Abstract:BackgroundDNA methylation is an important feature of plant epigenomes, involved in the formation of heterochromatin and affecting gene expression. Extensive variation of DNA methylation patterns within a species has been uncovered from studies of natural variation. However, the extent to which DNA methylation varies between flowering plant species is still unclear. To understand the variation in genomic patterning of DNA methylation across flowering plant species, we compared single base resolution DNA methylo… Show more
“…Indeed, if the total number of annotated repeat copies in each species is used as a proxy for genome size, similar associations are detectable (Fig. 1c), although the effect sizes are somewhat smaller possibly owing to variation in repeat annotation quality [3]. Fig.…”
Section: Methylome Evolution Over Long Timescalesmentioning
confidence: 81%
“…1a; see Additional file 2: Figure S1 for GMLs measured by HPLC and WGBS-seq). They range from as low as 5% in Theobroma cacao to as high as 43% in Beta vulgaris , with a mean of about 16% [3, 68]. While multiple factors probably contribute to these differences, interspecific variation in genome size is a strong predictor ([3, 68]; see Fig.…”
Section: Methylome Evolution Over Long Timescalesmentioning
Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1127-5) contains supplementary material, which is available to authorized users.
“…Indeed, if the total number of annotated repeat copies in each species is used as a proxy for genome size, similar associations are detectable (Fig. 1c), although the effect sizes are somewhat smaller possibly owing to variation in repeat annotation quality [3]. Fig.…”
Section: Methylome Evolution Over Long Timescalesmentioning
confidence: 81%
“…1a; see Additional file 2: Figure S1 for GMLs measured by HPLC and WGBS-seq). They range from as low as 5% in Theobroma cacao to as high as 43% in Beta vulgaris , with a mean of about 16% [3, 68]. While multiple factors probably contribute to these differences, interspecific variation in genome size is a strong predictor ([3, 68]; see Fig.…”
Section: Methylome Evolution Over Long Timescalesmentioning
Despite major progress in dissecting the molecular pathways that control DNA methylation patterns in plants, little is known about the mechanisms that shape plant methylomes over evolutionary time. Drawing on recent intra- and interspecific epigenomic studies, we show that methylome evolution over long timescales is largely a byproduct of genomic changes. By contrast, methylome evolution over short timescales appears to be driven mainly by spontaneous epimutational events. We argue that novel methods based on analyses of the methylation site frequency spectrum (mSFS) of natural populations can provide deeper insights into the evolutionary forces that act at each timescale.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1127-5) contains supplementary material, which is available to authorized users.
“…Genome-wide methylome studies have been performed in many plant species, such as Arabidopsis, tomato, poplar, soybean, rice, and cassava (2,3,(6)(7)(8)(9)(10)(11). These studies uncovered conserved DNA methylation patterns in genic regions and transposable element regions across plant genomes.…”
DNA methylation plays important roles in many biological processes, such as silencing of transposable elements, imprinting, and regulating gene expression. Many studies of DNA methylation have shown its essential roles in angiosperms (flowering plants). However, few studies have examined the roles and patterns of DNA methylation in gymnosperms. Here, we present genome-wide high coverage single-base resolution methylation maps of Norway spruce (Picea abies) from both needles and somatic embryogenesis culture cells via whole genome bisulfite sequencing. On average, DNA methylation levels of CG and CHG of Norway spruce were higher than most other plants studied. CHH methylation was found at a relatively low level; however, at least one copy of most of the RNA-directed DNA methylation pathway genes was found in Norway spruce, and CHH methylation was correlated with levels of siRNAs. In comparison with needles, somatic embryogenesis culture cells that are used for clonally propagating spruce trees showed lower levels of CG and CHG methylation but higher level of CHH methylation, suggesting that like in other species, these culture cells show abnormal methylation patterns.NA methylation is the most studied stable and heritable epigenetic modification of eukaryotes, and plays important roles in transcriptional regulation and silencing of repetitive elements and transposons (1). In plants, DNA methylation occurs in three contexts, CG, CHG (H is A, T, or C), and CHH (2-4). In Arabidopsis, forward genetic screens have uncovered many components that are required for DNA methylation. For example, the maintenance of CG, CHG, and a subset of CHH DNA