Sequencing and Analysis of a Reference Genome for the Model Plant Setaria

Background: Grasses from the genus Setaria, in particular the food crop S. italica (foxtail Millet) and the ancestral weed S. viridis (green foxtail) have served as informative model species for biofuel crops such as switchgrass (Panicum virgatum).

This BESC-JGI paper, with US and international collaborators, reports the sequencing and analysis of the Setaria genome.

Outcomes: The high quality whole genome assembly of the diploid S. italica is proving valuable as a framework in assisting with the genome assembly of other polyploid sequenced grasses, notably switchgrass.

Comparison between the genomes of S. italica and S. viridis, switchgrass, sorghum and rice have revealed both shared and unique properties of the independent adaptations of several grasses to life on earth.

Phylogenetic analysis of five nuclear genes shows that millet and Phylogenetic position of S. italica and S. viridis relative to a few switchgrass lineages underwent independent polyploidization events, both other important grass species. Left panel, relationships of the of which occurred after the divergence of Panicum from Setaria. commelinid monocots, showing the order Poales relative to the next closest order with a genome sequence, Arecales (http://www.mobot.org/MOBOT/research/APweb/). Middle The completed genome sequence enables the further development of panel, relationships among select grass genera (GPWG 2001). Right panel, phylogeny of selected Panicum, Setaria and

Setaria as a model plant, improves our understanding of cell wall Pennisetum species. Green, C4 lineage. composition, plant structure and development and traits that are pertinent to the development of biofuel crops.

Contacts: Jeff Bennetzen (maize@uga.edu, 706-583-0972), University of Georgia, Athens

Funding Source: DOE Office of Science BioEnergy Science Center, DOE Joint Genome Institute, National Institute of Food and Agriculture Plant Feedstock Genomics for Bioenergy Program, National Science Foundation, Oklahoma Center for Science and Technology and the University of Missouri Research Board.

59 Citation: Bennetzen, et al., “Reference genome sequence of the model plant Setaria”, Nature Biotechnology 30:6 (555-561) 2012. doi: 10.1038/nbt.2196