Mining RNAseq Data to Determine Differential Gene Expression in Populus Transgenic Lines using Kbase

To improve feedstock properties for biofuel conversion and production, several hundred genes have been selected to generate transgenic plants in the bioenergy crop Populus, as part of research performed by the BioEnergy Science Center. Transcriptomic profiling of these transgenic plants is an essential component of phenotypic characterization to uncover the molecular mechanism underlying biomass recalcitrance. We report here the transgenic effect of overexpression of a 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase-like transcriptional regulator (EPSP-TF) at the transcript level. Total RNAs were isolated from three independent transgenic lines and empty vector control plants, and subjected to RNAseq. Using the RNAseq data analysis methods available in the Department of Energy Systems Biology Knowledgebase (KBase) (https://kbase.us/), genes differentially expressed between transgenic lines and control plants are shown and discussed in light of their functions in secondary cell wall biosynthesis, along with the ease of using KBase for this analysis.