De novo assembly and annotation of the transcriptome of the agricultural weed Ipomoea purpurea uncovers gene expression changes associated with herbicide resistance.
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.
Affiliation: Department of Biological Sciences. University of Cincinnati, Cincinnati, Ohio 45221.Show MeSH
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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.
Affiliation: Department of Biological Sciences. University of Cincinnati, Cincinnati, Ohio 45221.