Dataset Information

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

ABSTRACT: Red maple (Acer rubum), a common deciduous tree species in Northern Ontario, has shown resistance to soil metal contamination. Previous reports have indicated that this plant does not accumulate metals in its tissue. However, low level of nickel and copper corresponding to the bioavailable levels in contaminated soils in Northern Ontario causes severe physiological damages. No differentiation between metal-contaminated and uncontaminated populations has been reported based on genetic analyses. The main objective of this study was to assess whether DNA methylation is involved in A. rubrum adaptation to soil metal contamination. Global cytosine and methylation-sensitive amplified polymorphism (MSAP) analyses were carried out in A. rubrum populations from metal-contaminated and uncontaminated sites. The global modified cytosine ratios in genomic DNA revealed a significant decrease in cytosine methylation in genotypes from a metal-contaminated site compared to uncontaminated populations. Other genotypes from a different metal-contaminated site within the same region appear to be recalcitrant to metal-induced DNA alterations even ?30 years of tree life exposure to nickel and copper. MSAP analysis showed a high level of polymorphisms in both uncontaminated (77%) and metal-contaminated (72%) populations. Overall, 205 CCGG loci were identified in which 127 were methylated in either outer or inner cytosine. No differentiation among populations was established based on several genetic parameters tested. The variations for nonmethylated and methylated loci were compared by analysis of molecular variance (AMOVA). For methylated loci, molecular variance among and within populations was 1.5% and 13.2%, respectively. These values were low (0.6% for among populations and 5.8% for within populations) for unmethylated loci. Metal contamination is seen to affect methylation of cytosine residues in CCGG motifs in the A. rubrum populations that were analyzed.

SUBMITTER: Kim NS

PROVIDER: S-EPMC4983588 | biostudies-literature | 2016 Aug

REPOSITORIES: biostudies-literature

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

Kim Nam-Soo NS Im Min-Ji MJ Nkongolo Kabwe K

Ecology and evolution 20160722 16

Red maple (Acer rubum), a common deciduous tree species in Northern Ontario, has shown resistance to soil metal contamination. Previous reports have indicated that this plant does not accumulate metals in its tissue. However, low level of nickel and copper corresponding to the bioavailable levels in contaminated soils in Northern Ontario causes severe physiological damages. No differentiation between metal-contaminated and uncontaminated populations has been reported based on genetic analyses. T ...[more]

PMID: 27547351

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Project description:The impacts of urbanization, such as urban heat island (UHI) and nutrient loads, can influence tree function through altered physiology and metabolism and stress response, which has implications for urban forest health in cities across the world. Our goal was to compare growth-stimulating and stress-mitigating acclimation patterns of red maple (Acer rubrum) trees in deciduous forests embedded in a small (Newark, DE, US) and a large (Philadelphia, PA, US) city. The study was conducted in a long-term urban forest network on seventy-nine mature red maple trees spanning ten forests across Newark and Philadelphia. We hypothesized that red maples in Philadelphia forests compared to Newark forests will be healthier and more acclimated to warmer temperatures, elevated CO2 concentrations and reactive nitrogen (Nr) deposition, and higher nutrient/heavy metal loads. Therefore, these red maples will have higher foliar pigments, nutrients, and stress-indicating elements, enriched ?15N isotopes and increased free polyamines and amino acids to support a growth-stimulating and stress-induced response to urbanization. Our results indicate red maples are potentially growth-stimulated and stress-acclimated in Philadelphia forests experiencing a greater magnitude of urban intensity. Red maples in Philadelphia forests contained higher concentrations of foliar chlorophyll, %N, ?15N, and nutrients than those in Newark forests. Similarly, lower foliar magnesium and manganese, and higher foliar zinc, cadmium, lead, and aluminum reflected the difference in soil biogeochemistry in Philadelphia forests. Accumulation patterns of foliar free amino acids, polyamines, phosphorous, and potassium ions in red maples in Philadelphia forests shows a reallocation in cellular metabolism and nutrient uptake pathways responsible for physiological acclimation. Our results suggest the approach used here can serve as a model for investigating 'plant physiology' and the use of urban trees as a biomonitor of the impacts of 'urban pollution' on urban forests. The results suggest that cellular oxidative stress in trees caused by pollutant uptake is mitigated by the accumulation of free amino acids, polyamines, and nutrients in a larger city. Our study provides a framework for determining whether trees respond to complex urban environments through stress memory and/or acclimation.

Project description:Knowledge of regulation of genes associated with metal resistance in higher plants is very limited. Many plant species have developed different genetic mechanisms and metabolic pathways to cope with metal toxicity. The main objectives of this study were to 1) assess gene expression dynamics of A. rubrum in response to nickel (Ni) stress and 2) describe gene function based on ontology. Certified A. rubrum genotypes were treated with 1,600 mg of Ni per 1 Kg of soil corresponding to a soil total nickel content in a metal-contaminated region in Ontario, Canada. Nickel resistant and susceptible genotypes were selected and used for transcriptome analysis. Overall, 223,610,443 bases were generated. Trinity reads were assembled to trinity transcripts. The transcripts were mapped to protein sequences and after quality controls and appropriate trimmings, 66,783 annotated transcripts were selected as expressed among the libraries. The study reveals that nickel treatment at a high dose of 1,600 mg/kg triggers regulation of several genes. When nickel-resistant genotypes were compared to water controls, 6,263 genes were upregulated and 3,142 were downregulated. These values were 3,308 and 2,176, respectively, when susceptible genotypes were compared to water control. The coping mechanism of A. rubrum to Ni toxicity was elucidated. Upregulation of genes associated with transport in cytosol was prevalent in resistant genotypes compared to controls while upregulation of genes associated with translation in the ribosome was higher in susceptible genotypes when compared to water. The analysis revealed no major gene associated with Ni resistance in A. rubrum. Overall, the results of this study suggest that the genetic mechanism controlling the resistance of this species to nickel is controlled by genes with limited expression. The subtle differences between resistant and susceptible genotypes in gene regulation were detected using water-treated genotypes as references.

Dataset Information

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

Publications

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

Similar Datasets

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