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Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Saccharomyces cerevisiae

PROVIDER: GSE171587 | GEO | 2021/04/07

REPOSITORIES: GEO

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Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [Bar-seq]

Project description:Genetic variation that underlies phenotypic differences provides the material on which evolutionary selection acts. Gene duplication/amplification is one type of genetic variation that can allow an organism to rapidly respond to environmental changes by increasing gene dosage. While the potential benefits afforded by gene amplification during evolution are well known, there is also a significant fitness cost to increasing gene dosage including resource shortages and burdening cellular systems. Although the evolutionary importance of gene duplication has long been appreciated, little is known about natural variation in the tolerance of duplication of specific genes. To investigate this question, we expressed the same high-copy gene overexpression (OE) library in a laboratory strain and 14 different wild S. cerevisiae isolates, together representing 4 lineages and several admixed strains, to explore the natural variation in tolerance to gene OE. Our results distinguish universal effects common to many studied strains versus strain-specific effects including broad-scale and gene-specific differences in the consequences of OE. These results raise important implications for the accessibility of evolutionary trajectories afforded by gene OE, depending on genetic background.

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Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [RNA-seq]

Project description:We used RNA-Seq to measure transcript abundance in 15 Saccharomyces cerevisiae strains from a diverse range of genetic lineages when growing in rich media (YPD) to characterize differential expression across strains.

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Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates

Project description:Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates

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Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

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Project description:Experimental evolution allows the observation of change over time as laboratory populations evolve in response to novel, controlled environments. Microbial evolution experiments take advantage of cryopreservation to archive experimental populations in glycerol media, creating a frozen, living "fossil" record. Prior research with Escherichia coli has shown that cryopreservation conditions can affect cell viability and that allele frequencies across the genome can change in response to a freeze-thaw event. We expand on these observations by characterizing fitness and genomic consequences of multiple freeze-thaw cycles in diploid yeast populations. Our study system is a highly recombinant Saccharomyces cerevisiae population (SGRP-4X) that harbors standing genetic variation that cryopreservation may threaten. We also investigate the four parental isogenic strains crossed to create the SGRP-4X. We measure cell viability over five consecutive freeze-thaw cycles; whereas we find that viability increases over time in the evolved recombinant populations, we observe no such viability improvements in the parental strains. We also collect genome-wide sequence data from experimental populations initially, after one freeze-thaw, and after five freeze-thaw cycles. In the recombinant evolved populations, we find a region of significant allele frequency change on chromosome 15 containing the ALR1 gene. In the parental strains, we find little evidence for new mutations. We conclude that cryopreserving yeast populations with standing genetic variation may have both phenotypic and genomic consequences, though the same cryopreservation practices may have only small impacts on populations with little or no initial variation.

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Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [Bar-seq]

Project description:Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [Bar-seq]

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Natural Variation in the Fitness Consequences of Gene Amplification in Wild Saccharomyces cerevisiae Isolates [RNA-seq]

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Project description:This SuperSeries is composed of the SubSeries listed below.

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