Genomic Convergence toward Diploidy in Saccharomyces cerevisiae

Gerstein, Aleeza C.; Chun, Hye Jung; Grant, Alex; Otto, Sarah P.

doi:10.1371/journal.pgen.0020145

Cited by 205 publications

(250 citation statements)

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“…A recent study in yeast Saccharomyces cerevisiae observed this phenomenon in an evolutionary context when isogenic 1x, 2x, and 4x yeast strains all converged toward diploid DNA levels over the course of 1766 mitotic cell divisions (Gerstein et al 2006). Further experimental evidence indicated that selection on genome size drove this convergence (Gerstein et al 2006). The exact mechanism of diploid superiority was unclear; however, the authors speculated that selection over evolutionary time has optimized organismal function at the diploid level, the historical ploidy state for this species (Gerstein et al 2006).…”

Section: Discussionmentioning

confidence: 88%

“…However, this does not seem to be true for synthetic autopolyploids. A recent study in yeast Saccharomyces cerevisiae observed this phenomenon in an evolutionary context when isogenic 1x, 2x, and 4x yeast strains all converged toward diploid DNA levels over the course of 1766 mitotic cell divisions (Gerstein et al 2006). Further experimental evidence indicated that selection on genome size drove this convergence (Gerstein et al 2006).…”

Section: Discussionmentioning

confidence: 91%

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Phenotypic and Transcriptomic Changes Associated With Potato Autopolyploidization

et al. 2007

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Polyploidy is remarkably common in the plant kingdom and polyploidization is a major driving force for plant genome evolution. Polyploids may contain genomes from different parental species (allopolyploidy) or include multiple sets of the same genome (autopolyploidy). Genetic and epigenetic changes associated with allopolyploidization have been a major research subject in recent years. However, we know little about the genetic impact imposed by autopolyploidization. We developed a synthetic autopolyploid series in potato (Solanum phureja) that includes one monoploid (1x) clone, two diploid (2x) clones, and one tetraploid (4x) clone. Cell size and organ thickness were positively correlated with the ploidy level. However, the 2x plants were generally the most vigorous and the 1x plants exhibited less vigor compared to the 2x and 4x individuals. We analyzed the transcriptomic variation associated with this autopolyploid series using a potato cDNA microarray containing $9000 genes. Statistically significant expression changes were observed among the ploidies for $10% of the genes in both leaflet and root tip tissues. However, most changes were associated with the monoploid and were within the twofold level. Thus, alteration of ploidy caused subtle expression changes of a substantial percentage of genes in the potato genome. We demonstrated that there are few genes, if any, whose expression is linearly correlated with the ploidy and can be dramatically changed because of ploidy alteration. Polyploids originate from either sexual reproduction via 2n gametes or somatic chromosome doubling. By traditional definition, there are two forms of polyploidy: allopolyploidy and autopolyploidy. These terms are often used to imply the mode of polyploid formation, but more accurately describe the degree of similarity between the subgenomes in polyploids. Allopolyploids have distinct subgenomes and typically originate from interspecific hybridization between divergent progenitor species. Autopolyploids have (nearly) identical subgenomes and typically originate from intraspecific hybridization (or self-fertilization through 2n gametes) or somatic chromosome doubling. Allo-and autopolyploids have traditionally been distinguished by modes of chromosome pairing and inheritance, with allopolyploids exhibiting bivalent pairing and disomic inheritance and autopolyploids exhibiting multivalent pairing and polysomic inheritance.A number of well-known polyploid plants of agricultural interest are classical allopolyploids, which include important crops such as bread wheat (2n ¼ 6x ¼ 42) and cotton (2n ¼ 4x ¼ 56). Studies of genetic and epigenetic changes associated with polyploidization have been focused mostly on newly synthesized allopolyploid materials 1 Present address:

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Section: Discussionmentioning

confidence: 88%

Section: Discussionmentioning

confidence: 91%

Phenotypic and Transcriptomic Changes Associated With Potato Autopolyploidization

et al. 2007

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“…In diploid cells, failure of correct chromosome disjunction produces cells that lack one homolog copy (monosomy) or have an extra copy (trisomy). In the yeast Saccharomyces cerevisiae, as in mammals, aneuploid cells grow slowly relative to euploid cells (1)(2)(3).…”

