title: A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop.
abstract: Field pennycress (Thlaspi arvense L.) is being domesticated as a new winter cover crop and biofuel species for the Midwestern United States that can be double-cropped between corn and soybeans. A genome sequence will enable the use of new technologies to make improvements in pennycress. To generate a draft genome, a hybrid sequencing approach was used to generate 47 Gb of DNA sequencing reads from both the Illumina and PacBio platforms. These reads were used to assemble 6,768 genomic scaffolds. The draft genome was annotated using the MAKER pipeline, which identified 27,390 predicted protein-coding genes, with almost all of these predicted peptides having significant sequence similarity to Arabidopsis proteins. A comprehensive analysis of pennycress gene homologues involved in glucosinolate biosynthesis, metabolism, and transport pathways revealed high sequence conservation compared with other Brassicaceae species, and helps validate the assembly of the pennycress gene space in this draft genome. Additional comparative genomic analyses indicate that the knowledge gained from years of basic Brassicaceae research will serve as a powerful tool for identifying gene targets whose manipulation can be predicted to result in improvements for pennycress.
authors: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
authors: Kevin M
authors: KM
authors: Dorn
authors: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.
authors: Johnathon D
authors: JD
authors: Fankhauser
authors: Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA.
authors: Donald L
authors: DL
authors: Wyse
authors: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA marks004@umn.edu.
authors: M David
authors: MD
authors: Marks
mesh_terms: D001483:Base Sequence; D056804:Biofuels; D018744:DNA, Plant / Q000737:chemistry; D017343:Genes, Plant; D018745:Genome, Plant; D053858:Metabolic Networks and Pathways; D008969:Molecular Sequence Data; D017422:Sequence Analysis, DNA; D031227:Thlaspi / Q000235:genetics*
chemical_list: D056804:Biofuels; D018744:DNA, Plant
keywords: Thlaspi arvense; comparative genomics; de novo assembly; field pennycress; whole genome sequencing
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