methylation is mediated by METHYLTRANSFERASE 1 (MET1), CHRO-MOMETHYLASE (CMT) 3, and CMT2, respectively, whereas the de novo establishment of DNA methylation in all three contexts and the maintenance of the rest of the CHH methylation is mediated by the RNA-directed DNA methylation (RdDM) pathway that employs DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2) (5).Genome-wide methylome studies have been performed in many plant species, such as Arabidopsis, tomato, poplar, soybean, rice, and cassava (2, 3, 6-11). These studies uncovered conserved DNA methylation patterns in genic regions and transposable element regions across plant genomes. However, the DNA methylation landscapes of gymnosperm species that have large genome sizes and high repeat content are relatively understudied. Takuno et al. have demonstrated that genic CHG methylation was correlated with genome size by studying gene body methylation in selected gymnosperm species (12). However, genome-wide high coverage single-base resolution DNA methylation maps of any gymnosperm are still lacking. It is known that transposable elements (TEs) are the main targets of DNA methylation. However, the roles of DNA methylation in TE-abundant gymnosperm species, for example Norway spruce (Picea abies), whose TEs comprise more than 70% of the genome, have not been studied in detail. Using next generation sequencing technology, the genome o...
“…We further included information on the presence of retained paralogs from the Brassicaceae α whole-genome duplication or the β and γ whole-genome duplication (37). We identified a set of genes with gbM in both C. rubella (33) and A. thaliana (17), which are highly likely to also harbor gbM in C. grandiflora. Finally, we included information on polymorphic TEs within 1 kb of genes in the rangewide sample.…”
Understanding the causes of cis-regulatory variation is a long-standing aim in evolutionary biology. Although cis-regulatory variation has long been considered important for adaptation, we still have a limited understanding of the selective importance and genomic determinants of standing cis-regulatory variation. To address these questions, we studied the prevalence, genomic determinants, and selective forces shaping cis-regulatory variation in the outcrossing plant Capsella grandiflora. We first identified a set of 1,010 genes with common cis-regulatory variation using analyses of allele-specific expression (ASE). Population genomic analyses of whole-genome sequences from 32 individuals showed that genes with common cis-regulatory variation (i) are under weaker purifying selection and (ii) undergo less frequent positive selection than other genes. We further identified genomic determinants of cis-regulatory variation. Gene body methylation (gbM) was a major factor constraining cis-regulatory variation, whereas presence of nearby transposable elements (TEs) and tissue specificity of expression increased the odds of ASE. Our results suggest that most common cis-regulatory variation in C. grandiflora is under weak purifying selection, and that gene-specific functional constraints are more important for the maintenance of cis-regulatory variation than genome-scale variation in the intensity of selection. Our results agree with previous findings that suggest TE silencing affects nearby gene expression, and provide evidence for a link between gbM and cis-regulatory constraint, possibly reflecting greater dosage sensitivity of body-methylated genes. Given the extensive conservation of gbM in flowering plants, this suggests that gbM could be an important predictor of cis-regulatory variation in a wide range of plant species.allele-specific expression | fitness effects | purifying selection | positive selection | gene body methylation U nderstanding the causes of regulatory variation is of major importance for many areas of biology and medicine (1). Much interest has centered on cis-regulatory variation, which has long been thought to be particularly important for adaptation (2-5). Like other quantitative traits, cis-regulatory variation is expected to be shaped by the interplay of mutation, selection, and drift. However, the relative importance of these forces remains unclear in most species.Recently, prospects for quantifying cis-regulatory variation have greatly improved, and, as a result, ample heritable cis-regulatory variation has been identified in many species (6); this is resulting in a growing consensus that a large amount of standing cis-regulatory variation is under weak purifying selection (7-9). Clarifying why the impact of purifying selection varies across the genome is therefore important to understand the maintenance of cis-regulatory variation.Variation in the intensity of purifying selection across the genome can result from differences in selective constraint that are due to the specific functions of...
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