Transcriptome and methylome analysis of trembling aspen (Populus tremuloides) under nickel stress.

Abstract

Nickel is an essential micronutrient required at low concentrations for adequate plant growth and health. However, excessive amounts of bioavailable nickel ions in the surrounding soil can result in plant toxicity symptoms. Plants have evolved heavy metal tolerance mechanisms to adapt and cope with this abiotic stressor. The main objectives of the present research were to 1) further characterize the P. tremuloides transcriptome 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing, 3) determine the effects of different nickel concentrations on P. tremuloides gene expression and, 4) assess global methylation levels in P. tremuloides under nickel stress. Trembling aspen (Populus tremuloides) seedlings treated with varying concentrations of nickel nitrates (150 mg Ni / 1 kg of dry soil, 800 mg / kg, and 1, 600 mg / kg) showed phenotypic segregation of physical toxicity symptoms at the highest nickel dose of 1, 600 mg / kg. This study revealed that a metal transport protein (Potrs038704g29436 – ATOX1-related copper transport) was among the top upregulated genes in resistant genotypes when compared to susceptible plants. Other upregulated genes associated with abiotic stress were identified including a Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase. Overall, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. The results of the dosage analysis suggested that the 800 mg / kg nickel dose is the threshold at which an early abiotic stress response may be triggered as seen by the highly upregulated LEA protein and two calcium binding proteins when compared to water. The cluster of genes that had increased gene expression with increasing nickel dose also had multiple enriched GO terms related to heavy metal and abiotic stress including metal ion transport, antioxidant activity, photosynthesis, and ribosomal activity. Lastly, the initial screen for potential global methylation differences between nickel-resistant genotypes and water showed no significant difference in overall methylation levels. However, the potassium nitrate control for the 1,600 mg / kg dose did show significantl hypomethylation in comparison to the nickel-treated or water control samples. Future experiments could use targetspecific methylation and gene expression assays to investigate the biological significance of the heavy metal stress candidate genes identified in this top-down study in trembling aspen. Understanding the heavy metal tolerance mechanisms and responses used by hardy species like trembling aspen is important for environment bioremediation and maintenance of healthy ecosystems.