The JGI Plant Gene Atlas Project: Special Emphasis on P. patens

In collaboration with scientific leaders from the plant genomics community, the Department of Energy Joint Genome Institute has begun a large-scale, coordinated effort to add functional information to the 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 from orthologous genes across the JGI Plant genomes.  The secondary goal is to provide a technology test bed to further develop genomic techniques that illuminate the function of plant genes and other plant regulatory and pathway elements. As such, this project includes test projects for amplification for micro-tissue and laser capture micro dissection derived samples, small RNA matched samples, and 5’ -> 3’ capture techniques. The initial pilot project includes samples from five major JGI Plant Flagship genomes: Chlamydomonas (algal model), Physcomitrella (moss model), Setaria (grass model), soybean (legume model and crop plant), and poplar (biomass tree crop). The initial set of Physcomitrella samples for transcriptome sequencing were contributed by 13 different groups using standardized growth and extraction protocols to minimize sample to sample variation.  We will present an overview of the Gene Atlas project and initial findings for Physcomitrella based on the samples completed to date.