Polyploidy and genome restructuring: a variety of outcomes

Hufton, Andrew L.; Panopoulou, Georgia

doi:10.1016/j.gde.2009.10.005

Cited by 63 publications

(53 citation statements)

References 58 publications

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“…Interestingly, only a very small fraction (7%) of these genes indicated pseudogenization, suggesting that despite different episodes of polyploidization and segmental duplications, the wheat genes were not affected by major structural rearrangements as previously observed by sequencing homeologous loci in wheat (Chalupska et al, 2008). Thus, in contrast with paleopolyploids such as maize, gene loss has not been that extensive in wheat since its polyploid origins, confirming that the mechanisms of coping with polyploidization have varied significantly for different genomes (Hufton and Panopoulou, 2009). Polyploidization events may have occurred too recently (;500,000 years) to observe massive loss of redundant functions by genetic drift; however, a more probable explanation is that most of the duplicated gene copies have been maintained by selection since they represent more than just redundant gene functions.…”

Section: Additional Noncollinear Genes Are Interspersed Within a Verysupporting

confidence: 55%

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

et al. 2010

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To improve our understanding of the organization and evolution of the wheat (Triticum aestivum) genome, we sequenced and annotated 13-Mb contigs (18.2 Mb) originating from different regions of its largest chromosome, 3B (1 Gb), and produced a 2x chromosome survey by shotgun Illumina/Solexa sequencing. All regions carried genes irrespective of their chromosomal location. However, gene distribution was not random, with 75% of them clustered into small islands containing three genes on average. A twofold increase of gene density was observed toward the telomeres likely due to high tandem and interchromosomal duplication events. A total of 3222 transposable elements were identified, including 800 new families. Most of them are complete but showed a highly nested structure spread over distances as large as 200 kb. A succession of amplification waves involving different transposable element families led to contrasted sequence compositions between the proximal and distal regions. Finally, with an estimate of 50,000 genes per diploid genome, our data suggest that wheat may have a higher gene number than other cereals. Indeed, comparisons with rice (Oryza sativa) and Brachypodium revealed that a high number of additional noncollinear genes are interspersed within a highly conserved ancestral grass gene backbone, supporting the idea of an accelerated evolution in the Triticeae lineages.

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Section: Additional Noncollinear Genes Are Interspersed Within a Verysupporting

confidence: 55%

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

et al. 2010

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“…Among these, the most striking are rapid genetic, epigenetic, and gene expression dynamics associated with nascent allopolyploidy, which are proposed to have played important roles in the immediate stabilization and longer-term establishment of newly formed allopolyploids as new species (Wendel 2000;Liu and Wendel 2003;Levy and Feldman 2004;Ma et al 2004;Pontes et al 2004;Adams and Wendel 2005b;Feldman and Levy 2005;Chen and Ni 2006;Adams 2007;Chen 2007;Otto 2007;Hegarty and Hiscock 2008;Feldman and Levy 2009;Jones and Hegarty 2009). Paradoxically, not all newly formed plant allopolyploids are associated with rapid genomic changes, albeit they all represent established species (Hufton and Panopoulou 2009;Jackson and Chen 2009). For example, negligible genomic instability was detected in a set of newly formed cotton allopolyploids involving various parental combinations at different ploidy levels (Liu et al 2001), and complete genetic stability at the microsatellite loci was found in a large number of newly synthesized allohexaploid wheat lines .…”

