De novo assembly of the pennycress (Thlaspi arvense) transcriptome provides tools for the development of a winter cover crop and biodiesel feedstock.
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.
Affiliation: Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN 55108, USA.Show MeSH
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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.
Affiliation: Department of Plant Biology, University of Minnesota, 1445 Gortner Avenue, 250 Biological Sciences Center, Saint Paul, MN 55108, USA.