Intertwined evolution of plant epigenomes and genomes

The methylome of clonal seagrass shoots shows age-associated variation and differentiation of roots from other tissues

Factors influencing variance of DNA methylation in vegetatively reproducing plants, both terrestrial plants and aquatic seagrasses, is just beginning to be understood. Improving our knowledge of these mechanisms will increase understanding of transgenerational epigenetics in plant clones, of the relationship between DNA methylation and seagrass development, and of the drivers of epigenetic variation, which may underly acclimation in clonally reproducing plants. Here, we sampled leaves, rhizomes and roots of three physically and spatially separated ramet sections from a clonally propagated field of the seagrass Zostera marina. Using reduced methylome sequencing, we studied variations in the methylome of seagrass Zostera marina between the sampled tissue types and across age groups. Our analysis of ramets of different ages showed variations in methylation between older and younger samples in both specific methylation patterns and global methylation levels. Our analysis of tissue types showed a marked differentiation of the roots from the rhizomes and leaves, which showed more similar methylation patterns. These findings are in agreement with the strong connection of DNA methylation and plant development and tissue differentiation. We also suggest an effect of differential environmental exposures on the methylome of the younger versus the older ramets due to the forming of molecular stress memories.

Genome-Wide Identification and Characterization of SNPs and InDels of Capsicum annuum var. glabriusculum from Mexico Based on Whole Genome Sequencing

Capsicum annuum var. glabriusculum is an economically important horticultural crop and is considered the wild genetic ancestor of chili peppers. The distribution range extends from southern North America, through Central America, to South America. Approximately 226 million 150 paired-end reads were generated from CHMX_Ch1 (a C. annuum from Chihuahua, Mexico). To compare with the CHMX_Ch1 genome, high-quality reads from QO (a C. annuum from Querétaro, Mexico) were downloaded from the NCBI database. A total of 210,324 variants were detected in CHMX_Ch1, whereas 169,718 variants were identified in QO, all compared to the domesticated C. annuum reference genome, UCD10Xv1.1. This comprised 203,990 SNPs and 6334 InDels in CHMX_Ch1 and 164,955 SNPs and 4763 InDels in QO. The variants with high and moderate impact were identified as missense, splice acceptor, splice donor, start lost, stop gain, stop lost, frameshift, insertion, and deletion effects. The candidate genes with the highest fold enrichment values among the SNPs were predominantly involved in gene regulation and metabolic processes. InDels were associated with nuclear and transcriptional regulator activity in both genomes. Overall, a greater number of variants were found in CHMX_Ch1 compared to QO. This study provides knowledge of the principal functions associated with high- and moderate-impact variants and supplies a resource for further investigations of the genetic characteristics of these chiltepin peppers.

Cause or effect: Probing the roles of epigenetics in plant development and environmental responses

Epigenetic modifications are inheritable, reversible changes that control gene expression without altering the DNA sequence itself. Recent advances in epigenetic and sequencing technologies have revealed key regulatory regions in genes with multiple epigenetic changes. However, causal associations between epigenetic changes and physiological events have rarely been examined. Epigenome editing enables alterations to the epigenome without changing the underlying DNA sequence. Modifying epigenetic information in plants has important implications for causality assessment of the epigenome. Here, we briefly review tools for selectively interrogating the epigenome. We highlight promising research on site-specific DNA methylation and histone modifications and propose future research directions to more deeply investigate epigenetic regulation, including cause-and-effect relationships between epigenetic modifications and the development/environmental responses of Arabidopsis thaliana.

The evolutionary consequences of interactions between the epigenome, the genome and the environment

