Determination of DNA methylation associated with Acer rubrum (red maple) adaptation to metals: analysis of global DNA modifications and methylation-sensitive amplified polymorphism

Reduced representation bisulfite sequencing (RRBS) analysis reveals variation in distribution and levels of DNA methylation in white birch (Betula papyrifera) exposed to nickel

Research in understanding the role of genetics and epigenetics in plant adaptations to environmental stressors such as metals is still in its infancy. The objective of the present study is to assess the effect of nickel on DNA methylation level and distribution in white birch (Betula papyrifera Marshall) using reduced representation bisulfite sequencing (RRBS). The distribution of methylated C sites of each sample revealed that the level of methylation was much higher in CG context varying between 54% and 65%, followed by CHG (24%-31.5%), and then CHH with the methylation rate between 3.3% and 5.2%. The analysis of differentially methylated regions (DMR) revealed that nickel induced both hypermethylation and hypomethylation when compared to water. Detailed analysis showed for the first time that nickel induced a higher level of hypermethylation compared to controls, while potassium triggers a higher level of hypomethylation compared to nickel. Surprisingly, the analysis of the distribution of DMRs revealed that 38%-42% were located in gene bodies, 20%-24% in exon, 19%-20% in intron, 16%-17% in promoters, and 0.03%-0.04% in transcription start site. RRBS was successful in detecting and mapping DMR in plants exposed to nickel.

Decrypting Molecular Mechanisms Involved in Counteracting Copper and Nickel Toxicity in Jack Pine (Pinus banksiana) Based on Transcriptomic Analysis

The remediation of copper and nickel-afflicted sites is challenged by the different physiological effects imposed by each metal on a given plant system. Pinus banksiana is resilient against copper and nickel, providing an opportunity to build a valuable resource to investigate the responding gene expression toward each metal. The objectives of this study were to (1) extend the analysis of the Pinus banksiana transcriptome exposed to nickel and copper, (2) assess the differential gene expression in nickel-resistant compared to copper-resistant genotypes, and (3) identify mechanisms specific to each metal. The Illumina platform was used to sequence RNA that was extracted from seedlings treated with each of the metals. There were 449 differentially expressed genes (DEGs) between copper-resistant genotypes (RGs) and nickel-resistant genotypes (RGs) at a high stringency cut-off, indicating a distinct pattern of gene expression toward each metal. For biological processes, 19.8% of DEGs were associated with the DNA metabolic process, followed by the response to stress (13.15%) and the response to chemicals (8.59%). For metabolic function, 27.9% of DEGs were associated with nuclease activity, followed by nucleotide binding (27.64%) and kinase activity (10.16%). Overall, 21.49% of DEGs were localized to the plasma membrane, followed by the cytosol (16.26%) and chloroplast (12.43%). Annotation of the top upregulated genes in copper RG compared to nickel RG identified genes and mechanisms that were specific to copper and not to nickel. NtPDR, AtHIPP10, and YSL1 were identified as genes associated with copper resistance. Various genes related to cell wall metabolism were identified, and they included genes encoding for HCT, CslE6, MPG, and polygalacturonase. Annotation of the top downregulated genes in copper RG compared to nickel RG revealed genes and mechanisms that were specific to nickel and not copper. Various regulatory and signaling-related genes associated with the stress response were identified. They included UGT, TIFY, ACC, dirigent protein, peroxidase, and glyoxyalase I. Additional research is needed to determine the specific functions of signaling and stress response mechanisms in nickel-resistant plants.

