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De novo assembly and annotation of the transcriptome of the agricultural weed Ipomoea purpurea uncovers gene expression changes associated with herbicide resistance.

Leslie T, Baucom RS - G3 (Bethesda) (2014)

Bottom Line: The differentially expressed genes also broadly implicated receptor-like kinases, which were down-regulated in the resistant lines, and other growth and defense genes, which were up-regulated in resistant lines.Overall, this work identifies potential candidate resistance loci for future investigations and dramatically increases genomic resources for this species.The assembled transcriptome presented herein will also provide a valuable resource to the Ipomoea community, as well as to those interested in utilizing the close relationship between the Convolvulaceae and the Solanaceae for phylogenetic and comparative genomics examinations.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences. University of Cincinnati, Cincinnati, Ohio 45221.

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Protein length coverage of translated sequences in the I. purpurea transcriptome compared with a database of maize, rice, tomato, and Arabidopsis proteins.
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fig3: Protein length coverage of translated sequences in the I. purpurea transcriptome compared with a database of maize, rice, tomato, and Arabidopsis proteins.

Mentions: We evaluated the quality and completeness of the I. purpurea transcriptome by assessing the number of core eukaryotic genes that were present among transcripts and by determining the percentage of full-length proteins that were sequenced. The Core Eukaryotic Genes Mapping Approach program identified a total of 240 of the 248 core eukaryotic genes, and 220 of these were considered complete (>70% of the protein identified). We next predicted open reading frames with the program OrfPredictor and performed a blastp (e−20) with a database of plant proteins (tomato, Arabidopsis, maize, rice) using the predicted peptide sequences. OrfPredictor predicted 63,857 open reading frames, leaving 1099 transcripts that did not return a potential ORF. Of these predicted ORFs, 29,615 returned a significant blastp hit to our database of plant proteins, and 21,371 of these sequences exhibited >90% alignment coverage (Figure 3). Thus, ~46% of the predicted peptide sequences in the I. purpurea transcriptome were nearly full-length.


De novo assembly and annotation of the transcriptome of the agricultural weed Ipomoea purpurea uncovers gene expression changes associated with herbicide resistance.

Leslie T, Baucom RS - G3 (Bethesda) (2014)

Protein length coverage of translated sequences in the I. purpurea transcriptome compared with a database of maize, rice, tomato, and Arabidopsis proteins.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4199709&req=5

fig3: Protein length coverage of translated sequences in the I. purpurea transcriptome compared with a database of maize, rice, tomato, and Arabidopsis proteins.
Mentions: We evaluated the quality and completeness of the I. purpurea transcriptome by assessing the number of core eukaryotic genes that were present among transcripts and by determining the percentage of full-length proteins that were sequenced. The Core Eukaryotic Genes Mapping Approach program identified a total of 240 of the 248 core eukaryotic genes, and 220 of these were considered complete (>70% of the protein identified). We next predicted open reading frames with the program OrfPredictor and performed a blastp (e−20) with a database of plant proteins (tomato, Arabidopsis, maize, rice) using the predicted peptide sequences. OrfPredictor predicted 63,857 open reading frames, leaving 1099 transcripts that did not return a potential ORF. Of these predicted ORFs, 29,615 returned a significant blastp hit to our database of plant proteins, and 21,371 of these sequences exhibited >90% alignment coverage (Figure 3). Thus, ~46% of the predicted peptide sequences in the I. purpurea transcriptome were nearly full-length.

Bottom Line: The differentially expressed genes also broadly implicated receptor-like kinases, which were down-regulated in the resistant lines, and other growth and defense genes, which were up-regulated in resistant lines.Overall, this work identifies potential candidate resistance loci for future investigations and dramatically increases genomic resources for this species.The assembled transcriptome presented herein will also provide a valuable resource to the Ipomoea community, as well as to those interested in utilizing the close relationship between the Convolvulaceae and the Solanaceae for phylogenetic and comparative genomics examinations.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences. University of Cincinnati, Cincinnati, Ohio 45221.

Show MeSH
Related in: MedlinePlus