Limits...
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.

Show MeSH

Related in: MedlinePlus

Confirmation of RNA-seq results. (A) Bar plot of edgeR and quantitative polymerase chain reaction (qPCR) log2 fold changes from resistant to susceptible lines (positive fold change indicates greater expression in resistant lines). Top blast descriptors are as follows: ceram is ceramidase family protein, brass is brassinosteroid insensitive 1−associated receptor kinase 1, pecmet is pectin methylesterase, serthre is receptor serine-threonine protein, vichyd is vicianin hydrolase-live, p450_0 is cytochrome p450 82a3-like, germd is (-)-germacrene d synthase, and helica is u5 small nuclear ribonucleoprotein helicase. B) Confirmation of 14 edgeR differentially expressed genes by qPCR (r = 0.632, P = 0.000675).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC4199709&req=5

fig7: Confirmation of RNA-seq results. (A) Bar plot of edgeR and quantitative polymerase chain reaction (qPCR) log2 fold changes from resistant to susceptible lines (positive fold change indicates greater expression in resistant lines). Top blast descriptors are as follows: ceram is ceramidase family protein, brass is brassinosteroid insensitive 1−associated receptor kinase 1, pecmet is pectin methylesterase, serthre is receptor serine-threonine protein, vichyd is vicianin hydrolase-live, p450_0 is cytochrome p450 82a3-like, germd is (-)-germacrene d synthase, and helica is u5 small nuclear ribonucleoprotein helicase. B) Confirmation of 14 edgeR differentially expressed genes by qPCR (r = 0.632, P = 0.000675).

Mentions: Analysis using edgeR detected 19 genes that were differentially expressed between resistant and susceptible individuals following P-value adjustments (Figure 6). Twelve transcripts were down-regulated, and seven transcripts were up-regulated in the resistant compared to susceptible families (Figure 6). Seven of these were annotated by Blast2GO as simply “protein” (Table 4). Five of the seven transcripts that were up-regulated in the resistant families could be annotated—one exhibited homology to a member of the cytochrome P450 family, two were germacrene D-synthases, one a protein kinase, and the final up-regulated transcript exhibited homology to a ribonucleoprotein helicase (Table 4). Seven of the 12 transcripts that were down-regulated in resistant compared to susceptible families were annotated as a viacianin hydrolase-like protein, a pectin methylesterase, a ceramidase family protein, an ATP-binding protein, and a brassinosteroid insensitive 1-associated receptor kinase (Table 4). There was no evidence that the scaffold identified as EPSP synthase exhibited differential expression between the R and S lines (edgeR Log Fold Change = 0.013, P-value = 0.74) indicating that resistance in this species is not conferred by overexpression of EPSP synthase as in other species. Finally, the qPCR analysis of the expression patterns of 14 genes support our RNA-seq results (Figure 7). The expression patterns of transcripts identified as differentially expressed exhibit the same patterns in the qPCR validation (Figure 7A); over all loci tested, the relationship between the two methods was positive and significant (r = 0.632, P < 0.001, Figure 7B).


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)

Confirmation of RNA-seq results. (A) Bar plot of edgeR and quantitative polymerase chain reaction (qPCR) log2 fold changes from resistant to susceptible lines (positive fold change indicates greater expression in resistant lines). Top blast descriptors are as follows: ceram is ceramidase family protein, brass is brassinosteroid insensitive 1−associated receptor kinase 1, pecmet is pectin methylesterase, serthre is receptor serine-threonine protein, vichyd is vicianin hydrolase-live, p450_0 is cytochrome p450 82a3-like, germd is (-)-germacrene d synthase, and helica is u5 small nuclear ribonucleoprotein helicase. B) Confirmation of 14 edgeR differentially expressed genes by qPCR (r = 0.632, P = 0.000675).
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig7: Confirmation of RNA-seq results. (A) Bar plot of edgeR and quantitative polymerase chain reaction (qPCR) log2 fold changes from resistant to susceptible lines (positive fold change indicates greater expression in resistant lines). Top blast descriptors are as follows: ceram is ceramidase family protein, brass is brassinosteroid insensitive 1−associated receptor kinase 1, pecmet is pectin methylesterase, serthre is receptor serine-threonine protein, vichyd is vicianin hydrolase-live, p450_0 is cytochrome p450 82a3-like, germd is (-)-germacrene d synthase, and helica is u5 small nuclear ribonucleoprotein helicase. B) Confirmation of 14 edgeR differentially expressed genes by qPCR (r = 0.632, P = 0.000675).
Mentions: Analysis using edgeR detected 19 genes that were differentially expressed between resistant and susceptible individuals following P-value adjustments (Figure 6). Twelve transcripts were down-regulated, and seven transcripts were up-regulated in the resistant compared to susceptible families (Figure 6). Seven of these were annotated by Blast2GO as simply “protein” (Table 4). Five of the seven transcripts that were up-regulated in the resistant families could be annotated—one exhibited homology to a member of the cytochrome P450 family, two were germacrene D-synthases, one a protein kinase, and the final up-regulated transcript exhibited homology to a ribonucleoprotein helicase (Table 4). Seven of the 12 transcripts that were down-regulated in resistant compared to susceptible families were annotated as a viacianin hydrolase-like protein, a pectin methylesterase, a ceramidase family protein, an ATP-binding protein, and a brassinosteroid insensitive 1-associated receptor kinase (Table 4). There was no evidence that the scaffold identified as EPSP synthase exhibited differential expression between the R and S lines (edgeR Log Fold Change = 0.013, P-value = 0.74) indicating that resistance in this species is not conferred by overexpression of EPSP synthase as in other species. Finally, the qPCR analysis of the expression patterns of 14 genes support our RNA-seq results (Figure 7). The expression patterns of transcripts identified as differentially expressed exhibit the same patterns in the qPCR validation (Figure 7A); over all loci tested, the relationship between the two methods was positive and significant (r = 0.632, P < 0.001, Figure 7B).

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