The genomic and phenotypic diversity of Schizosaccharomyces pombe

Jeffares, Daniel C.; Rallis, Charalampos; Rieux, Adrien; Speed, Doug; Převorovský, Martin; Mourier, Tobias; Marsellach, Xavi; Iqbal, Zamin; Lau, Winston; Cheng, Tammy M.K.; Pracana, Rodrigo; Mülleder, Michael; Lawson, John; Chessel, Anatole; Bala, Sendu; Hellenthal, Garrett; O’Fallon, Brendan D.; Keane, Thomas; Simpson, Jared T.; Bischof, Leanne; Tomiczek, Bartłomiej; Bitton, Danny A.; Sideri, Theodora; Codlin, Sandra; Hellberg, Josephine E. E. U.; Trigt, Laurent van; Jeffery, Linda; Li, Juan Juan; Atkinson, Sophie; Thodberg, Malte; Febrer, Melanie; McLay, Kirsten; Drou, Nizar; Brown, William R. A.; Hayles, Jacqueline; Carazo-Salas, Rafael E.; Ralser, Markus; Maniatis, Nikolas; Balding, David J.; Balloux, François; Durbin, Richard; Bähler, Jürg

doi:10.1038/ng.3215

Cited by 180 publications

(382 citation statements)

References 61 publications

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“…This line shows the maximum cell length and calcofluor staining (a marker of incomplete cell division and filamentous growth) among 160 lines that were recently phenotyped (Jeffares et al 2015). However, no overt morphologic differences were observed between MA lines with and without mutations in this gene.…”

Section: Resultsmentioning

confidence: 88%

“…fewer than 3 kb in S. cerevisiae (Liti et al 2009), the same drop in S. pombe requires between 20 kb (Jeffares et al 2015) and 50 kb (data not shown). A possible explanation is that S. pombe undergoes less frequent outcrossing in the wild.…”

Section: Similarities and Differences Between Fission And Budding Yeastsmentioning

confidence: 79%

“…Here, using the polymorphism observed in a worldwide collection of S. pombe (Table S3) (Fawcett et al 2014;Jeffares et al 2015) and assuming a predominantly haploid life history, we estimate the N e of S. pombe to be 12 million. In comparison, less polymorphism is observed at noncoding sites in S. cerevisiae (Schacherer et al 2009), leading to an N e estimate of 3.4 million.…”

Section: Similarities and Differences Between Fission And Budding Yeastsmentioning

confidence: 99%

“…In the wild, S. pombe occurs in small, incompletely isolated populations with only weak population structure resulting from recent global dispersal (Brown et al 2011;Jeffares et al 2015). Beyond this, little is known of its natural ecology.…”

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confidence: 99%

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The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

et al. 2015

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The rate at which new mutations arise in the genome is a key factor in the evolution and adaptation of species. Here we describe the rate and spectrum of spontaneous mutations for the fission yeast Schizosaccharomyces pombe, a key model organism with many similarities to higher eukaryotes. We undertook an 1700-generation mutation accumulation (MA) experiment with a haploid S. pombe, generating 422 single-base substitutions and 119 insertion-deletion mutations (indels) across the 96 replicates. This equates to a base-substitution mutation rate of 2.00 3 10 210 mutations per site per generation, similar to that reported for the distantly related budding yeast Saccharomyces cerevisiae. However, these two yeast species differ dramatically in their spectrum of base substitutions, the types of indels (S. pombe is more prone to insertions), and the pattern of selection required to counteract a strong AT-biased mutation rate. Overall, our results indicate that GC-biased gene conversion does not play a major role in shaping the nucleotide composition of the S. pombe genome and suggest that the mechanisms of DNA maintenance may have diverged significantly between fission and budding yeasts. Unexpectedly, CpG sites appear to be excessively liable to mutation in both species despite the likely absence of DNA methylation.KEYWORDS mutation accumulation; effective population size; biased gene conversion; fission yeast M UTATION is the ultimate source of all genetic differences within and among species. Mutation may alter the sequence of the genome via single-base substitutions; change the length of the genome by means of insertions, deletions, and duplications; or alter genome architecture via changes in chromosomal ploidy. The rate at which each of these events occurs in nature is largely obscured in a comparison of individuals or species owing to the action of natural selection and drift. An unbiased estimate of the rate and spectrum of spontaneous mutations can be obtained by passing replicate individuals through thousands of generations of mutation accumulation (MA). Under this protocol, which imposes a very small effective population size during passage, selection will have little influence on the fate of new mutations.The fission yeast Schizosaccharomyces pombe is a member of the largest and most diverse fungal phylum, Ascomycota, and is a key model system in cell biology. In the wild, S. pombe occurs in small, incompletely isolated populations with only weak population structure resulting from recent global dispersal (Brown et al. 2011;Jeffares et al. 2015). Beyond this, little is known of its natural ecology. It is, however, often recovered from natural fermentations and was isolated originally from East African millet beer.Notwithstanding the uncertainty regarding its ecology, the life cycle of S. pombe in the wild is likely to be predominantly haploid. In a collection of 81 natural isolates, all but one were haploid, with the sole diploid most likely resulting from biparental inbreeding (Brown et al. 2011). ...

