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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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The cytochrome P450 genes identified in the I. purpurea transcriptome by a blast analysis using the cytochrome P450 family and subfamily sequences from tomato. Each circle, or node, represents a transcript from I. purpurea, with the tomato cytochrome P450 families indicated by separate colors.
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fig5: The cytochrome P450 genes identified in the I. purpurea transcriptome by a blast analysis using the cytochrome P450 family and subfamily sequences from tomato. Each circle, or node, represents a transcript from I. purpurea, with the tomato cytochrome P450 families indicated by separate colors.

Mentions: The cytochrome P450gene family is one of the largest families in plant genomes with as many as 300 genes belonging to 50 gene families (Nelson et al. 2004; Hamberger and Bak 2013). Given the diversity of functions that cytochrome P450 genes perform in plant genomes, we elected to explore the number of cytochrome P450 genes, and their assembly quality in the I. purpurea transcriptome to provide further context for expression patterns detected in our RNA-seq screen (presented below). Of the ~35K transcripts in the I. purpurea transcriptome that exhibited a significant blast hit, 289 were identified as a cytochrome P450 gene, and a blastx to a curated database of tomato cytochrome P450 proteins further identified 34 families and 121 subfamilies of P450 gene within I. purpurea. Families homologous to the tomato cytochrome P450 gene families, and their relative sizes in the I. purpurea transcriptome, are shown in Figure 5. Of these 121 subfamilies, 7 exhibited homology to subfamilies that are pseudogenes in tomato (Table S6). Seven transcripts did not exhibit homology to a curated tomato P450 protein and could not be assigned to a family. The CYP82 superfamily is the most highly represented P450 gene family in the I. purpurea transcriptome, with 53 transcripts belonging to seven different subfamilies (Figure 5). The sequencing and assembly effort presented herein thus produced a large number of P450 genes for downstream analysis, and the majority (~250) of these transcripts were sequenced at almost the full length of other plant cytochrome P450 proteins (i.e., >90% length; Figure S5).


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)

The cytochrome P450 genes identified in the I. purpurea transcriptome by a blast analysis using the cytochrome P450 family and subfamily sequences from tomato. Each circle, or node, represents a transcript from I. purpurea, with the tomato cytochrome P450 families indicated by separate colors.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

fig5: The cytochrome P450 genes identified in the I. purpurea transcriptome by a blast analysis using the cytochrome P450 family and subfamily sequences from tomato. Each circle, or node, represents a transcript from I. purpurea, with the tomato cytochrome P450 families indicated by separate colors.
Mentions: The cytochrome P450gene family is one of the largest families in plant genomes with as many as 300 genes belonging to 50 gene families (Nelson et al. 2004; Hamberger and Bak 2013). Given the diversity of functions that cytochrome P450 genes perform in plant genomes, we elected to explore the number of cytochrome P450 genes, and their assembly quality in the I. purpurea transcriptome to provide further context for expression patterns detected in our RNA-seq screen (presented below). Of the ~35K transcripts in the I. purpurea transcriptome that exhibited a significant blast hit, 289 were identified as a cytochrome P450 gene, and a blastx to a curated database of tomato cytochrome P450 proteins further identified 34 families and 121 subfamilies of P450 gene within I. purpurea. Families homologous to the tomato cytochrome P450 gene families, and their relative sizes in the I. purpurea transcriptome, are shown in Figure 5. Of these 121 subfamilies, 7 exhibited homology to subfamilies that are pseudogenes in tomato (Table S6). Seven transcripts did not exhibit homology to a curated tomato P450 protein and could not be assigned to a family. The CYP82 superfamily is the most highly represented P450 gene family in the I. purpurea transcriptome, with 53 transcripts belonging to seven different subfamilies (Figure 5). The sequencing and assembly effort presented herein thus produced a large number of P450 genes for downstream analysis, and the majority (~250) of these transcripts were sequenced at almost the full length of other plant cytochrome P450 proteins (i.e., >90% length; Figure S5).

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