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Gene retention, fractionation and subgenome differences in polyploid plants

Cheng, Feng, Wu, Jian, Cai, Xu, Liang, Jianli, Freeling, Michael, Wang, Xiaowu·2018·Nature Plants
DOI 10.1038/s41477-018-0136-7
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Abstract

All natural plant species are evolved from ancient polyploids. Polyloidization plays an important role in plant genome evolution, species divergence and crop domestication. We review how the pattern of polyploidy within the plant phylogenetic tree has engendered hypotheses involving mass extinctions, lag-times following polyploidy, and epochs of asexuality. Polyploidization has happened repeatedly in plant evolution and, we conclude, is important for crop domestication. Once duplicated, the effect of purifying selection on any one duplicated gene is relaxed, permitting duplicate gene and regulatory element loss (fractionation). We review the general topic of fractionation, and how some gene categories are retained more than others. Several explanations, including neofunctionalization, subfunctionalization and gene product dosage balance, have been shown to influence gene content over time. For allopolyploids, genetic differences between parental lines immediately manifest as subgenome dominance in the wide-hybrid, and persist and propagate for tens of millions of years. While epigenetic modifications are certainly involved in genome dominance, it has been difficult to determine which came first, the chromatin marks being measured or gene expression. Data support the conclusion that genome dominance and heterosis are antagonistic and mechanically entangled; both happen immediately in the synthetic wide-cross hybrid. Also operating in this hybrid are mechanisms of 'paralogue in…

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  • After allotetraploidization, one of the two subgenomes often loses more genes than the other.

    “After allotetraploidization, one of the two subgenomes often loses more genes than the other (Garsmeur et al. 2014; Session et al. 2016; Cheng et al. 2018), although not always (Sun et al. 2017).”

    From An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication (2022) · cites this paper as Cheng et al. 2018

  • Biased gene retention is a character more frequently observed in allopolyploids.

    “In summary, we find that genes were preferentially retained on one duplicated chromosome in a subset of ancestral chromosomes, a character more frequently observed in allopolyploids (Garsmeur et al. 2014; Cheng et al. 2018).”

    From An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication (2022) · cites this paper as Cheng et al. 2018

  • Previous studies have highlighted that allopolyploid subgenomes are often subjected to asymmetrical evolution, whereas in autopolyploids all chromosome copies are highly similar and equally affected by rediploidization.

    “Previous studies have highlighted the contrasting genomic implications of allopolyploidization and autopolyploidization, in which the two subgenomes of allopolyploids are often—although not systematically—subjected to asymmetrical evolution, whereas in autopolyploids all chromosome copies are highly similar and equally affected by the rediploidization process (Garsmeur et al. 2014; Cheng et al. 2”

    From An atlas of fish genome evolution reveals delayed rediploidization following the teleost whole-genome duplication (2022) · cites this paper as Cheng et al. 2018

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Metadata

Authors
Cheng, F., Wu, J., Cai, X., Liang, J., Freeling, M., & Wang, X.
ORCID
Venue
Nature Plants
Publisher
Springer Science and Business Media LLC
Published
2018-04-30
Volume
4
Issue
5
Pages
258-268
ISSN
2055-0278
DOI
10.1038/s41477-018-0136-7
Cited by
398
References
7
Language
en
Licence

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