Comparative epigenetic and genetic spatial structure in Mediterranean mountain plants: a multispecies study

Changes in epigenetic states can allow individuals to cope with environmental changes. If such changes are heritable, this may lead to epigenetic adaptation. Thus, it is likely that in sessile organisms such as plants, part of the spatial epigenetic variation found across individuals will reflect the environmental heterogeneity within populations. The departure of the spatial epigenetic structure from the baseline genetic variation can help in understanding the value of epigenetic regulation in species with different breadth of optimal environmental requirements. Here, we hypothesise that in plants with narrow environmental requirements, epigenetic variability should be less structured in space given the lower variability in suitable environmental conditions. We performed a multispecies study that considered seven pairs of congeneric plant species, each encompassing a narrow endemic with habitat specialisation and a widespread species. In three populations per species we used AFLP and methylation-sensitive AFLP markers to characterise the spatial genetic and epigenetic structures. Narrow endemics showed a significantly lower epigenetic than genetic differentiation between populations. Within populations, epigenetic variation was less spatially structured than genetic variation, mainly in narrow endemics. In these species, structural equation models revealed that such pattern was associated to a lack of correlation between epigenetic and genetic information. Altogether, these results show a greater decoupling of the spatial epigenetic variation from the baseline spatial genetic pattern in endemic species. These findings highlight the value of studying genetic and epigenetic spatial variation to better understand habitat specialisation in plants.

A review of metal contamination in seagrasses with an emphasis on metal kinetics and detoxification

Seagrasses are important foundation species in coastal ecosystems, and they provide food and habitat that supports high biodiversity. However, seagrasses are increasingly subjected to anthropogenic disturbances such as metal pollution, which has been implicated as a significant factor driving seagrass losses. There have been several reviews synthesizing the metal concentrations in seagrasses and evaluating their utility as biomonitors for metal pollution in the coastal environment at the local scale. However, the interpretation of metal data in seagrass biomonitors requires a more mechanistic understanding of the processes governing metal bioaccumulation and detoxification. In this review, the progress and trends in metal studies in seagrasses between 1973 and 2022 were analyzed to identify frontier topics in this field. In addition, we tried to (1) analyze and assess the current status of metal contamination in seagrasses on a global scale by incorporating more metal data from tropical and Indo-Pacific seagrasses, (2) summarize the geochemical and biological factors governing metal uptake and loss in seagrasses, and (3) provide an up-to-date understanding of metals' effects on seagrasses and their physiological responses to metal challenges. This review improves our understanding of the highly variable metal concentrations observed in the field.

DNA methylation and histone modifications induced by abiotic stressors in plants

BACKGROUND

A review of research shows that methylation in plants is more complex and sophisticated than in microorganisms and animals. Overall, studies on the effects of abiotic stress on epigenetic modifications in plants are still scarce and limited to few species. Epigenetic regulation of plant responses to environmental stresses has not been elucidated. This study summarizes key effects of abiotic stressors on DNA methylation and histone modifications in plants.

DISCUSSION

Plant DNA methylation and histone modifications in responses to abiotic stressors varied and depended on the type and level of stress, plant tissues, age, and species. A critical analysis of the literature available revealed that 44% of the epigenetic modifications induced by abiotic stressors in plants involved DNA hypomethylation, 40% DNA hypermethylation, and 16% histone modification. The epigenetic changes in plants might be underestimated since most authors used methods such as methylation-sensitive amplification polymorphism (MSAP), High performance liquid chromatography (HPLC), and immunolabeling that are less sensitive compared to bisulfite sequencing and single-base resolution methylome analyses. More over, mechanisms underlying epigenetic changes in plants have not yet been determined since most reports showed only the level or/and distribution of DNA methylation and histone modifications.

CONCLUSIONS

Various epigenetic mechanisms are involved in response to abiotic stressors, and several of them are still unknown. Integrated analysis of the changes in the genome by omic approaches should help to identify novel components underlying mechanisms involved in DNA methylation and histone modifications associated with plant response to environmental stressors.