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Section: Resultsmentioning

confidence: 88%

Section: Similarities and Differences Between Fission And Budding Yeastsmentioning

confidence: 79%

Section: Similarities and Differences Between Fission And Budding Yeastsmentioning

confidence: 99%

mentioning

confidence: 99%

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The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

et al. 2015

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“…Indeed, Schizosaccharomyces has been described to be isolated from wines showing strong organoleptic and chemical deviations such as high levels of acetic acid, sulfidric acid, acetaldehyde, acetoin and ethyl acetate [12]. Due to the enormous variability in the genetic composition of any species such as S. pombe [18], recent selection processes have been performed in order to obtain proper strains for winemaking purposes [19,20]. The last studies regarding Schizosaccharomyces genus have demonstrated that it is possible to produce quality wines through the combination of wild Schizosaccharomyces strains with selected Saccharomyces strains or more recently through the use of selected Schizosaccharomyces strains that are able to perform by themselves a complete proper fermentation process, especially under very acidic conditions.…”

Section: Introductionmentioning

confidence: 99%

New Trends in Schizosaccharomyces Use for Winemaking

Benito¹,

Calderón²,

Benito³

2016

Grape and Wine Biotechnology

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Several researchers are studying the winemaking potential of non-Saccharomyces yeast strains in order to improve wine quality. For that purpose, yeast species such as Torulaspora delbrueckii, Lachancea thermotolerans, Metschnikowia pulcherrima, Candida zemplinina, Kloeckera apiculata, Hansenula anomala and Pichia guilliermondii were studied in the past. Yeasts from the genus Schizosaccharomyces have been traditionally studied from a winemaking point of view due to its rapid malic acid deacidification, by converting malic acid to ethanol and CO 2 . Nevertheless, during the last 5 years, it has been discovered that Schizosaccharomyces pombe possesses several remarkable metabolic properties different from its traditional malic acid deacidification that may be useful in modern quality winemaking, including a malic dehydrogenase activity, high autolytic polysaccharides release, ability of gluconic acid reduction, urease activity in order to avoid ethyl carbamate formation, elevated production of pyruvic acid related to colour improvement, and low production of biogenic amines.

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The evolution of mating‐type switching for reproductive assurance

Nieuwenhuis

Immler

2016

BioEssays

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Alternative ways to ensure mate compatibility, such as hermaphroditism and the breakdown of self-incompatibility, evolved repeatedly when finding a mating partner is difficult. In a variety of microorganisms where compatibility is determined by mating-types, a highly regulated form of universal compatibility system called mating-type switching has evolved several times. This sophisticated system allows for the genetic adjustment of the mating type during asexual growth, and it most likely evolved for reproductive assurance of immotile species under low densities. In this review, we compare the switching strategy to other universal compatibility systems such as "unisexual mating" and homothallism. We identify the costs of switching, including genome instability, and mechanistic costs, as well as the benefits, mainly the maintenance of important mating-type functions. Given the potential benefits of mating-type switching, we speculate that switching is likely to have evolved many times independently, and may be more common in groups where genetic mating types regulate mate compatibility than assumed so far.

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The genomic and phenotypic diversity of Schizosaccharomyces pombe

Cited by 180 publications

References 61 publications

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

The Spontaneous Mutation Rate in the Fission Yeast Schizosaccharomyces pombe

New Trends in Schizosaccharomyces Use for Winemaking

The evolution of mating‐type switching for reproductive assurance

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