A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop.
Bottom Line: 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.
Affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.Show MeSH
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Mentions: CAPS49 analysis using DNA isolated from progeny of the individual plants that were used to generate the draft genome was performed to distinguish between these three hypotheses. Primer sequences used to amplify regions used in the CAPS analysis shown in Fig. 2A are listed in Supplementary Table S4. Individuals were shown to either distinctly contain or lack the variant at four restriction enzyme sites, which eliminated the first hypothesis that these SNPs represented divergence in paralogous genes or misassembly of duplicated regions. Furthermore, none of the samples showed evidence of heterozygosity. Plants 3, 5, and 7 lacked the cut sites at the polymorphic regions, and plants 1, 2, 4, 6, 8, and 9 were homozygous for the cut sites (Fig. 2B). This supports the third hypothesis that the original MN106 population contained at least two distinct, highly homogenous populations. The fact that three individuals lacked all the cut sites and six individuals contained all the cut sites is likely due to the fact that at every CAPS locus, one prominent variant was detected in the variant detection analysis. Loci with the prominent variant that contained the six base restriction site were chosen for the CAPS analysis.Figure 2.
Affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.