The epigenome is the suite of interacting chemical marks and molecules that helps to shape patterns of development, phenotypic plasticity and gene regulation, in part due to its responsiveness to environmental stimuli. There is increasing interest in understanding the functional and evolutionary importance of this sensitivity under ecologically realistic conditions. Observations that epigenetic variation abounds in natural populations have prompted speculation that it may facilitate evolutionary responses to rapid environmental perturbations, such as those occurring under climate change. A frequent point of contention is whether epigenetic variants reflect genetic variation or are independent of it. The genome and epigenome often appear tightly linked and interdependent. While many epigenetic changes are genetically determined, the converse is also true, with DNA sequence changes influenced by the presence of epigenetic marks. Understanding how the epigenome, genome and environment interact with one another is therefore an essential step in explaining the broader evolutionary consequences of epigenomic variation. Drawing on results from experimental and comparative studies carried out in diverse plant and animal species, we synthesize our current understanding of how these factors interact to shape phenotypic variation in natural populations, with a focus on identifying similarities and differences between taxonomic groups. We describe the main components of the epigenome and how they vary within and between taxa. We review how variation in the epigenome interacts with genetic features and environmental determinants, with a focus on the role of transposable elements (TEs) in integrating the epigenome, genome and environment. And we look at recent studies investigating the functional and evolutionary consequences of these interactions. Although epigenetic differentiation in nature is likely often a result of drift or selection on stochastic epimutations, there is growing evidence that a significant fraction of it can be stably inherited and could therefore contribute to evolution independently of genetic change.

The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary studies. Poplars, among the world's most widely distributed and cultivated trees, exhibit extensive phenotypic diversity and environmental adaptability. In this study, we present a genus-level super-pangenome comprising 19 Populus genomes, revealing the likely pivotal role of private genes in facilitating local environmental and climate adaptation. Through the integration of pangenomes with transcriptomes, methylomes, and chromatin accessibility mapping, we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures, notably CG methylation in gene-body regions. Further comparative genomic analyses have enabled the identification of 142 202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive divergence. We have experimentally validated a ∼180-bp presence/absence variant affecting the expression of the CUC2 gene, crucial for leaf serration formation. Finally, we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome (http://www.populus-superpangenome.com). Together, the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

The unusual predominance of maintenance DNA methylation in Spirodela polyrhiza

Duckweeds are among the fastest reproducing plants, able to clonally divide at exponential rates. However, the genetic and epigenetic impact of clonality on plant genomes is poorly understood. 5-methylcytosine (5mC) is a modified base often described as necessary for the proper regulation of certain genes and transposons and for the maintenance of genome integrity in plants. However, the extent of this dogma is limited by the current phylogenetic sampling of land plant species diversity. Here we analyzed DNA methylomes, small RNAs, mRNA-seq, and H3K9me2 histone modification for Spirodela polyrhiza. S. polyrhiza has lost highly conserved genes involved in de novo methylation of DNA at sites often associated with repetitive DNA, and within genes, however, symmetrical DNA methylation and heterochromatin are maintained during cell division at certain transposons and repeats. Consequently, small RNAs that normally guide methylation to silence repetitive DNA like retrotransposons are diminished. Despite the loss of a highly conserved methylation pathway, and the reduction of small RNAs that normally target repetitive DNA, transposons have not proliferated in the genome, perhaps due in part to the rapid, clonal growth lifestyle of duckweeds.

Profiling genome-wide methylation in two maples: Fine-scale approaches to detection with nanopore technology

DNA methylation is critical to the regulation of transposable elements and gene expression and can play an important role in the adaptation of stress response mechanisms in plants. Traditional methods of methylation quantification rely on bisulfite conversion that can compromise accuracy. Recent advances in long-read sequencing technologies allow for methylation detection in real time. The associated algorithms that interpret these modifications have evolved from strictly statistical approaches to Hidden Markov Models and, recently, deep learning approaches. Much of the existing software focuses on methylation in the CG context, but methylation in other contexts is important to quantify, as it is extensively leveraged in plants. Here, we present methylation profiles for two maple species across the full range of 5mC sequence contexts using Oxford Nanopore Technologies (ONT) long-reads. Hybrid and reference-guided assemblies were generated for two new Acer accessions: Acer negundo (box elder; 65x ONT and 111X Illumina) and Acer saccharum (sugar maple; 93x ONT and 148X Illumina). The ONT reads generated for these assemblies were re-basecalled, and methylation detection was conducted in a custom pipeline with the published Acer references (PacBio assemblies) and hybrid assemblies reported herein to generate four epigenomes. Examination of the transposable element landscape revealed the dominance of LTR Copia elements and patterns of methylation associated with different classes of TEs. Methylation distributions were examined at high resolution across gene and repeat density and described within the broader angiosperm context, and more narrowly in the context of gene family dynamics and candidate nutrient stress genes.