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confidence: 99%

Reciprocal uniparental disomy in yeast

Andersen

Petes

2012

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

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In the diploid cells of most organisms, including humans, each chromosome is usually distinguishable from its partner homolog by multiple single-nucleotide polymorphisms. One common type of genetic alteration observed in tumor cells is uniparental disomy (UPD), in which a pair of homologous chromosomes are derived from a single parent, resulting in loss of heterozygosity for all single-nucleotide polymorphisms while maintaining diploidy. Somatic UPD events are usually explained as reflecting two consecutive nondisjunction events. Here we report a previously undescribed mode of chromosome segregation in Saccharomyces cerevisiae in which one cell division produces daughter cells with reciprocal UPD for the same pair of chromosomes without an aneuploid intermediate. One pair of sister chromatids is segregated into one daughter cell and the other pair is segregated into the other daughter cell, mimicking a meiotic chromosome segregation pattern. We term this process “reciprocal uniparental disomy.”

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“…In certain eukaryotic lineages such as in unicellular fungi, genome size is clearly under selective pressure. 13 In order to study deletions, it is necessary to accurately detect them. Small deletions of only a few bases can be detected by sequencing.…”

Section: Introductionmentioning

confidence: 99%

“…In certain eukaryotic lineages such as in unicellular fungi, genome size is clearly under selective pressure. 13 A small genome size is assumed to have been of adaptive advantage due to its ability to replicate faster. Such evolution can only occur in the presence of deletions as the basic mutational events.…”

Section: Introductionmentioning

confidence: 99%

The effect of pedigree structure on detection of deletions and other null alleles

Johansson

Säll

2008

Eur J Hum Genet

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Deletions and other null alleles for genetic markers can be detected as a special case of non-Mendelian inheritance, ie when a parent and a child appear to be homozygous for different alleles. The probability to detect a deletion for a fixed overall number of investigated individuals was calculated for biallelic and multiallelic markers with varying allele frequencies. To determine the effect of increasing the number of parents and grandparents, the probability for this event was derived for a parent and one child, a trio, a trio with one grandparent and a trio with two grandparents. The results for biallelic markers show that for a fixed total number of individuals, a sample of trios with two grandparents is always more efficient than the other family types, despite a lower total number of founder chromosomes in the sample. For multiallelic markers the outcome varies. The effect of adding additional children to a nuclear family was also investigated. For nuclear families, the optimal number of children is two or three, depending on the allele frequencies. It is shown that adding children is more efficient than adding grandparents. European Journal of Human Genetics (2008Genetics ( ) 16, 1225Genetics ( -1234 doi:10.1038/ejhg.2008 published online 16 April 2008 Keywords: deletion; null allele; pedigree; genetic marker IntroductionDeletions are one of the many types of mutations that can affect a genome. The observed size of a deletion range from a single base pair up to an entire arm of a chromosome (see Lewis 1 ). In recent years, there has been an increasing interest in investigating structural variants, including deletions. 2 One reason is because deletions may be the cause of some diseases. One such case is the occurrence of somatic deletions involved in cancer, which can be detected through 'loss of heterozygosity' in the tumour when compared to other tissues. 3 Another situation where deletions may be observed is when they occur as de novo deletions. These are notable when they subsequently cause disease in the offspring of the person within whom the deletion occurred in the germline. 4 Finally, deletions causing disease may be inherited. Such deletions may act as directly causing in one end of the spectrum, but may also act as risk alleles in complex diseases. 5,6 However, just as in the case with other types of mutations deletions may have no phenotypic effect. 7,8 Alternatively, the effect is so weak that it is effectively undetectable. Such mutations may then appear as polymorphisms within populations. The presence of deletion polymorphisms in the human genome have recently been investigated in a number of large-scale projects. 5,9 -12 These investigations demonstrate that a large number of deletion polymorphisms occur in humans. They also show that, although with few exceptions the deletion constitutes the rare allele, the frequency of the deletion may be relatively high. The presence and frequency of deletion polymorphisms is of interest for a number of reasons. In certain eukaryotic lineages such...

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Genomic Convergence toward Diploidy in Saccharomyces cerevisiae

Cited by 205 publications

References 32 publications

Phenotypic and Transcriptomic Changes Associated With Potato Autopolyploidization

Phenotypic and Transcriptomic Changes Associated With Potato Autopolyploidization

Reciprocal uniparental disomy in yeast

The effect of pedigree structure on detection of deletions and other null alleles

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