Epigenetics and plant genome evolution

Díez, Concepción M.; Roessler, Kyria; Gaut, Brandon S.

doi:10.1016/j.pbi.2013.11.017

Cited by 90 publications

(65 citation statements)

References 68 publications

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“…Genomic analyses of Arabidopsis provided evidence for an evolutionary trade-off between silencing of transposons and maintaining expression for nearby genes (Hollister and Gaut, 2009;Diez et al, 2014). There is evidence for spreading of DNA methylation from transposons to adjacent sequences in Arabidopsis (Ahmed et al, 2011) and maize (Eichten et al, 2012).…”

Section: Living With a New Genome Structurementioning

confidence: 99%

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Springer

Lisch

2016

Plant Cell

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ORCID IDs: 0000-0002-7301-4759 (N.M.S.); 0000-0003-3232-9479 (Q.L.)Flowering plants have strikingly distinct genomes, although they contain a similar suite of expressed genes. The diversity of genome structures and organization is largely due to variation in transposable elements (TEs) and whole-genome duplication (WGD) events. We review evidence that chromatin modifications and epigenetic regulation are intimately associated with TEs and likely play a role in mediating the effects of WGDs. We hypothesize that the current structure of a genome is the result of various TE bursts and WGDs and it is likely that the silencing mechanisms and the chromatin structure of a genome have been shaped by these events. This suggests that the specific mechanisms targeting chromatin modifications and epigenomic patterns may vary among different species. Many crop species have likely evolved chromatin-based mechanisms to tolerate silenced TEs near actively expressed genes. These interactions of heterochromatin and euchromatin are likely to have important roles in modulating gene expression and variability within species.

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Section: Living With a New Genome Structurementioning

confidence: 99%

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Springer

Lisch

2016

Plant Cell

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“…TEs and other heterochromatic sequences are methylated in all three contexts, whereas gene body methylation occurs primarily at CG sites (Diez et al, 2014). Unlike Arabidopsis, numerous genes in both soybean and common bean were found to contain densely methylated TE insertions that could complicate analysis.…”

Section: Cg Body Methylation Was High In Transcriptionally Active Sinmentioning

confidence: 99%

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

et al. 2015

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Soybean (Glycine max) and common bean (Phaseolus vulgaris) share a paleopolyploidy (whole-genome duplication [WGD]) event, approximately 56.5 million years ago, followed by a genus Glycine-specific polyploidy, approximately 10 million years ago. Cytosine methylation is an epigenetic mark that plays an important role in the regulation of genes and transposable elements (TEs); however, the role of DNA methylation in the fate/evolution of genes following polyploidy and speciation has not been fully explored. Whole-genome bisulfite sequencing was used to produce nucleotide resolution methylomes for soybean and common bean. We found that, in soybean, CG body-methylated genes were abundant in WGD genes, which were, on average, more highly expressed than single-copy genes and had slower evolutionary rates than unmethylated genes, suggesting that WGD genes evolve more slowly than single-copy genes. CG body-methylated genes were also enriched in shared single-copy genes (single copy in both species) that may be responsible for the broad and high expression patterns of this class of genes. In addition, diverged methylation patterns in non-CG contexts between paralogs were due mostly to TEs in or near genes, suggesting a role for TEs and non-CG methylation in regulating gene expression post polyploidy. Reference methylomes for both soybean and common bean were constructed, providing resources for investigating epigenetic variation in legume crops. Also, the analysis of methylation patterns of duplicated and single-copy genes has provided insights into the functional consequences of polyploidy and epigenetic regulation in plant genomes.

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“…Many examples of segregating epimutations have been documented in experimental and wild populations of plants and in some cases contribute to heritable variation in phenotypes independently of DNA sequence variation (4,5). These observations have led to much speculation about the role of DNA methylation in plant evolution (6)(7)(8), and its potential in breeding programs (9). In the model plant Arabidopsis thaliana, spontaneous methylation changes at CG dinucleotides accumulate in a rapid but nonlinear fashion over generations (2,3,10), thus pointing to high forward-backward epimutation rates (11).…”

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confidence: 99%

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

Graaf

Wardenaar

Neumann

et al. 2015

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

238

278

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Stochastic changes in cytosine methylation are a source of heritable epigenetic and phenotypic diversity in plants. Using the model plant Arabidopsis thaliana, we derive robust estimates of the rate at which methylation is spontaneously gained (forward epimutation) or lost (backward epimutation) at individual cytosines and construct a comprehensive picture of the epimutation landscape in this species. We demonstrate that the dynamic interplay between forward and backward epimutations is modulated by genomic context and show that subtle contextual differences have profoundly shaped patterns of methylation diversity in A. thaliana natural populations over evolutionary timescales. Theoretical arguments indicate that the epimutation rates reported here are high enough to rapidly uncouple genetic from epigenetic variation, but low enough for new epialleles to sustain long-term selection responses. Our results provide new insights into methylome evolution and its population-level consequences.epigenetics | epimutation | DNA methylation | evolution | Arabidopsis P lant genomes make extensive use of cytosine methylation to control the expression of transposable elements (TEs) and genes (1). Despite its tight regulation, methylation losses or gains at individual cytosines or clusters of cytosines can emerge spontaneously, in an event termed "epimutation" (2, 3). Many examples of segregating epimutations have been documented in experimental and wild populations of plants and in some cases contribute to heritable variation in phenotypes independently of DNA sequence variation (4, 5). These observations have led to much speculation about the role of DNA methylation in plant evolution (6-8), and its potential in breeding programs (9). In the model plant Arabidopsis thaliana, spontaneous methylation changes at CG dinucleotides accumulate in a rapid but nonlinear fashion over generations (2,3,10), thus pointing to high forward-backward epimutation rates (11). Precise estimates of these rates are necessary to be able to quantify the long-term dynamics of epigenetic variation under laboratory or natural conditions, and to understand the molecular mechanisms that drive methylome evolution (12-14). Here we combine theoretical modeling with high-resolution methylome analysis of multiple independent A. thaliana mutation accumulation (MA) lines (15), including measurements of methylation changes in continuous generations, to obtain robust estimates of forward and backward epimutation rates. ResultsWe joined whole-genome MethylC-seq (16) data from two earlier MA studies (2, 3) with extensive multigenerational MethylC-seq measurements from three additional MA lines (Fig. 1A and SI Appendix, Tables S1-S6). The first of these new MA lines (MA1 3) was propagated for 30 generations and includes measurements for 13 (nearly) consecutive generations (Fig. 1A). The other two MA lines (MA2 3) were propagated for 17 generations and were measured every four generations on average (Fig. 1A). These new data therefore allowed us to track epimutation...

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Epigenetics and plant genome evolution

Cited by 90 publications

References 68 publications

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

Creating Order from Chaos: Epigenome Dynamics in Plants with Complex Genomes

A Comparative Epigenomic Analysis of Polyploidy-Derived Genes in Soybean and Common Bean

Rate, spectrum, and evolutionary dynamics of spontaneous epimutations

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