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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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Related in: MedlinePlus

Average expression (fragments per kilo bases of transcripts per million mapped reads [FPKM]) values according to Gene Ontology (GO) Slim categories within the (A) Molecular Function, (B) Biological Process, and (C) Cellular Component GO categories.
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fig4: Average expression (fragments per kilo bases of transcripts per million mapped reads [FPKM]) values according to Gene Ontology (GO) Slim categories within the (A) Molecular Function, (B) Biological Process, and (C) Cellular Component GO categories.

Mentions: Following assignment of the top blast hit via blastx and the screen for TE sequences, we loaded the xml formatted blast results into the Blast2GO program to assign GO terms and performed further annotation of the transcripts. Of the 33,118 transcripts with at least one GO-term assignment, 28,156 were annotated in the level 1 GO categories of biological process, molecular function, and cellular component. The GOSlim category assignments of transcripts are presented in Figure S4, and the overall assignments are available in the supplemental annotation file (Table S1). The GOSlim categories that exhibit highest expression, on average, in the I. purpurea transcriptome are associated with photosynthesis (Figure 4) (structural molecule activity (Figure 4A), photosynthesis and generation of precursor metabolites (Figure 4B) and thylakoid (Figure 4C)—this result is in line with our expectations since the majority of the plant tissue used for RNA extraction was leaf tissue. Flower bud and stem tissues were also included in this bulk sample and as a result we were able to recover expressed transcripts that belong to, for example, the ‘pollen tube’ GOSlim category (Figure 4C).


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)

Average expression (fragments per kilo bases of transcripts per million mapped reads [FPKM]) values according to Gene Ontology (GO) Slim categories within the (A) Molecular Function, (B) Biological Process, and (C) Cellular Component GO categories.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig4: Average expression (fragments per kilo bases of transcripts per million mapped reads [FPKM]) values according to Gene Ontology (GO) Slim categories within the (A) Molecular Function, (B) Biological Process, and (C) Cellular Component GO categories.
Mentions: Following assignment of the top blast hit via blastx and the screen for TE sequences, we loaded the xml formatted blast results into the Blast2GO program to assign GO terms and performed further annotation of the transcripts. Of the 33,118 transcripts with at least one GO-term assignment, 28,156 were annotated in the level 1 GO categories of biological process, molecular function, and cellular component. The GOSlim category assignments of transcripts are presented in Figure S4, and the overall assignments are available in the supplemental annotation file (Table S1). The GOSlim categories that exhibit highest expression, on average, in the I. purpurea transcriptome are associated with photosynthesis (Figure 4) (structural molecule activity (Figure 4A), photosynthesis and generation of precursor metabolites (Figure 4B) and thylakoid (Figure 4C)—this result is in line with our expectations since the majority of the plant tissue used for RNA extraction was leaf tissue. Flower bud and stem tissues were also included in this bulk sample and as a result we were able to recover expressed transcripts that belong to, for example, the ‘pollen tube’ GOSlim category (Figure 4C).

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