The JGI was originally formed to carry out the DOE’s share of the Human Genome Project. Upon completion of that effort, on the basis of various advisory groups and white papers, and with the approval of DOE, JGI undertook a series of animal sequencing projects selected for their comparative value against human, and as foundational genomes for understanding metazoan evolution and development. These included puffer fish (the first vertebrate genome sequenced by the whole genome shotgun method in the public sector), sea squirt, sea anemone, amphioxus, limpet, leech, polychaete, demosponge, frog, and water flea. As DOE turned its focus toward bioenergy and the environment, these JGI efforts to sequence and analyze eukaryotic genomes morphed into sustained programmatic efforts directed largely towards plants and fungi. In addition, a range of microbial eukaryotes (primarily various types of alga) were taken on as individual projects, but this challenging effort has received only intermittent support from DOE program management.
The scientific aims of the eukaryotic program are to produce, annotate, and analyze plant, fungal, and other eukaryotic genomes that are either directly relevant to DOE mission, or underlie fundamental biology related to this mission. These aims include (1) production and continued improvement of selected “flagship” genomes as a platform for bioenergy studies, (2) the draft sequence of additional genomes for comparative and exploratory purposes, and (3) the elucidation of functional elements in these genomes through the generation of large-scale datasets including studies of gene expression and intra- and inter-specific sequence variation.
From their inception in 2008 until quite recently, the plant and fungal programs were organized as quasi-independent programs. The Programs coordinate sequencing and execute the assembly and annotation of reference genomes as well as maintaining “flagship” genomes with significant additional efforts to improve these genomes and provide additional value. The programs each have been successful, not just in these endeavors, but also in gathering and supporting vibrant user communities that have significant experience with and expectations of the JGI. Each program has a scientific advisory board that meets 3-4 times a year to review program activities and provide guidance on prioritization of ongoing activities and new projects.
In summer of 2011, the two programs were unified into a Eukaryotic “Super-Program,” in parallel to the unification of (prokaryotic) microbial and metagenomes programs into a microbial super-program. The goal of this merger is not to force complete integration of their activities, which would have major costs and be disruptive to users and ongoing projects, but rather to encourage long-term coordination of development activities and to leverage the significant strengths of each program for the benefit of both.
The Eukaryotic Super-Program comprises the Plant and Fungal Genomics Programs, each responsible for administrating and coordinating the sequencing and analysis of the projects approved through the CSP and Bioenergy Research Centers, and for developing sustained programmatic efforts coordinated with the appropriate user community, such as the Plant Gene Atlas and Encyclopedia of Fungal Genomes.