De Novo Assembly and Characterization of Transcriptome of Red Maple (Acer rubrum) Genotypes Resistant to Nickel Toxicity.

Knowledge of regulation of genes associated with metal resistance in higher plants is very sketchy. The main objectives of this study are to 1) develop and characterize the Acer rubrum transcriptome, 2) assess gene expression dynamics of A. rubrumin response to nickel stress, and 3) describe gene function based on ontology. Nickel resistant and susceptible genotypes were selected and used for transcriptome analysis. Overall, 223,610,443 bases were generated. A total of 261,907 trinity genes were identified and assembled to 412,831 total trinity transcripts. The average read length was 546.50. The transcripts were mapped to protein sequences and based on best match; we annotated the A. rubrum transcriptome and assigned gene ontology. Expression profiles were generated and 66,783 genes were selected as expressed among the libraries. When nickel resistant genotypes were compared to water controls, 6,263 transcripts were upregulated and 3,142 were downregulated. These values were 3,308 and 2,176, respectively when susceptible genotypes were compared to water control. 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.