Limits...
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.

Show MeSH

Related in: MedlinePlus

Comparative genomics of pennycress and other Brassicaceae species. (A) Syntenic path assembly dot plots comparing pennycress scaffolds >75 kilobases long to the seven Eutrema salsugineum pseudochromosomes fromYang et al.1 (B) BLASTp analysis of the 27,390 predicted pennycress peptides against predicted peptide sets from Capsella rubella,5Brassica rapa,43Arabidopsis thaliana (Bevan and Initiative, 2000), Arabidopsis lyrata,42 and Eutrema salsugineum. Highly similar is defined as pennycress predicted peptide having at least one BLASTp hit e < 1 × 10−5 and positive sequence similarity >70%. (C) BLASTp analysis of predicted pennycress peptides against a protein database containing the predicted peptides of the five Brassicaceae species listed. Predicted peptides with top hits (e ≤ 1 × 10−5 and >70% hit length) to a predicted protein from the corresponding species are shown, with pennycress peptides with hits falling below this threshold shown in the lower right half of the pie chart.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4401323&req=5

DSU045F1: Comparative genomics of pennycress and other Brassicaceae species. (A) Syntenic path assembly dot plots comparing pennycress scaffolds >75 kilobases long to the seven Eutrema salsugineum pseudochromosomes fromYang et al.1 (B) BLASTp analysis of the 27,390 predicted pennycress peptides against predicted peptide sets from Capsella rubella,5Brassica rapa,43Arabidopsis thaliana (Bevan and Initiative, 2000), Arabidopsis lyrata,42 and Eutrema salsugineum. Highly similar is defined as pennycress predicted peptide having at least one BLASTp hit e < 1 × 10−5 and positive sequence similarity >70%. (C) BLASTp analysis of predicted pennycress peptides against a protein database containing the predicted peptides of the five Brassicaceae species listed. Predicted peptides with top hits (e ≤ 1 × 10−5 and >70% hit length) to a predicted protein from the corresponding species are shown, with pennycress peptides with hits falling below this threshold shown in the lower right half of the pie chart.

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.


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)

Comparative genomics of pennycress and other Brassicaceae species. (A) Syntenic path assembly dot plots comparing pennycress scaffolds >75 kilobases long to the seven Eutrema salsugineum pseudochromosomes fromYang et al.1 (B) BLASTp analysis of the 27,390 predicted pennycress peptides against predicted peptide sets from Capsella rubella,5Brassica rapa,43Arabidopsis thaliana (Bevan and Initiative, 2000), Arabidopsis lyrata,42 and Eutrema salsugineum. Highly similar is defined as pennycress predicted peptide having at least one BLASTp hit e < 1 × 10−5 and positive sequence similarity >70%. (C) BLASTp analysis of predicted pennycress peptides against a protein database containing the predicted peptides of the five Brassicaceae species listed. Predicted peptides with top hits (e ≤ 1 × 10−5 and >70% hit length) to a predicted protein from the corresponding species are shown, with pennycress peptides with hits falling below this threshold shown in the lower right half of the pie chart.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4401323&req=5

DSU045F1: Comparative genomics of pennycress and other Brassicaceae species. (A) Syntenic path assembly dot plots comparing pennycress scaffolds >75 kilobases long to the seven Eutrema salsugineum pseudochromosomes fromYang et al.1 (B) BLASTp analysis of the 27,390 predicted pennycress peptides against predicted peptide sets from Capsella rubella,5Brassica rapa,43Arabidopsis thaliana (Bevan and Initiative, 2000), Arabidopsis lyrata,42 and Eutrema salsugineum. Highly similar is defined as pennycress predicted peptide having at least one BLASTp hit e < 1 × 10−5 and positive sequence similarity >70%. (C) BLASTp analysis of predicted pennycress peptides against a protein database containing the predicted peptides of the five Brassicaceae species listed. Predicted peptides with top hits (e ≤ 1 × 10−5 and >70% hit length) to a predicted protein from the corresponding species are shown, with pennycress peptides with hits falling below this threshold shown in the lower right half of the pie chart.
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.

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