BSXplorer: analytical framework for exploratory analysis of BS-seq data

BACKGROUND

Bisulfite sequencing detects and quantifies DNA methylation patterns, contributing to our understanding of gene expression regulation, genome stability maintenance, conservation of epigenetic mechanisms across divergent taxa, epigenetic inheritance and, eventually, phenotypic variation. Graphical representation of methylation data is crucial in exploring epigenetic regulation on a genome-wide scale in both plants and animals. This is especially relevant for non-model organisms with poorly annotated genomes and/or organisms where genome sequences are not yet assembled on chromosome level. Despite being a technology of choice to profile DNA methylation for many years now there are surprisingly few lightweight and robust standalone tools available for efficient graphical analysis of data in non-model systems. This significantly limits evolutionary studies and agrigenomics research. BSXplorer is a tool specifically developed to fill this gap and assist researchers in explorative data analysis and in visualising and interpreting bisulfite sequencing data more easily.

RESULTS

BSXplorer provides in-depth graphical analysis of sequencing data encompassing (a) profiling of methylation levels in metagenes or in user-defined regions using line plots and heatmaps, generation of summary statistics charts, (b) enabling comparative analyses of methylation patterns across experimental samples, methylation contexts and species, and (c) identification of modules sharing similar methylation signatures at functional genomic elements. The tool processes methylation data quickly and offers API and CLI capabilities, along with the ability to create high-quality figures suitable for publication.

CONCLUSIONS

BSXplorer facilitates efficient methylation data mining, contrasting and visualization, making it an easy-to-use package that is highly useful for epigenetic research.

How do threatened plant species with low genetic diversity respond to environmental stress? Insights from comparative conservation epigenomics and phenotypic plasticity

Many threatened plants have low genetic diversity, which may reduce their capacity for genetically based adaptation, increasing their extinction risk. Non-genetic variation (e.g. epigenomic modifications such as DNA methylation) and plasticity may facilitate the persistence of threatened plants, yet are rarely incorporated into conservation assessments. We present a case study investigating variation and plasticity in DNA methylation and phenotypic traits in four genetically depauperate species of Leavenworthia (Brassicaceae), including one widespread species and one asexual, threatened species. We grew individuals from several maternal lines and populations per species in contrasting watering treatments, measured phenotypic traits and analysed DNA methylation using whole-genome bisulphite sequencing. We addressed four questions: (1) How do patterns of DNA methylation differ within and among species? (2) Within species, how do phenotypic traits and patterns of DNA methylation vary in response to drought? (3) Does variation in DNA methylation correspond to phenotypic variation? (4) What are the implications for conservation? We found that taxa were epigenomically distinct and that each species exhibited variation in DNA methylation among populations that could be relevant for conservation. Within species, the DNA methylation response to environmental stress corresponded to its phenotypic response. Species differed in their DNA methylation and phenotypic responses to environmental stress, with the extent of plasticity possibly related to species geographic range size. We also found phenotypic and DNA methylation variation in the asexual, threatened species that may be relevant for conservation. Our results suggest that variation in DNA methylation may promote the persistence of genetically depauperate threatened plants, highlighting its potential as a novel conservation target to reduce extinction risk.

SlSAMS1 enhances salt tolerance through regulation DNA methylation of SlGI in tomato

S-adenosylmethionine (SAM), which is synthesized from methionine and ATP catalyzed by S-adenosylmethionine synthetase (SAMS), is an important methyl donor in plants. SAMS and DNA methylation play an important role in the plant response to abiotic stresses. Previous studies have shown that SAMS improves salt tolerance in tomato plants, but it is not clear whether the DNA methylation pathway mediates SAMS-induced salt tolerance. This study confirmed that SlSAMS1-overexpressing plants exhibited improved salt tolerance. Through whole-genome bisulfite sequencing (WGBS) and transcriptome sequencing (RNA-seq) analysis, the study screened the circadian rhythm pathway and identified the gene SlGI in this pathway, which was regulated by SlSAMS1. The gene body region of SlGI, the core gene of the circadian rhythm pathway, was hypermethylated in SlSAMS1-overexpressing plants, and its expression level was significantly increased. Furthermore, the SlGI-overexpressing plants showed higher salt tolerance, less reduction in plant height and fresh weight, lower electrolyte leakage, malondialdehyde and H2O2 content, and higher antioxidant enzyme activity compared to wild type plants. Therefore, SlSAMS1-overexpressing plants regulated significant changes in CHG-type methylation sites of the SlGI gene body and its expression levels, leading to an enhanced salt tolerance of tomato plants.

