<i>Saccharomyces cerevisiae</i>and<i>Saccharomyces paradoxus</i>coexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics

Sniegowski, Paul D.; Dombrowski, Peter G; Fingerman, Ethan G.

doi:10.1111/j.1567-1364.2002.tb00048.x

Cited by 184 publications

(100 citation statements)

References 30 publications

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“…Introgression between YJM789 and S. paradoxus or a closely related species is a possibility that can account for these observations. Indeed, S. paradoxus and S. cerevisiae share similar habitats (39), and hybrids between the two are found in nature (40). Although hybrids between S. cerevisiae and other members of the Saccharomyces sensu stricto are predominantly sterile, rare viable offspring containing DNA from both species have been produced (41)(42)(43), providing a putative way for introgression to occur.…”

Section: Resultsmentioning

confidence: 99%

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

McCusker

Hyman

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

244

291

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We sequenced the genome of Saccharomyces cerevisiae strain YJM789, which was derived from a yeast isolated from the lung of an AIDS patient with pneumonia. The strain is used for studies of fungal infections and quantitative genetics because of its extensive phenotypic differences to the laboratory reference strain, including growth at high temperature and deadly virulence in mouse models. Here we show that the Ϸ12-Mb genome of YJM789 contains Ϸ60,000 SNPs and Ϸ6,000 indels with respect to the reference S288c genome, leading to protein polymorphisms with a few known cases of phenotypic changes. Several ORFs are found to be unique to YJM789, some of which might have been acquired through horizontal transfer. Localized regions of high polymorphism density are scattered over the genome, in some cases spanning multiple ORFs and in others concentrated within single genes. The sequence of YJM789 contains clues to pathogenicity and spurs the development of more powerful approaches to dissecting the genetic basis of complex hereditary traits.comparative genomics ͉ genome architecture ͉ introgression ͉ lateral gene transfer T here is extensive genetic and phenotypic diversity within species. Determining which of the vast amounts of sequence differences that are found among individuals of a species contribute to heritable traits will allow diseases to be tackled at the molecular level and aid in the development of novel therapies. Saccharomyces cerevisiae, commonly known as baker's or brewer's yeast, plays a central role in food production and is one of the most studied genetic model species. It is not only widely used in biotechnology but also is a powerful model system that has been applied to identify multigenetic factors of hereditary traits (1-7). The genome sequence of one laboratory strain, a derivative of S288c, was the first genome of a free-living eukaryotic organism to be sequenced (8). Over the last 10 years, this genome has served as the reference for the S. cerevisiae species and has catalyzed the development of whole-genome approaches to biology (9, 10). Despite frequent laboratory use of alternative strains, sequence information for S. cerevisiae beyond the domesticated strain S288c has been fragmentary. S288c, which originated from a strain isolated from a rotten fig, was chosen for sequencing because it possesses properties that make it easy to work with, such as minimal colony morphology switching, consistent growth rates in glucose media, and no flocculence (11). At several loci, S288c contains polymorphisms not found in natural isolates, which could be hallmarks of domestication (12,13). A growing number of S. cerevisiae infections in humans have recently been reported (14). As a result, S. cerevisiae is also regarded as an emerging opportunistic pathogen that can cause clinically relevant infections in different patient types and body sites (15)(16)(17). One clinical strain (YJM145), derived from a yeast isolated from an AIDS patient with S. cerevisiae pneumonia (18), has been studied extensively as ...

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Section: Resultsmentioning

confidence: 99%

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

McCusker

Hyman

et al. 2007

Proc. Natl. Acad. Sci. U.S.A.

244

291

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“…This high copy number may result from the evolution of yeast and its population of retrotransposons under laboratory conditions; most wild yeast strains typically harbor lower Ty1 copy numbers (10)(11)(12).…”

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confidence: 99%

Transposon insertion site profiling chip (TIP-chip)

Wheelan

Scheifele

Martínez-Murillo

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

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Mobile elements are important components of our genomes, with diverse and significant effects on phenotype. Not only can transposons inactivate genes by direct disruption and shuffle the genome through recombination, they can also alter gene expression subtly or powerfully. Currently active transposons are highly polymorphic in host populations, including, among hundreds of others, L1 and Alu elements in humans and Ty1 elements in yeast. For this reason, we wished to develop a simple genome-wide method for identifying all transposons in any given sample. We have designed a transposon insertion site profiling chip (TIP-chip), a microarray intended for use as a high-throughput technique for mapping transposon insertions. By selectively amplifying transposon flanking regions and hybridizing them to the array, we can locate all transposons present in a sample. We have tested the TIP-chip extensively to map Ty1 retrotransposon insertions in yeast and have achieved excellent results in two laboratory strains as well as in evolved Ty1 high-copy strains. We are able to identify all of the theoretically detectable transposons in the FY2 lab strain, with essentially no false positives. In addition, we mapped many new transposon copies in the high-copy Ty1 strain and determined its Ty1 insertion pattern.

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“…Smooth strains and biofilm‐forming strains with distinct colony morphologies and from different ecological niches were identified. Two biofilm strains—YJM311 (clinical) (McCusker, Clemons, Stevens, & Davis, 1994), YJM224 (distillery yeast)—and three smooth strains—YJM981 (clinical) (McCullough, Clemons, Farina, McCusker, & Stevens, 1998), SK1 (lab/soil) (Liti et al., 2009), YPS681 (woodland) (Sniegowski, Dombrowski, & Fingerman, 2002)—were selected for fitness assays.…”

Section: Methodsmentioning

confidence: 99%

Biofilm formation and toxin production provide a fitness advantage in mixed colonies of environmental yeast isolates

Deschaine

Heysel

Lenhart

et al. 2018

Ecology and Evolution

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Microbes can engage in social interactions ranging from cooperation to warfare. Biofilms are structured, cooperative microbial communities. Like all cooperative communities, they are susceptible to invasion by selfish individuals who benefit without contributing. However, biofilms are pervasive and ancient, representing the first fossilized life. One hypothesis for the stability of biofilms is spatial structure: Segregated patches of related cooperative cells are able to outcompete unrelated cells. These dynamics have been explored computationally and in bacteria; however, their relevance to eukaryotic microbes remains an open question. The complexity of eukaryotic cell signaling and communication suggests the possibility of different social dynamics. Using the tractable model yeast, Saccharomyces cerevisiae, which can form biofilms, we investigate the interactions of environmental isolates with different social phenotypes. We find that biofilm strains spatially exclude nonbiofilm strains and that biofilm spatial structure confers a consistent and robust fitness advantage in direct competition. Furthermore, biofilms may protect against killer toxin, a warfare phenotype. During biofilm formation, cells are susceptible to toxin from nearby competitors; however, increased spatial use may provide an escape from toxin producers. Our results suggest that yeast biofilms represent a competitive strategy and that principles elucidated for the evolution and stability of bacterial biofilms may apply to more complex eukaryotes.

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Saccharomyces cerevisiaeandSaccharomyces paradoxuscoexist in a natural woodland site in North America and display different levels of reproductive isolation from European conspecifics

Cited by 184 publications

References 30 publications

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

Genome sequencing and comparative analysis of Saccharomyces cerevisiae strain YJM789

Transposon insertion site profiling chip (TIP-chip)

Biofilm formation and toxin production provide a fitness advantage in mixed colonies of environmental yeast isolates

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