Genetic and epigenetic changes during the invasion of a cosmopolitan species (Phragmites australis)

While many introduced invasive species can increase genetic diversity through multiple introductions and/or hybridization to colonize successfully in new environments, others with low genetic diversity have to persist by alternative mechanisms such as epigenetic variation. Given that Phragmites australis is a cosmopolitan reed growing in a wide range of habitats and its invasion history, especially in North America, has been relatively well studied, it provides an ideal system for studying the role and relationship of genetic and epigenetic variation in biological invasions. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive (MS) AFLP methods to evaluate genetic and epigenetic diversity and structure in groups of the common reed across its range in the world. Evidence from analysis of molecular variance (AMOVA) based on AFLP and MS-AFLP data supported the previous conclusion that the invasive introduced populations of P. australis in North America were from European and Mediterranean regions. In the Gulf Coast region, the introduced group harbored a high level of genetic variation relative to originating group from its native location, and it showed epigenetic diversity equal to that of the native group, if not higher, while the introduced group held lower genetic diversity than the native. In the Great Lakes region, the native group displayed very low genetic and epigenetic variation, and the introduced one showed slightly lower genetic and epigenetic diversity than the original one. Unexpectedly, AMOVA and principal component analysis did not demonstrate any epigenetic convergence between native and introduced groups before genetic convergence. Our results suggested that intertwined changes in genetic and epigenetic variation were involved in the invasion success in North America. Although our study did not provide strong evidence proving the importance of epigenetic variation prior to genetic, it implied the similar role of stable epigenetic diversity to genetic diversity in the adaptation of P. australis to local environment.

Epigenetic modifications preserve the hyperaccumulator Noccaea caerulescens from Ni geno-toxicity

The Ni hyperaccumulator Noccaea caerulescens has adapted to live in a naturally stressed environment, evolving a complex pattern of traits to cope with adverse conditions. Evidence is accumulating regarding the important role of epigenetic modifications in regulating plant responses to stress. In this study, we present data from the natural "open-field" adaptation of the Ni hyperaccumulator N. caerulescens to serpentine soil and provide the first evidence of the involvement of epigenetic changes in response to the high Ni content present in plant leaves. The alkaline comet assay revealed the integrity of the nuclei of leaf cells of N. caerulescens grown in a Ni-rich environment, while in the non-tolerant Arabidopsis thaliana exposed to Ni, the nuclei were severely damaged. DNA of N. caerulescens plants grown in situ were considerably hyper-methylated compared to A. thaliana plants exposed to Ni. In addition, qRT-PCR revealed that N. caerulescens MET1, DRM2, and HDA8 genes involved in epigenetic DNA and histone modification were up-regulated in the presence of high Ni content in leaves. Such epigenetic modifications may constitute a defense strategy that prevents genome instability and direct damage to the DNA structure by Ni ion, enabling plants to survive in an extreme environment. Further studies will be necessary to analyze in detail the involvement of DNA methylation and other epigenetic mechanisms in the complex process of metal hyperaccumulation and plants' adaptive response. Environ. Mol. Mutagen. 59:464-475, 2018. © 2018 Wiley Periodicals, Inc.

Genetic and epigenetic variations associated with adaptation to heterogeneous habitat conditions in a deciduous shrub

Environmentally induced phenotypic plasticity is thought to play an important role in the adaption of plant populations to heterogeneous habitat conditions, and yet the importance of epigenetic variation as a mechanism of adaptive plasticity in natural plant populations still merits further research. In this study, we investigated populations of Vitex negundo var. heterophylla (Chinese chastetree) from adjacent habitat types at seven sampling sites. Using several functional traits, we detected a significant differentiation between habitat types. With amplified fragment length polymorphisms (AFLP) and methylation-sensitive AFLP (MSAP), we found relatively high levels of genetic and epigenetic diversity but very low genetic and epigenetic differences between habitats within sites. Bayesian clustering showed a remarkable habitat-related differentiation and more genetic loci associated with the habitat type than epigenetic, suggesting that the adaptation to the habitat is genetically based. However, we did not find any significant correlation between genetic or epigenetic variation and habitat using simple and partial Mantel tests. Moreover, we found no correlation between genetic and ecologically relevant phenotypic variation and a significant correlation between epigenetic and phenotypic variation. Although we did not find any direct relationship between epigenetic variation and habitat environment, our findings suggest that epigenetic variation may complement genetic variation as a source of functional phenotypic diversity associated with adaptation to the heterogeneous habitat in natural plant populations.