Advances in Plant Epigenome Editing Research and Its Application in Plants

Plant epistatic regulation is the DNA methylation, non-coding RNA regulation, and histone modification of gene sequences without altering the genome sequence, thus regulating gene expression patterns and the growth process of plants to produce heritable changes. Epistatic regulation in plants can regulate plant responses to different environmental stresses, regulate fruit growth and development, etc. Genome editing can effectively improve plant genetic efficiency by targeting the design and efficient editing of genome-specific loci with specific nucleases, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALEN), and clustered regularly interspaced short palindromic repeats/CRISPR-associated 9 (CRISPR/Cas9). As research progresses, the CRISPR/Cas9 system has been widely used in crop breeding, gene expression, and epistatic modification due to its high editing efficiency and rapid translation of results. In this review, we summarize the recent progress of CRISPR/Cas9 in epigenome editing and look forward to the future development direction of this system in plant epigenetic modification to provide a reference for the application of CRISPR/Cas9 in genome editing.

Epigenetic and Genetic Population Structure is Coupled in a Marine Invertebrate

Delineating the relative influence of genotype and the environment on DNA methylation is critical for characterizing the spectrum of organism fitness as driven by adaptation and phenotypic plasticity. In this study, we integrated genomic and DNA methylation data for two distinct Olympia oyster (Ostrea lurida) populations while controlling for within-generation environmental influences. In addition to providing the first characterization of genome-wide DNA methylation patterns in the oyster genus Ostrea, we identified 3,963 differentially methylated loci between populations. Our results show a clear coupling between genetic and epigenetic patterns of variation, with 27% of variation in interindividual methylation differences explained by genotype. Underlying this association are both direct genetic changes in CpGs (CpG-SNPs) and genetic variation with indirect influence on methylation (mQTLs). When comparing measures of genetic and epigenetic population divergence at specific genomic regions this relationship surprisingly breaks down, which has implications for the methods commonly used to study epigenetic and genetic coupling in marine invertebrates.

Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements

Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression patterns. Precise identification of functional TF binding sites in time and space not only will revolutionize our understanding of regulatory networks governing cell fate decisions but is also instrumental to uncover how genetic variations cause morphological diversity or disease. In this review, we discuss recent advances in mapping TF binding sites and characterizing the various parameters underlying the complexity of binding site recognition by TFs.

Plant DNA Methylation Responds to Nutrient Stress

Nutrient stress as abiotic stress has become one of the important factors restricting crop yield and quality. DNA methylation is an essential epigenetic modification that can effectively regulate genome stability. Exploring DNA methylation responses to nutrient stress could lay the foundation for improving plant tolerance to nutrient stress. This article summarizes the plant DNA methylation patterns, the effects of nutrient stress, such as nitrogen, phosphorus, iron, zinc and sulfur stress, on plant DNA methylation and research techniques for plant DNA methylation, etc. Our discussion provides insight for further research on epigenetics response to nutrient stress in the future.

Histone H1 prevents non-CG methylation-mediated small RNA biogenesis in Arabidopsis heterochromatin

Flowering plants utilize small RNA (sRNA) molecules to guide DNA methyltransferases to genomic sequences. This RNA-directed DNA methylation (RdDM) pathway preferentially targets euchromatic transposable elements. However, RdDM is thought to be recruited by methylation of histone H3 at lysine 9 (H3K9me), a hallmark of heterochromatin. How RdDM is targeted to euchromatin despite an affinity for H3K9me is unclear. Here, we show that loss of histone H1 enhances heterochromatic RdDM, preferentially at nucleosome linker DNA. Surprisingly, this does not require SHH1, the RdDM component that binds H3K9me. Furthermore, H3K9me is dispensable for RdDM, as is CG DNA methylation. Instead, we find that non-CG methylation is specifically associated with sRNA biogenesis, and without H1 sRNA production quantitatively expands to non-CG-methylated loci. Our results demonstrate that H1 enforces the separation of euchromatic and heterochromatic DNA methylation pathways by excluding the sRNA-generating branch of RdDM from non-CG-methylated heterochromatin.

