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: Of the sequenced Brassicaceae genomes, pennycress is most closely related to E. salsugineum, which possesses a much smaller genome (241 Mb), but the same karyotype (n = 7).1,48 To evaluate the relative completeness of the genome assembly, we used a syntenic path assembly comparison of the pennycress assembly to the E. salsugineum reference genome.1 Pennycress genomic scaffolds >75 kb long, representing 241 Mb (>70%) of the assembly were compared with the 241 Mb reference genome of E. salsugineum. Large portions of the seven E. salsugineum pseudochromosomes possess a high degree of synteny with the pennycress assembly, indicative of the close evolutionary relationship between these two species, as well as a high level of completeness of conserved regions in the pennycress genome (Fig. 1A).Figure 1.
Affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.