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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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Similarity and coverage of pennycress transcripts versus Arabidopsis genes.(a) Histogram showing frequency versus percentage similarity (positive amino acid identity) of pennycress contigs versus an Arabidopsis peptide.(b) Histogram showing frequency versus percentage coverage (longest positive hit/peptide length) of pennycress contigs versus an Arabidopsis peptide. Most assembled pennycress transcripts have high coverage which greatly skews the histogram to the right.(c) Smoothed color density representation of the percentage similarity (x axis) of each pennycress transcript plotted against the percent coverage of the Arabidopsis protein similarity (y axis). The plot was produced using the ‘smoothScatter’ function in r (R Development Core Team, 2008), which produces a smoothed density representation of the scatterplot using a kernel density estimate (nbin = 100). Darker color indicates a higher density of transcripts in a given position, with the darkest ‘bin’ containing over 700 transcripts. Boxes encompassing transcripts encoding peptides with 70, 80 and 95% sequence similarity and coverage are shown in the upper right corner. Raw similarity and coverage data are provided in Table S2.
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fig03: Similarity and coverage of pennycress transcripts versus Arabidopsis genes.(a) Histogram showing frequency versus percentage similarity (positive amino acid identity) of pennycress contigs versus an Arabidopsis peptide.(b) Histogram showing frequency versus percentage coverage (longest positive hit/peptide length) of pennycress contigs versus an Arabidopsis peptide. Most assembled pennycress transcripts have high coverage which greatly skews the histogram to the right.(c) Smoothed color density representation of the percentage similarity (x axis) of each pennycress transcript plotted against the percent coverage of the Arabidopsis protein similarity (y axis). The plot was produced using the ‘smoothScatter’ function in r (R Development Core Team, 2008), which produces a smoothed density representation of the scatterplot using a kernel density estimate (nbin = 100). Darker color indicates a higher density of transcripts in a given position, with the darkest ‘bin’ containing over 700 transcripts. Boxes encompassing transcripts encoding peptides with 70, 80 and 95% sequence similarity and coverage are shown in the upper right corner. Raw similarity and coverage data are provided in Table S2.

Mentions: To more closely examine the level of global sequence conservation between pennycress and A. thaliana, we further examined a BLASTx comparison of the pennycress transcriptome assembly to the Arabidopsis TAIR10 peptide database (primary transcripts only). The relative homology of each predicted peptide to the most similar Arabidopsis protein was measured by the percentage of positive sequence similarity (Figure 3a) and percentage coverage (Figure 3b). A smooth scatter plot representing the percentage similarity and percentage coverage for each pennycress sequence compared to the closest Arabidopsis peptide sequence is shown in Figure 3(c). A large proportion (>85%) of transcripts show at least 70% similarity to an Arabidopsis protein. A total of 16 556 pennycress predicted peptides had at least one match to an Arabidopsis gene with >70% similarity/>70% coverage (Figure 3c, boxes), of which 4846 pennycress transcripts showed ≥95% similarity and coverage, 9685 transcripts showed between 80 and 95% similarity and coverage, and 2025 transcripts showed between 70 and 80% similarity and coverage. A total of 17 317 transcripts showed <70% similarity and coverage, and 4783 transcripts lacked a significant BLASTx hit (e ≤ 0.05) to an Arabidopsis peptide.


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)

Similarity and coverage of pennycress transcripts versus Arabidopsis genes.(a) Histogram showing frequency versus percentage similarity (positive amino acid identity) of pennycress contigs versus an Arabidopsis peptide.(b) Histogram showing frequency versus percentage coverage (longest positive hit/peptide length) of pennycress contigs versus an Arabidopsis peptide. Most assembled pennycress transcripts have high coverage which greatly skews the histogram to the right.(c) Smoothed color density representation of the percentage similarity (x axis) of each pennycress transcript plotted against the percent coverage of the Arabidopsis protein similarity (y axis). The plot was produced using the ‘smoothScatter’ function in r (R Development Core Team, 2008), which produces a smoothed density representation of the scatterplot using a kernel density estimate (nbin = 100). Darker color indicates a higher density of transcripts in a given position, with the darkest ‘bin’ containing over 700 transcripts. Boxes encompassing transcripts encoding peptides with 70, 80 and 95% sequence similarity and coverage are shown in the upper right corner. Raw similarity and coverage data are provided in Table S2.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3824206&req=5

fig03: Similarity and coverage of pennycress transcripts versus Arabidopsis genes.(a) Histogram showing frequency versus percentage similarity (positive amino acid identity) of pennycress contigs versus an Arabidopsis peptide.(b) Histogram showing frequency versus percentage coverage (longest positive hit/peptide length) of pennycress contigs versus an Arabidopsis peptide. Most assembled pennycress transcripts have high coverage which greatly skews the histogram to the right.(c) Smoothed color density representation of the percentage similarity (x axis) of each pennycress transcript plotted against the percent coverage of the Arabidopsis protein similarity (y axis). The plot was produced using the ‘smoothScatter’ function in r (R Development Core Team, 2008), which produces a smoothed density representation of the scatterplot using a kernel density estimate (nbin = 100). Darker color indicates a higher density of transcripts in a given position, with the darkest ‘bin’ containing over 700 transcripts. Boxes encompassing transcripts encoding peptides with 70, 80 and 95% sequence similarity and coverage are shown in the upper right corner. Raw similarity and coverage data are provided in Table S2.
Mentions: To more closely examine the level of global sequence conservation between pennycress and A. thaliana, we further examined a BLASTx comparison of the pennycress transcriptome assembly to the Arabidopsis TAIR10 peptide database (primary transcripts only). The relative homology of each predicted peptide to the most similar Arabidopsis protein was measured by the percentage of positive sequence similarity (Figure 3a) and percentage coverage (Figure 3b). A smooth scatter plot representing the percentage similarity and percentage coverage for each pennycress sequence compared to the closest Arabidopsis peptide sequence is shown in Figure 3(c). A large proportion (>85%) of transcripts show at least 70% similarity to an Arabidopsis protein. A total of 16 556 pennycress predicted peptides had at least one match to an Arabidopsis gene with >70% similarity/>70% coverage (Figure 3c, boxes), of which 4846 pennycress transcripts showed ≥95% similarity and coverage, 9685 transcripts showed between 80 and 95% similarity and coverage, and 2025 transcripts showed between 70 and 80% similarity and coverage. A total of 17 317 transcripts showed <70% similarity and coverage, and 4783 transcripts lacked a significant BLASTx hit (e ≤ 0.05) to an Arabidopsis peptide.

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