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De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock.

Dorn KM, Fankhauser JD, Wyse DL, Marks MD - Plant J. (2013)

Bottom Line: A global comparison of homology between the pennycress and Arabidopsis transcriptomes, along with four other Brassicaceae species, revealed a high level of global sequence conservation within the family.Identification of these genes leads to testable hypotheses concerning their conserved function and to rational strategies to improve agronomic properties in pennycress.Future work to characterize isoform variation between diverse pennycress lines and develop a draft genome sequence for pennycress will further direct trait improvement.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN 55108, USA.

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Comparative transcriptomics of pennycress versus five Brassicaceae species.(a) Representation of the Brassicaceae phylogeny, adapted from Beilstein et al. (2010) and Franzke et al. (2011).(b) BLASTx comparison of the pennycress transcriptome assembly versus A. thaliana, Arabidopsis lyrata, Brassica rapa, Capsella rubella and Thellungiella halophila. The top blast hit (e ≤ 0.05) for each pennycress transcript versus the five species is shown. Contigs without significant hits were then compared to the NCBI peptide non-redundant database.(c) Five pairwise tBLASTn comparisons of Brassicaceae species to the pennycress transcriptome assembly. Sequences with significant homology (e ≤ 0.05 and positive match percentage ≧70%) shared between the five Brassicaceae species and pennycress (Thlaspi arvense) are shown in the inner circle.
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fig02: Comparative transcriptomics of pennycress versus five Brassicaceae species.(a) Representation of the Brassicaceae phylogeny, adapted from Beilstein et al. (2010) and Franzke et al. (2011).(b) BLASTx comparison of the pennycress transcriptome assembly versus A. thaliana, Arabidopsis lyrata, Brassica rapa, Capsella rubella and Thellungiella halophila. The top blast hit (e ≤ 0.05) for each pennycress transcript versus the five species is shown. Contigs without significant hits were then compared to the NCBI peptide non-redundant database.(c) Five pairwise tBLASTn comparisons of Brassicaceae species to the pennycress transcriptome assembly. Sequences with significant homology (e ≤ 0.05 and positive match percentage ≧70%) shared between the five Brassicaceae species and pennycress (Thlaspi arvense) are shown in the inner circle.

Mentions: Previous molecular analyzes of the Brassicaceae have divided the family into three basic lineages, recently reviewed by Franzke et al. (2011). Thlaspi arvense is a member of expanded lineage 2, and is more closely related to Thellungiella halophila and other Eutrema/Thellungiella species than the Brassica species in lineage 2 (Figure 2a). Arabidopsis thaliana, A. lyrata and Capsella rubella are members of lineage 1. To explore the relationship between pennycress and other Brassicaceae at the transcriptome level, we compared the assembled translated pennycress transcriptome to a peptide database derived from the sequenced genomes of A. thaliana, A. lyrata, C. rubella, B. rapa and T. halophila. A BLASTx comparison of the pennycress transcriptome with this peptide database showed that 16 298 of the 33 873 pennycress contigs had significant (e ≤ 0.05) top hits to T. halophila (Figure 2b). B. rapa had the next highest number of top hits (4972), with the lineage 1 species having approximately 3000 top hits each. A BLASTx comparison of the remaining sequences without significant hits to one of the five Brassicaceae species revealed that 3386 sequences had no significant hit in the NCBI non-redundant peptide database. This blast search returned 779 pennycress contigs with significant hits in the non-redundant peptide database, including 424 fungi. Many of these fungal hits (273) were to fungal plant pathogens, including Fusarium, Pyrenophora, Phaeosphaeria, Leptosphaeria and Bipolaris species (Table S3). These fungal transcripts were left in the assembly as the association between pennycress and these fungi may be informative in future analyzes.


De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock.

Dorn KM, Fankhauser JD, Wyse DL, Marks MD - Plant J. (2013)

Comparative transcriptomics of pennycress versus five Brassicaceae species.(a) Representation of the Brassicaceae phylogeny, adapted from Beilstein et al. (2010) and Franzke et al. (2011).(b) BLASTx comparison of the pennycress transcriptome assembly versus A. thaliana, Arabidopsis lyrata, Brassica rapa, Capsella rubella and Thellungiella halophila. The top blast hit (e ≤ 0.05) for each pennycress transcript versus the five species is shown. Contigs without significant hits were then compared to the NCBI peptide non-redundant database.(c) Five pairwise tBLASTn comparisons of Brassicaceae species to the pennycress transcriptome assembly. Sequences with significant homology (e ≤ 0.05 and positive match percentage ≧70%) shared between the five Brassicaceae species and pennycress (Thlaspi arvense) are shown in the inner circle.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
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getmorefigures.php?uid=PMC3824206&req=5

fig02: Comparative transcriptomics of pennycress versus five Brassicaceae species.(a) Representation of the Brassicaceae phylogeny, adapted from Beilstein et al. (2010) and Franzke et al. (2011).(b) BLASTx comparison of the pennycress transcriptome assembly versus A. thaliana, Arabidopsis lyrata, Brassica rapa, Capsella rubella and Thellungiella halophila. The top blast hit (e ≤ 0.05) for each pennycress transcript versus the five species is shown. Contigs without significant hits were then compared to the NCBI peptide non-redundant database.(c) Five pairwise tBLASTn comparisons of Brassicaceae species to the pennycress transcriptome assembly. Sequences with significant homology (e ≤ 0.05 and positive match percentage ≧70%) shared between the five Brassicaceae species and pennycress (Thlaspi arvense) are shown in the inner circle.
Mentions: Previous molecular analyzes of the Brassicaceae have divided the family into three basic lineages, recently reviewed by Franzke et al. (2011). Thlaspi arvense is a member of expanded lineage 2, and is more closely related to Thellungiella halophila and other Eutrema/Thellungiella species than the Brassica species in lineage 2 (Figure 2a). Arabidopsis thaliana, A. lyrata and Capsella rubella are members of lineage 1. To explore the relationship between pennycress and other Brassicaceae at the transcriptome level, we compared the assembled translated pennycress transcriptome to a peptide database derived from the sequenced genomes of A. thaliana, A. lyrata, C. rubella, B. rapa and T. halophila. A BLASTx comparison of the pennycress transcriptome with this peptide database showed that 16 298 of the 33 873 pennycress contigs had significant (e ≤ 0.05) top hits to T. halophila (Figure 2b). B. rapa had the next highest number of top hits (4972), with the lineage 1 species having approximately 3000 top hits each. A BLASTx comparison of the remaining sequences without significant hits to one of the five Brassicaceae species revealed that 3386 sequences had no significant hit in the NCBI non-redundant peptide database. This blast search returned 779 pennycress contigs with significant hits in the non-redundant peptide database, including 424 fungi. Many of these fungal hits (273) were to fungal plant pathogens, including Fusarium, Pyrenophora, Phaeosphaeria, Leptosphaeria and Bipolaris species (Table S3). These fungal transcripts were left in the assembly as the association between pennycress and these fungi may be informative in future analyzes.

Bottom Line: A global comparison of homology between the pennycress and Arabidopsis transcriptomes, along with four other Brassicaceae species, revealed a high level of global sequence conservation within the family.Identification of these genes leads to testable hypotheses concerning their conserved function and to rational strategies to improve agronomic properties in pennycress.Future work to characterize isoform variation between diverse pennycress lines and develop a draft genome sequence for pennycress will further direct trait improvement.

View Article: PubMed Central - PubMed

Affiliation: Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN 55108, USA.

Show MeSH
Related in: MedlinePlus