Flagship Plant Genomes

The Department of Energy Joint Genome Institute (DOE JGI) is placing special emphasis on improving the accuracy and completeness of plant genomes that have been selected because of their DOE mission-relevance and economic importance. These “flagship” plants are switchgrass, sorghum, poplar, soybean, foxtail millet, physcomitrella, and chlamydomonas. Unlocking the genetic information from these plants has the potential for facilitating improved crop yields, disease and insect resistance and drought tolerance for the crops, as well as better understanding of oil synthesis and cell walls for biofuel feedstocks. By sequencing the DNA of these plants, DOE JGI is making significant contributions toward meeting the world’s energy needs.

Typically, the initial draft of the plant genomes is carried out at the JGI in Walnut Creek. Genome improvement, for flagship genomes, takes place here at the HAGSC in Huntsville. Assembly and annotation of the sequence is a collaborative effort between the JGI Phytozome Annotation group and HudsonAlpha.

Currently, plant whole genomes are drafted using 3 and 6 kb plasmid, fosmid and BAC Sanger libraries. Following the initial assembly of the draft end-reads, the customary protocol for plant genome improvement at HA begins with the selection of targeted areas of the genome. The target area is isolated as a subset of the whole to allow for a more workable subproject size. The subprojects range from either fosmid- or BAC-size to 2 MB. Targets may be selected for a variety of reasons that include gene-rich areas, QTL regions, or a region with significant number of gaps in the sequence and unresolved repetitive sequence.

The objective is to completely (or as near as possible) resolve each base call in the target subproject and then incorporate that “complete” sequence back into the entire genome assembly. Methods for making this improvement include primer walks with a variety of chemistries and templates, transposons, and shatters of clones (the latter two techniques being essentially subprojects of the subprojects). Efforts are currently underway to explore practical uses of next-generation sequencing technologies for the extremely large and multi-copied plant genomes.

New public releases of plant genomes occur periodically for each flagship genome, as significant iterative improvements are made to the entire sequence. The DOE JGI strives to provide a greater understanding of the genetic variation and functional adaptations of flagship plant genomes, thus improving our nation’s biofuel capabilities. The sequence and analysis is made public through the phytozome web site at www.phytozome.net.