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

Abstract

Plants have evolved heavy metal tolerance mechanisms to adapt and cope with nickel (Ni) toxicity. Decrypting whole gene expression of Trembling Aspen (Pinus tremuloides) under nickel stress could elucidate the nickel resistance/tolerance mechanisms. The main objectives of the present research were to 1) characterize the P. tremuloides transcriptome, and 2) compare gene expression dynamics between nickel-resistant and nickel-susceptible P. tremuloides genotypes with Whole Transcriptome (WT) sequencing. Illumina Sequencing generated 27–45 million 2X150 paired-end reads of raw data per sample. The alignment performed with StringTie Software added two groups of transcripts to the draft genome annotation. One group contained 32,677 new isoforms that match to 17,254 genes. The second group contained 17,349 novel transcripts that represent 16,157 novel genes. Overall, 52,987 genes were identified from which 36,770 genes were selected as differently expressed. With the high stringency (two-fold change, FDR value ≤ 0.05 and logFC value ≥1 (upregulated) or ≤ -1 (downregulated), after GSEA analysis and filtering for gene set size, 575 gene sets were upregulated and 146 were downregulated in nickel resistant phenotypes compared to susceptible genotypes. For biological process, genes associated with translation were significantly upregulated while signal transduction and cellular protein process genes were downregulated in resistant compared to susceptible genotypes. For molecular function, there was a significant downregulation of genes associated with DNA binding in resistant compared to susceptible lines. Significant upregulation was observed in genes located in ribosome while downregulation of genes in chloroplast and mitochondrion were preponderant in resistant genotypes compared to susceptible. Hence, from a whole transcriptome level, an upregulation in ribosomal and translation activities was identified as the main response to Ni toxicity in the resistant plants. More importantly, 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 identified upregulated genes associated with abiotic stress include genes coding for Dirigent Protein 10, GATA transcription factor, Zinc finger protein, Auxin response factor, Bidirectional sugar transporter, and thiamine thiazole synthase.

Gene expression profiling of Jack Pine (Pinus banksiana) under copper stress: Identification of genes associated with copper resistance

“…This raises the possibility that DEGs in SG were also associated with death coping mechanisms responding to copper induced stress and tissue damage. This pattern of gene expression was also observed in Populus tremuloides when exposed to excess nickel [34].…”

Transcriptome Analysis Reveals Changes in Whole Gene Expression, Biological Process, and Molecular Functions Induced by Nickel in Jack Pine (Pinus banksiana)

“…Pinus banksiana is able to accumulate nickel in the needles, roots and branches, albeit to a lesser extent than would be required to be classified as an accumulator [22,28]. Previous reports have provided differences in gene expression between nickel-treated and -untreated hardwood genotypes [29][30][31]. The greater number of upregulated genes compared to downregulated genes in the present study indicates that excess nickel mostly elicited an increase in protein production.…”

“…Under the same nickel-treatment regimen, the transcriptomes of Populus tremuloides, Betula papyrifera and Acer rubrum elicited the majority of the gene expression in nickel transport, cellular component organization and the carbohydrate metabolic process [29][30][31]. Gene expression associated with metabolic function was similar among the different species.…”

“…The small proportion of genes associated with transport indicates that the majority of genes were not associated with nickel transporters (Figures 3 and 4). Unlike Pinus banksiana, the transcriptomes of the aforementioned angiosperms had the majority of genes associated with the ribosome, attributed to increased protein translation [29][30][31]. Overall, the large functional differences between the transcriptomes of angiosperms and Pinus banksiana demonstrate that Pinus banksiana manages excess nickel differently from angiosperms.…”