Preferential elimination of repeated DNA sequences from the paternal, <i>Nicotiana tomentosiformis</i> genome donor of a synthetic, allotetraploid tobacco

Skalická, Kamila; Lim, K. Yoong; Matyášek, Roman; Matzke, Marjori; Leitch, Andrew R.; Kovařı́k, Aleš

doi:10.1111/j.1469-8137.2004.01297.x

Cited by 135 publications

(131 citation statements)

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“…The ascendancy of the B. rapa genome over B. oleracea has already been described by Chen and Pikaard (1997), who observed a nucleolar dominance of B. rapa rRNA genes in reciprocal crosses of synthetic oilseed rape. Directed parental genome modifications seem to be a recurrent feature of allopolyploid formation: in several synthetic allopolyploids (Song et al 1995;Adams et al 2004;Skalicka et al 2005), a bias toward one genome has been reported, frequently in favor of the maternal genome, suggesting that genome changes might by influenced by nucleocytoplasmic interactions. However, in our synthetic B. napus, the predominant gene expression pattern was of paternal origin and there was no bias in the cellular localization of proteins displaying nonadditive value.…”

Section: Discussionmentioning

confidence: 99%

Numerous and Rapid Nonstochastic Modifications of Gene Products in Newly SynthesizedBrassica napusAllotetraploids

et al. 2006

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Polyploidization is a widespread process that results in the merger of two or more genomes in a common nucleus. To investigate modifications of gene expression occurring during allopolyploid formation, the Brassica napus allotetraploid model was chosen. Large-scale analyses of the proteome were conducted on two organs, the stem and root, so that .1600 polypeptides were screened. Comparative proteomics of synthetic B. napus and its homozygous diploid progenitors B. rapa and B. oleracea showed that very few proteins disappeared or appeared in the amphiploids (,1%), but a strikingly high number (25-38%) of polypeptides displayed quantitative nonadditive pattern. Nonstochastic gene expression repatterning was found since 99% of the detected variations were reproducible in four independently created amphiploids. More than 60% of proteins displayed a nonadditive pattern closer to the paternal parent B. rapa. Interspecific hybridization triggered the majority of the deviations (89%), whereas very few variations ($3%) were associated with genome doubling and more significant alterations arose from selfing ($9%). Some nonadditive proteins behaved similarly in both organs, while others exhibited contrasted behavior, showing rapid organ-specific regulation. B. napus formation was therefore correlated with immediate and directed nonadditive changes in gene expression, suggesting that the early steps of allopolyploidization repatterning are controlled by nonstochastic mechanisms.

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Section: Discussionmentioning

confidence: 99%

Numerous and Rapid Nonstochastic Modifications of Gene Products in Newly SynthesizedBrassica napusAllotetraploids

et al. 2006

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“…Studies of genetic and epigenetic changes associated with polyploidization have been focused mostly on newly synthesized allopolyploid materials 1 (Song et al 1995;Liu et al 1998;Comai et al 2000;Ozkan et al 2001;Kashkush et al 2002;Madlung et al 2002Madlung et al , 2005He et al 2003;Kashkush et al 2003;Adams et al 2004;Wang et al 2004Wang et al , 2006Skalicka et al 2005;Albertin et al 2006;Lukens et al 2006). However, in allopolyploids, ploidy level per se is difficult to tease apart from many other variables, such as diverged suites of regulatory factors from different genomes.…”

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confidence: 99%

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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“…In these genomes, natural selection and stochastic processes govern the genetic fate of each paralog-fates that include redundancy, subfunctionalization, neofunctionalization, and gene silencing (Ohno 1970;Hughes and Hughes 1993;Force et al 1999;Lynch and Force 2000;Lynch et al 2001;Gu 2003). After allopolyploidization, interactions between the subgenomes derived from each ancestral species included exchange of chromosome segments (Moscone et al 1996;Skalická et al 2005), concerted evolution (Wendel et al 1995;Volkov et al 1999), recombination (Zwierzykowski et al 1998), and epistasis ( Jiang et al 2000). Restructuring can then alter the stoichiometry of protein interactions by modifying regulatory elements or changing gene copy number.…”

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confidence: 99%

Ancestry Influences the Fate of Duplicated Genes Millions of Years After Polyploidization of Clawed Frogs (Xenopus)

Evans

2007

Genetics

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Allopolyploid species form through the fusion of two differentiated genomes and, in the earliest stages of their evolution, essentially all genes in the nucleus are duplicated. Because unique mutations occur in each ancestor prior to allopolyploidization, duplicate genes in these species potentially are not interchangeable, and this could influence their genetic fates. This study explores evolution and expression of a simple duplicated complex-a heterodimer between RAG1 and RAG2 proteins in clawed frogs (Xenopus). Results demonstrate that copies of RAG1 degenerated in different polyploid species in a phylogenetically biased fashion, predominately in only one lineage of closely related paralogs. Surprisingly, as a result of an early deletion of one RAG2 paralog, it appears that in many species RAG1/RAG2 heterodimers are composed of proteins that were encoded by unlinked paralogs. If the tetraploid ancestor of extant species of Xenopus arose through allopolyploidization and if recombination between paralogs was rare, then the genes that encode functional RAG1 and RAG2 proteins in many polyploid species were each ultimately inherited from different diploid progenitors. These observations are consistent with the notion that ancestry can influence the fate of duplicate genes millions of years after duplication, and they uncover a dimension of natural selection in allopolyploid genomes that is distinct from other genetic phenomena associated with polyploidization or segmental duplication.

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Preferential elimination of repeated DNA sequences from the paternal, Nicotiana tomentosiformis genome donor of a synthetic, allotetraploid tobacco

Cited by 135 publications

References 72 publications

Numerous and Rapid Nonstochastic Modifications of Gene Products in Newly SynthesizedBrassica napusAllotetraploids

Numerous and Rapid Nonstochastic Modifications of Gene Products in Newly SynthesizedBrassica napusAllotetraploids

Phenotypic and Transcriptomic Changes Associated With Potato Autopolyploidization

Ancestry Influences the Fate of Duplicated Genes Millions of Years After Polyploidization of Clawed Frogs (Xenopus)

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