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

Analysis of genes involved in glucosinolate metabolism and transport. (A) Overview of glucosinolate biosynthesis core structure (top) via methionine and tryptophan and breakdown (bottom) and corresponding orthologues in the pennycress genome pathway derived from Liu et al.4 Expression values (RPKM, in parentheses) are shown for each putative orthologues derived from the global RNAseq reads previously described.19 (B–G) Neighbour joining trees of TGG1/TGG2, MVP1, ESP, ESM1, GTR1, and GTR2-like predicted peptides (100 bootstrap replicates) from pennycress (identified in this study), Brassica rapa, and Brassica oleraceae.4
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSU045F3: Analysis of genes involved in glucosinolate metabolism and transport. (A) Overview of glucosinolate biosynthesis core structure (top) via methionine and tryptophan and breakdown (bottom) and corresponding orthologues in the pennycress genome pathway derived from Liu et al.4 Expression values (RPKM, in parentheses) are shown for each putative orthologues derived from the global RNAseq reads previously described.19 (B–G) Neighbour joining trees of TGG1/TGG2, MVP1, ESP, ESM1, GTR1, and GTR2-like predicted peptides (100 bootstrap replicates) from pennycress (identified in this study), Brassica rapa, and Brassica oleraceae.4

Mentions: BLASTp analyses were used to identify putative orthologues to known glucosinolate genes in Arabidopsis (Supplementary Dataset S2). Genes involved in the GSL core biosynthesis and breakdown pathway were derived from A. thaliana, B. rapa, and B. oleraceae.4 Putative orthologues were identified for GSL biosynthesis from methionine and tryptophan (Fig. 3A), along with several putative myrosinases (thioglucoside glucohydrolase—TGGs and atypical myrosinases—PEN2 and PEN3). Potential orthologues to several interesting specifier proteins were also identified (Fig. 3A—top). To obtain a semi-quantitative estimate of these predicted genes, RNAseq reads from the previously described transcriptome were used to obtain rough expression values for each gene model (Supplementary Dataset S1). As these RNAseq reads represent a global library representing various tissues, this analysis provides an initial probe into the pennycress genes potentially responsible for the unique glucosinolate composition of pennycress. For example, two putative myrosinases (Ta16900 and Ta16899) represent the 120th and 129th most highly expressed gene models, respectively (Fig. 3A and B; Supplementary Dataset S1). A modified vacuole phenotype1 (MVP1)-like pennycress gene was also identified (Ta16960—Fig. 3A). MVP1 in Arabidopsis interacts with the myrosinase TGG2 to modulate myrosinase activity.57Figure 3.


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)

Analysis of genes involved in glucosinolate metabolism and transport. (A) Overview of glucosinolate biosynthesis core structure (top) via methionine and tryptophan and breakdown (bottom) and corresponding orthologues in the pennycress genome pathway derived from Liu et al.4 Expression values (RPKM, in parentheses) are shown for each putative orthologues derived from the global RNAseq reads previously described.19 (B–G) Neighbour joining trees of TGG1/TGG2, MVP1, ESP, ESM1, GTR1, and GTR2-like predicted peptides (100 bootstrap replicates) from pennycress (identified in this study), Brassica rapa, and Brassica oleraceae.4
© Copyright Policy - creative-commons
Related In: Results  -  Collection

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

DSU045F3: Analysis of genes involved in glucosinolate metabolism and transport. (A) Overview of glucosinolate biosynthesis core structure (top) via methionine and tryptophan and breakdown (bottom) and corresponding orthologues in the pennycress genome pathway derived from Liu et al.4 Expression values (RPKM, in parentheses) are shown for each putative orthologues derived from the global RNAseq reads previously described.19 (B–G) Neighbour joining trees of TGG1/TGG2, MVP1, ESP, ESM1, GTR1, and GTR2-like predicted peptides (100 bootstrap replicates) from pennycress (identified in this study), Brassica rapa, and Brassica oleraceae.4
Mentions: BLASTp analyses were used to identify putative orthologues to known glucosinolate genes in Arabidopsis (Supplementary Dataset S2). Genes involved in the GSL core biosynthesis and breakdown pathway were derived from A. thaliana, B. rapa, and B. oleraceae.4 Putative orthologues were identified for GSL biosynthesis from methionine and tryptophan (Fig. 3A), along with several putative myrosinases (thioglucoside glucohydrolase—TGGs and atypical myrosinases—PEN2 and PEN3). Potential orthologues to several interesting specifier proteins were also identified (Fig. 3A—top). To obtain a semi-quantitative estimate of these predicted genes, RNAseq reads from the previously described transcriptome were used to obtain rough expression values for each gene model (Supplementary Dataset S1). As these RNAseq reads represent a global library representing various tissues, this analysis provides an initial probe into the pennycress genes potentially responsible for the unique glucosinolate composition of pennycress. For example, two putative myrosinases (Ta16900 and Ta16899) represent the 120th and 129th most highly expressed gene models, respectively (Fig. 3A and B; Supplementary Dataset S1). A modified vacuole phenotype1 (MVP1)-like pennycress gene was also identified (Ta16960—Fig. 3A). MVP1 in Arabidopsis interacts with the myrosinase TGG2 to modulate myrosinase activity.57Figure 3.

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