechanism for whole-genome duplication and restoration of fertility to interspecies hybrids. The events that occurred in Z. parabailii strongly resemble those postulated to have caused ancient whole-genome duplication in an ancestor of Saccharomyces cerevisiae.

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“…There are 12 formally described species in the genus Zygosaccharomyces [22]. The most studied of these is Z .…”

Section: Introductionmentioning

confidence: 99%

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch

et al. 2017

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“…The economic importance of Zygosaccharomyces spp. as spoilage organisms makes their rapid identification a high priority because an informed decision on cleaning procedures can be made only after the causative agent has been defined …”

Section: Resultsmentioning

confidence: 99%

“…as spoilage organisms makes their rapid identification a high priority because an informed decision on cleaning procedures can be made only after the causative agent has been defined. 26 To optimize cleaning and sanitation procedures, the 21 isolates were further tested for their susceptibility to seven commercial disinfectants and cleaning agents commonly used in the food industry.…”

Section: Resultsmentioning

confidence: 99%

The occurrence of spoilage yeasts in cream-filled bakery products

Osimani

Milanović

Taccari

et al. 2016

J. Sci. Food Agric.

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“…Here, we present the first genome-scale model reconstruction and analysis of Zygosaccharomyces parabailii, which is one of the 3 species described in the Z. bailii sensu lato clade and one of the 12 formally described species in the Zygosaccharomyces genus [25,26].…”

Section: Introductionmentioning

confidence: 99%

“…In the case of Z. bailii, high tolerance to low pH and weak acids make these yeasts notorious as frequent agents of food spoilage [22,23]. However, the same tolerance traits can also be seen as beneficial for the microbial-based production of otherwise aggressive compounds such as lactic acid [24].Here, we present the first genome-scale model reconstruction and analysis of Zygosaccharomyces parabailii, which is one of the 3 species described in the Z. bailii sensu lato clade and one of the 12 formally described species in the Zygosaccharomyces genus [25,26].This work is based on our recent genome assembly and annotation, which we have improved by producing functional annotations and used to obtain transcriptional profiles upon lactic acid stress [27]. Our model does not necessarily reflects the hybrid nature of Z. parabailii ATCC60483, but it can be pivotal for making progress into the simulation and MARZIA DI FILIPPO ET AL 3 understanding of the high stress tolerance and metabolism of this yeast species, unveiling how to better exploit its nature for industrial purposes.…”

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confidence: 99%

Genome-scale metabolic reconstruction of the stress-tolerant hybrid yeast Zygosaccharomyces parabailii

Filippo

Ortiz‐Merino

Damiani

et al. 2018

Preprint

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Funding informationGenome-scale metabolic models are powerful tools to understand and engineer cellular systems facilitating their use as cell factories. This is especially true for microorganisms with known genome sequences from which nearly complete sets of enzymes and metabolic pathways are determined, or can be inferred. Yeasts are highly diverse eukaryotes whose metabolic traits have long been exploited in industry, and although many of their genome sequences are available, few genome-scale metabolic models have so far been produced. For the first time, we reconstructed the genomescale metabolic model of the hybrid yeast Zygosaccharomyces parabailii, which is a member of the Z. bailii sensu lato clade notorious for stress-tolerance and therefore relevant to industry. The model comprises 3096 reactions, 2091 metabolites, and 2413 genes. Our own laboratory data were then used to establish a biomass synthesis reaction, and constrain the extracellular environment. Through constraint-based modeling, our model reproduces the co-consumption and catabolism of acetate and glucose posing it as a promising platform for understanding and exploiting the metabolic po-1 2 MARZIA DI FILIPPO ET AL tential of Z. parabailii. K E Y W O R D SGenome-scale metabolic model/ constraint-based modeling / hybrid yeast / stress tolerance / Zygosaccharomyces parabailii 1 | INTRODUCTION Current genome sequencing technologies allow a fast and cheap overview into the genetic composition of virtually any organism, but connecting such genotypes to observed phenotypes remains a challenge. The reconstruction of genome-scale metabolic networks provide structured frameworks to represent the biochemical transformations within a target organism as complex genotype-phenotype relationships. Afterwards, different modeling approaches can be used to simulate, understand, predict and eventually control the behavior of such genome-scale metabolic networks.Flux Balance Analysis (FBA) is a widely used constraint-based modeling approach that relies on linear programming and the optimization of a given objective function (e.g., maximization of growth) for the determination of the metabolic model flux distribution [1,2]. This approach is based on the assumption that organisms operate under a series of constraints limiting their possible functions, and leading to the definition of allowable cell phenotypes from defined metabolic networks [3].In the last two decades, genome-wide reconstructions of metabolism have been produced for a plethora of model organisms, spanning from bacteria to higher eukaryotes [4]. The original versions of these models typically undergo incremental improvements. In particular, 10 different versions of the Saccharomyces cerevisiae metabolic network have been produced to date, by implementing cellular compartments, curated reactions, standard nomenclature, and even transcriptional regulation, as reviewed in [5]. However, less extensive efforts have been dedicated to other so-called non-conventional or non-Saccharomyces yeast species, de...

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Rapid identification of Zygosaccharomyces with genus-specific primers

Cited by 21 publications

References 24 publications

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch

Evolutionary restoration of fertility in an interspecies hybrid yeast, by whole-genome duplication after a failed mating-type switch

The occurrence of spoilage yeasts in cream-filled bakery products

Genome-scale metabolic reconstruction of the stress-tolerant hybrid yeast Zygosaccharomyces parabailii

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