title: Reference genome sequence of the model plant Setaria.
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).
authors.affiliation: The BioEnergy Science Center and the Department of Genetics, University of Georgia, Athens, Georgia, USA. maize@uga.edu
authors.forename: Jeffrey L
authors.initials: JL
authors.lastname: Bennetzen
authors.forename: Jeremy
authors.initials: J
authors.lastname: Schmutz
authors.forename: Hao
authors.initials: H
authors.lastname: Wang
authors.forename: Ryan
authors.initials: R
authors.lastname: Percifield
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hawkins
authors.forename: Ana C
authors.initials: AC
authors.lastname: Pontaroli
authors.forename: Matt
authors.initials: M
authors.lastname: Estep
authors.forename: Liang
authors.initials: L
authors.lastname: Feng
authors.forename: Justin N
authors.initials: JN
authors.lastname: Vaughn
authors.forename: Jane
authors.initials: J
authors.lastname: Grimwood
authors.forename: Jerry
authors.initials: J
authors.lastname: Jenkins
authors.forename: Kerrie
authors.initials: K
authors.lastname: Barry
authors.forename: Erika
authors.initials: E
authors.lastname: Lindquist
authors.forename: Uffe
authors.initials: U
authors.lastname: Hellsten
authors.forename: Shweta
authors.initials: S
authors.lastname: Deshpande
authors.forename: Xuewen
authors.initials: X
authors.lastname: Wang
authors.forename: Xiaomei
authors.initials: X
authors.lastname: Wu
authors.forename: Therese
authors.initials: T
authors.lastname: Mitros
authors.forename: Jimmy
authors.initials: J
authors.lastname: Triplett
authors.forename: Xiaohan
authors.initials: X
authors.lastname: Yang
authors.forename: Chu-Yu
authors.initials: CY
authors.lastname: Ye
authors.forename: Margarita
authors.initials: M
authors.lastname: Mauro-Herrera
authors.forename: Lin
authors.initials: L
authors.lastname: Wang
authors.forename: Pinghua
authors.initials: P
authors.lastname: Li
authors.forename: Manoj
authors.initials: M
authors.lastname: Sharma
authors.forename: Rita
authors.initials: R
authors.lastname: Sharma
authors.forename: Pamela C
authors.initials: PC
authors.lastname: Ronald
authors.forename: Olivier
authors.initials: O
authors.lastname: Panaud
authors.forename: Elizabeth A
authors.initials: EA
authors.lastname: Kellogg
authors.forename: Thomas P
authors.initials: TP
authors.lastname: Brutnell
authors.forename: Andrew N
authors.initials: AN
authors.lastname: Doust
authors.forename: Gerald A
authors.initials: GA
authors.lastname: Tuskan
authors.forename: Daniel
authors.initials: D
authors.lastname: Rokhsar
authors.forename: Katrien M
authors.initials: KM
authors.lastname: Devos
mesh_terms: D000220:Adaptation, Biological / Q000235:genetics; D002874:Chromosome Mapping; D018745:Genome, Plant; D008969:Molecular Sequence Data; D008897:Panicum / Q000235:genetics; D010802:Phylogeny; D017422:Sequence Analysis, DNA; D032983:Setaria Plant / Q000235:genetics*