Salix purpurea cv. Fish Creek De Novo Transcriptome Evaluation and Gene Expression Analysis Using RNA-Seq Data

Emmanuel Gonzalez, Julie Marleau, Frederic Pitre, Michel Labrecque, Simon Joly

Several agronomical, physiological and ecological attributes make willow species suitable for their use in land reclamation and phytoremediation of polluted soils. Their ability to reduce inorganic and organic contamination in soils of brownfields is studied as part of a large-scale genomics phytoremediation project (GENOREM). A pot experiment, where Salix purpurea cv. Fish Creek plants were cultivated in a contaminated soil, was performed to evaluate the phytoremediation potential of this cultivar through genomic approaches. Recent advances in high-throughput sequencing of transcriptomes (RNA-Seq) and computational methods make it possible to assemble a transcriptome even when a reference genome or transcriptome is not available. These also allow the analysis of differential gene expression that represents a good way to explore genetic variation and understand tree responses to environmental pollution. We present the Fish Creek de novo transcriptome bioinformatic pipeline using leaves, flower buds, and cambium sequences obtained from high throughput sequencing approaches. Differential gene expression is compared among several conditions. More than simply analyzing gene expression distribution patterns relying on available pipelines, we describe here how we evaluated and improved the Fish Creek de novo transcriptome through several bioinformatic steps.