Cells adapt to different roles by turning different groups of genes on and off. One way cells control which genes are on or off is by creating regions of active and inactive DNA, which are created and maintained by different groups of proteins. Genes in active DNA regions can be turned on, while genes in inactive regions are switched off or silenced. Silenced DNA regions also turn off ‘transposable elements’: pieces of DNA that can copy themselves and move to other regions of the genome if they become active. Transposons can be dangerous if they are activated, because they can disrupt genes or regulatory sequences when they move.

There are different types of active and inactive DNA, but it is not always clear why these differences exist, or how they are maintained over time. In plants, such as the commonly-studied weed Arabidopsis thaliana, there are two types of inactive DNA, called E and H, that can silence transposons. In both types, DNA has small chemicals called methyl groups attached to it, which help inactivate the DNA. Type E DNA is methylated by a process called RNA-directed DNA methylation (RdDM), but RdDM is rarely seen in type H DNA.

Choi, Lyons and Zilberman showed that RdDM is attracted to E and H regions by previously existing methylated DNA. However, in the H regions, a protein called histone H1 blocks RdDM from attaching methyl groups. This helps focus RdDM onto E regions where it is most needed, because E regions contain the types of transposons RdDM is best suited to silence.

When Choi, Lyons and Zilberman examined genetically modified A. thaliana plants that do not produce histone H1, they found that RdDM happened in both E and H regions. There are many more H regions than E regions, so stretching RdDM across both made it less effective at silencing DNA.

This work shows how different DNA silencing processes are focused onto specific genetic regions, helping explain why there are different types of active and inactive DNA within cells. RdDM has been studied as a way to affect crop growth and yield by altering DNA methylation. These results may help such studies by explaining how RdDM is naturally targeted.

The Dynamism of Transposon Methylation for Plant Development and Stress Adaptation

Plant development processes are regulated by epigenetic alterations that shape nuclear structure, gene expression, and phenotypic plasticity; these alterations can provide the plant with protection from environmental stresses. During plant growth and development, these processes play a significant role in regulating gene expression to remodel chromatin structure. These epigenetic alterations are mainly regulated by transposable elements (TEs) whose abundance in plant genomes results in their interaction with genomes. Thus, TEs are the main source of epigenetic changes and form a substantial part of the plant genome. Furthermore, TEs can be activated under stress conditions, and activated elements cause mutagenic effects and substantial genetic variability. This introduces novel gene functions and structural variation in the insertion sites and primarily contributes to epigenetic modifications. Altogether, these modifications indirectly or directly provide the ability to withstand environmental stresses. In recent years, many studies have shown that TE methylation plays a major role in the evolution of the plant genome through epigenetic process that regulate gene imprinting, thereby upholding genome stability. The induced genetic rearrangements and insertions of mobile genetic elements in regions of active euchromatin contribute to genome alteration, leading to genomic stress. These TE-mediated epigenetic modifications lead to phenotypic diversity, genetic variation, and environmental stress tolerance. Thus, TE methylation is essential for plant evolution and stress adaptation, and TEs hold a relevant military position in the plant genome. High-throughput techniques have greatly advanced the understanding of TE-mediated gene expression and its associations with genome methylation and suggest that controlled mobilization of TEs could be used for crop breeding. However, development application in this area has been limited, and an integrated view of TE function and subsequent processes is lacking. In this review, we explore the enormous diversity and likely functions of the TE repertoire in adaptive evolution and discuss some recent examples of how TEs impact gene expression in plant development and stress adaptation.

The epigenome and beyond: How does non-genetic inheritance change our view of evolution?

Evidence from across the tree of life suggests that epigenetic inheritance is more common than previously thought. If epigenetic inheritance is indeed as common as the data suggest, this finding has potentially important implications for evolutionary theory and our understanding of how evolution and adaptation progress. However, we currently lack an understanding of how common various epigenetic inheritance types are, and how they impact phenotypes. In this perspective, we review the open questions that need to be addressed to fully integrate epigenetic inheritance into evolutionary theory and to develop reliable predictive models for phenotypic evolution. We posit that addressing these challenges will require the collaboration of biologists from different disciplines and a focus on the exploration of data and phenomena without preconceived limits on potential mechanisms or outcomes.