Abstract
We generated a high-quality reference genome sequence for foxtail millet (Setaria italica). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis, the ancestral wild relative of S. italica, and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass (Panicum virgatum).
Original language | English |
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Pages (from-to) | 555-561 |
Number of pages | 7 |
Journal | Nature Biotechnology |
Volume | 30 |
Issue number | 6 |
DOIs | |
State | Published - Jun 2012 |
Funding
The studies conducted by the US Department of Energy Joint Genome Institute, the BioEnergy Science Center and the Joint Bioenergy Institute are supported by the Office of Science of the US Department of Energy under contract numbers DEAC0205CH11231, DEAC0500OR22725 and DEAC0205CH11231, respectively. This research was also supported by grants from the Department of Energy (DEFG0208ER64636), National Institute of Food and Agriculture Plant Feedstock Genomics for Bioenergy Program (no. 20083550404851), National Science Foundation (IOS0701736 and DBI0607123), the Oklahoma Center for the Advancement of Science and Technology (PSB08007, PS11035B), and the University of Missouri Research Board. We thank C. Saski at Clemson University for the construction of the Setaria italica and switchgrass BAC libraries, M. Udvardi at the Noble Foundation for providing switchgrass genomic DNA and B. Meyers at the University of Delaware for small RNA annotation advice.