Comprehensive Transcriptome Analysis of Response to Nickel Stress in White Birch (Betula papyrifera).

White birch (Betula papyrifera) is one of the dominant tree species of the Boreal Forest. Recent studies have shown that birch is fairly resistant to heavy metal contamination, specifically to nickel. Knowledge of regulation of genes associated with metal resistance in higher plants is very sketchy. Availability and annotation of the dwarf birch (Betula nana) enables the use of throughout sequencing approaches to understanding responses to environmental challenges in other Betula species such as B. papyrifera. The main objectives of this study are to 1) develop and characterize the white birch transcriptome, 2) to assess gene expression dynamics of white birch in response to nickel stress, and 3) to describe gene function based on ontology. Nickel resistant and susceptible genotypes were selected and used for transcriptome analysis. A total of 209802 trinity genes were identified and were assembled to 278264 total trinity transcripts. The transcripts were mapped to protein sequences and based on best match; we annotate the white birch genes and assign gene ontology. In total, 215700 transcripts were annotated and were compared to the published dwarf birch genome. Overall, a genomic match for 61% transcripts (169052 out 278264) with the reference genome was found. Expression profiles were generated and 62587 genes were found to be significantly differentially expressed among the nickel resistant, susceptible, and untreated libraries. The main nickel resistance mechanism in B. papyrifera is a down regulation of genes associated with translation (in ribosome), binding, and transporter activity. Five candidate genes associated to nickel resistance were identified. They include Glutathione S –transferase (GST), thioredoxin family protein, putative transmembrane protein and two Nramp transporters. These genes can be useful for genetic engineering of birch trees.