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A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop.

Dorn KM, Fankhauser JD, Wyse DL, Marks MD - DNA Res. (2015)

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.

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CAPS analysis of Thlaspi arvense line MN106 (A) Schematic of the four PCR fragments produced by the primer sets listed in Supplementary Table S4. The largest fragments used to distinguish between individuals containing the SNP (MN106 A genotype fragment—top, and MN106 B genotype fragment—bottom). (B) DNA was isolated from progeny of each of the nine plants used to produce the draft genome assembly, and analysed using four CAPS markers. PCR products for each plant are shown side-by-side undigested (uncut) and post-digestion (cut) with the corresponding restriction endonucleases. In all cases, samples 3, 5, and 7 share restriction digest patterns, corresponding to the MN106-B genotype. A negative control for the PCR reaction is shown in the last lane. (C) Morphology of developing T. arvense flowers. The top panel (1–3) shows the morphology of the unaltered flowers, while the bottom panel (4–6) shows the same series of flowers with sepals and petals either removed or rearranged to reveal the status of the stamens with regard to filament elongation and the shedding of pollen. (4) Neither filament elongation nor pollen shedding has commenced in (1). (5) Filaments have elongated, and pollen is being shed inside of the closed flower shown in (2). (5) Pollen densely covers the stigmatic surface by the time the flower is fully open in (6). All scale bars equal 1 mm.
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DSU045F2: CAPS analysis of Thlaspi arvense line MN106 (A) Schematic of the four PCR fragments produced by the primer sets listed in Supplementary Table S4. The largest fragments used to distinguish between individuals containing the SNP (MN106 A genotype fragment—top, and MN106 B genotype fragment—bottom). (B) DNA was isolated from progeny of each of the nine plants used to produce the draft genome assembly, and analysed using four CAPS markers. PCR products for each plant are shown side-by-side undigested (uncut) and post-digestion (cut) with the corresponding restriction endonucleases. In all cases, samples 3, 5, and 7 share restriction digest patterns, corresponding to the MN106-B genotype. A negative control for the PCR reaction is shown in the last lane. (C) Morphology of developing T. arvense flowers. The top panel (1–3) shows the morphology of the unaltered flowers, while the bottom panel (4–6) shows the same series of flowers with sepals and petals either removed or rearranged to reveal the status of the stamens with regard to filament elongation and the shedding of pollen. (4) Neither filament elongation nor pollen shedding has commenced in (1). (5) Filaments have elongated, and pollen is being shed inside of the closed flower shown in (2). (5) Pollen densely covers the stigmatic surface by the time the flower is fully open in (6). All scale bars equal 1 mm.

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.


A draft genome of field pennycress (Thlaspi arvense) provides tools for the domestication of a new winter biofuel crop.

Dorn KM, Fankhauser JD, Wyse DL, Marks MD - DNA Res. (2015)

CAPS analysis of Thlaspi arvense line MN106 (A) Schematic of the four PCR fragments produced by the primer sets listed in Supplementary Table S4. The largest fragments used to distinguish between individuals containing the SNP (MN106 A genotype fragment—top, and MN106 B genotype fragment—bottom). (B) DNA was isolated from progeny of each of the nine plants used to produce the draft genome assembly, and analysed using four CAPS markers. PCR products for each plant are shown side-by-side undigested (uncut) and post-digestion (cut) with the corresponding restriction endonucleases. In all cases, samples 3, 5, and 7 share restriction digest patterns, corresponding to the MN106-B genotype. A negative control for the PCR reaction is shown in the last lane. (C) Morphology of developing T. arvense flowers. The top panel (1–3) shows the morphology of the unaltered flowers, while the bottom panel (4–6) shows the same series of flowers with sepals and petals either removed or rearranged to reveal the status of the stamens with regard to filament elongation and the shedding of pollen. (4) Neither filament elongation nor pollen shedding has commenced in (1). (5) Filaments have elongated, and pollen is being shed inside of the closed flower shown in (2). (5) Pollen densely covers the stigmatic surface by the time the flower is fully open in (6). All scale bars equal 1 mm.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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Show All Figures
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DSU045F2: CAPS analysis of Thlaspi arvense line MN106 (A) Schematic of the four PCR fragments produced by the primer sets listed in Supplementary Table S4. The largest fragments used to distinguish between individuals containing the SNP (MN106 A genotype fragment—top, and MN106 B genotype fragment—bottom). (B) DNA was isolated from progeny of each of the nine plants used to produce the draft genome assembly, and analysed using four CAPS markers. PCR products for each plant are shown side-by-side undigested (uncut) and post-digestion (cut) with the corresponding restriction endonucleases. In all cases, samples 3, 5, and 7 share restriction digest patterns, corresponding to the MN106-B genotype. A negative control for the PCR reaction is shown in the last lane. (C) Morphology of developing T. arvense flowers. The top panel (1–3) shows the morphology of the unaltered flowers, while the bottom panel (4–6) shows the same series of flowers with sepals and petals either removed or rearranged to reveal the status of the stamens with regard to filament elongation and the shedding of pollen. (4) Neither filament elongation nor pollen shedding has commenced in (1). (5) Filaments have elongated, and pollen is being shed inside of the closed flower shown in (2). (5) Pollen densely covers the stigmatic surface by the time the flower is fully open in (6). All scale bars equal 1 mm.
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.

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.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, Saint Paul, MN 55108, USA.

Show MeSH
Related in: MedlinePlus