A RNA-Seq and Microarray Combined Gene Atlas Database for Perennial Bioenergy Crop Switchgrass

Switchgrass (Panicum virgatum) has been used as a model crop for sustainable bioenergy research for more than a decade. The switchgrass Affymetrix chip based Gene Atlas database (http://switchgrassgenomics.noble.org/), along with the reference genome at JGI Phytozome portal, contributed significantly to the annotation of gene/gene family for switchgrass during these years of bioenergy research. To date 31 major organs, including root, leaf and stem as well as developmental serial for inflorescence and seeds have been included in the database, providing rich information for functional analysis of the switchgrass genome. Now using RNA-seq expression analysis, along with the release of the switchgrass reference genome V3.1, the switchgrass Gene Atlas is being updated with the addition of the RNA-seq derived expression data. By combining the RNA-seq data and the re-annotated microarray chip expression data against genome v3.1, the switchgrass Gene Atlas database will continue to serve the community for genome functional analysis. Examples of comparing different tissues with RNA-seq analysis tools will be shown from KBase.