JGI Plant Gene Atlas: Adding Experimentally Derived Functional Annotations to JGI Plants

The JGI Plant Gene Atlas is a large, coordinated effort to add functional information to JGI Plant Flagship Genomes. The primary goal of this project is to develop dense RNA-seq data sets for Plant Flagships to form reference transcriptomes across common tissues and conditions and to provide the ability to compare expression across conditions within a plant and from orthologous genes across the JGI Plant genomes. This substantial amount of updateable transcriptomic resource is directly available to JGI users through the JGI Plant Portal at phytozome.jgi.doe.gov. The secondary goal is to provide a technology test bed to further develop genomic techniques that illuminate the function of plant genes and plant regulatory and pathway elements. Gene Atlas project currently comprises 1,078 samples from twelve JGI Plant Flagship genomes: Chlamydomonas (algal model), Physcomitrella (moss model), Brachypodium (a C3 grass model), switchgrass (a woody perennial crop plant), Hall’s panicgrass (grass model), Setaria italica (grain and forage crop), Setaria viridis (model C4 grass), Sorghum (a C4 grass bioenergy crop and model) [6 monocots], Arabidopsis (model for plant genetics and biology), soybean (legume model and crop plant), Medicago (legume model) and poplar (biomass tree crop).

 We will present results from our genome version controlled data analysis pipelines which facilitates identifying gene clusters showing tissue/condition specific expression patterns, visualize expression profiles of gene sets across Gene Atlas plants and adding experimental and orthologous based functional annotations.

 In addition to standard tissues and conditions, the Gene Atlas includes a comparative condition across the plants focused on nitrogen metabolism providing a single condition that can be compared broadly from the minimal Chlamydomonas, into the early plant model Physcomitrella, and through the dicots and monocots included in the study. Our results on transcriptional modulation in response to changes in available nitrogen source and conserved gene expression networks across the phylogeny will also be discussed.