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Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection - PubMed

  • ️Tue Jan 01 2019

Combined De Novo Transcriptome and Metabolome Analysis of Common Bean Response to Fusarium oxysporum f. sp. phaseoli Infection

Limin Chen et al. Int J Mol Sci. 2019.

Abstract

Molecular changes elicited by common bean (Phaseolus vulgaris L.) in response to Fusarium oxysproum f. sp. Phaseoli (FOP) remain elusive. We studied the changes in root metabolism during common bean-FOP interactions using a combined de novo transcriptome and metabolome approach. Our results demonstrated alterations of transcript levels and metabolite concentrations in common bean roots 24 h post infection as compared to control. The transcriptome and metabolome responses in common bean roots revealed significant changes in structural defense i.e., cell-wall loosening and weakening characterized by hyper accumulation of cell-wall loosening and degradation related transcripts. The levels of pathogenesis related genes were significantly higher upon FOP inoculation. Interestingly, we found the involvement of glycosylphosphatidylinositol- anchored proteins (GPI-APs) in signal transduction in response to FOP infection. Our results confirmed that hormones have strong role in signaling pathways i.e., salicylic acid, jasmonate, and ethylene pathways. FOP induced energy metabolism and nitrogen mobilization in infected common bean roots as compared to control. Importantly, the flavonoid biosynthesis pathway was the most significantly enriched pathway in response to FOP infection as revealed by the combined transcriptome and metabolome analysis. Overall, the observed modulations in the transcriptome and metabolome flux as outcome of several orchestrated molecular events are determinant of host's role in common bean-FOP interactions.

Keywords: Fusarium oxysproum; common bean; metabolome; plant–pathogen interaction; transcriptome.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1

Fusarium oxysproum f. sp. phaseoli infected (FO) and non-infected (CK) common bean roots and seedlings at 4, 8, 12, 18, and 24 h post infection.

Figure 2
Figure 2

(a) Overall distribution of sample gene expression, (b) principle component analysis of expressed genes, and (c) Pearson correlations between CK-24 and FO-24 replicates.

Figure 3
Figure 3

(a) Differential gene MA map. The ordinate represents the log2 fold change value; the abscissa represents the average value of gene expression in the two samples; the red dot represents the upregulation of the gene expression, and the green dot represents the downregulation of the expression. Blue indicates no significant difference in gene expression. (b) Kyoto encyclopedia of genes and genomes (KEGG) enrichment scatter plot. The ordinate represents the KEGG pathway. The abscissa represents the Rich factor. The larger the Rich factor, the greater the enrichment. The larger the point, the greater the number of differential genes enriched in the pathway. The redder the color of the dots, the more significant the enrichment.

Figure 4
Figure 4

KEGG orthology map (ko04626, plant–pathogen interaction) of common bean-Fusarium oxysproum f. sp. Phaseoli (FOP) pathosystem. For the treatment group, the red box labeled enzyme is associated with the upregulated gene, and the green box labeled enzyme is associated with the downregulated gene. The blue labeled enzyme is related to both upregulation and downregulation. This pathway map is associated with DEGs. The enzymes are all marked with different colors.

Figure 5
Figure 5

qRT-PCR validation of the selected common bean differentially expressed genes (DEGs) in control (CK-24) and FOP infected plants (FO-24) 24 h post infection.

Figure 6
Figure 6

(a) Heatmap hierarchical clustering of differentially expressed metabolites. Hierarchical trees were drawn based on differentially accumulated metabolites in CK-24 and FO-24. (b) Top 10 differentially accumulated metabolites in CK-24 and FO-24.

Figure 7
Figure 7

Differential metabolite KEGG enrichment. The larger value indicates that the degree of enrichment is greater. The closer the p-value is to 0, the more significant the enrichment is. The size of the points in the graph represents the number of distinct significant metabolites enriched into the corresponding pathway.

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