Section: Discussionmentioning

confidence: 99%

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

Zhao

Zhu

et al. 2011

Genetics

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Allopolyploidy has played a prominent role in organismal evolution, particularly in angiosperms. Allohexaploidization is a critical step leading to the formation of common wheat as a new species, Triticum aestivum, as well as for bestowing its remarkable adaptability. A recent study documented that the initial stages of wheat allohexaploidization was associated with rampant genetic and epigenetic instabilities at genomic regions flanking a retrotransposon family named Veju. Although this finding is in line with the prevailing opinion of rapid genomic instability associated with nascent plant allopolyploidy, its relevance to speciation of T. aestivum remains unclear. Here, we show that genetic instability at genomic regions flanking the Veju, flanking a more abundant retroelement BARE-1, as well as at a large number of randomly sampled genomic loci, is all extremely rare or nonexistent in preselected individuals representing three sets of independently formed nascent allohexaploid wheat lines, which had a transgenerationally stable genomic constitution analogous to that of T. aestivum. In contrast, extensive and transgenerationally heritable repatterning of DNA methylation at all three kinds of genomic loci were reproducibly detected. Thus, our results suggest that rampant genetic instability associated with nascent allohexaploidization in wheat likely represents incidental and anomalous phenomena that are confined to by-product individuals inconsequential to the establishment of the newly formed plants toward speciation of T. aestivum; instead, extensive and heritable epigenetic remodeling coupled with preponderant genetic stability is generally associated with nascent wheat allohexaploidy, and therefore, more likely a contributory factor to the speciation event(s).

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“…Whole-genome duplication events have also been assocaited with genome rearrangement, including aberrant recombination, transposable element activation, meiotic/ mitotic defects, and intron expansions and contractions (Hufton and Panopoulou 2009). Evidence currently available suggests that autopolyploids neither experience strong genome restructuring nor extensive reorganization during the first few generations following genome doubling, but that these processes may become more important in the longer term (Parisod et al 2010a, b).…”

Section: Genomic Rearrangement In Polyploid Plantsmentioning

confidence: 99%

“…Given the extensive body of literature that exists on polyploid genomics, this review is not meant to be exhaustive. Please refer to some excellent review articles for more complete and detailed information related to genomics research in polyploid plants (Birchler and Veitia 2010;Chen 2010;Freeling 2009;Hegarty and Hiscock 2008;Hufton and Panopoulou 2009;Parisod et al 2010a, b;Salmon and Ainouche 2010;; Van de Peer et al 2009). …”

Section: Introductionmentioning

confidence: 99%

Genomic aspects of research involving polyploid plants

Yang

Cheng

et al. 2010

Plant Cell Tiss Organ Cult

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Almost all extant plant species have doubled their genomes at least once in their evolutionary histories, resulting in polyploidy which provided a rich genomic resource for evolutionary processes. Moreover, superior polyploid clones have been developed during the process of crop domestication. Polyploid plants generated by evolutionary processes and/or crop domestication have been the intentional or serendipitous focus of research dealing with the dynamics and consequences of genome evolution. One of the new trends in genomics research is to create synthetic polyploid plants which provide materials for studying the initial genomic changes/responses immediately after polyploid formation. Polyploid plants are also used in functional genomics research to study gene expression in a complex genomic background. In this review, we summarize recent progress in genomics research involving ancient, young, and synthetic polyploid plants, with a focus on genome size evolution, genomic diversity, genomic rearrangement, genetic and epigenetic changes in duplicated genes, gene discovery, and comparative genomics. Implications on plant sciences including evolution, functional genomics, and plant breeding are presented. Polyploids will be a focus of genomic research in the future as rapid advances in DNA sequencing technology create unprecedented opportunities for discovering and monitoring genomic and transcriptomic changes. The accumulation of knowledge on polyploid formation, maintenance, and divergence at whole-genome and subgenome levels will not only help plant biologists understand how plants have evolved and diversified, but also assist plant breeders in designing new strategies for crop improvement.

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Polyploidy and genome restructuring: a variety of outcomes

Cited by 63 publications

References 58 publications

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

Megabase Level Sequencing Reveals Contrasted Organization and Evolution Patterns of the Wheat Gene and Transposable Element Spaces

Extensive and Heritable Epigenetic Remodeling and Genetic Stability Accompany Allohexaploidization of Wheat

Genomic aspects of research involving polyploid plants

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