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. 2022 Dec 22:13:1106123.
doi: 10.3389/fpls.2022.1106123. eCollection 2022.

A transcriptome analysis of Benincasa hispida revealed the pathways and genes involved in response to Phytophthora melonis infection

Jinsen Cai  1 , Songguang Yang  1 , Wenrui Liu  1 , Jinqiang Yan  1 , Biao Jiang  1 , Dasen Xie  1   2
Affiliations

A transcriptome analysis of Benincasa hispida revealed the pathways and genes involved in response to Phytophthora melonis infection

Jinsen Cai et al. Front Plant Sci. .

Abstract

Wilt disease caused by Phytophthora melonis infection is one of the most serious threats to Benincasa hispida production. However, the mechanism of the response of B. hispida to a P. melonis infection remains largely unknown. In the present study, two B. hispida cultivars with different degrees of resistance to P. melonis were identified: B488 (a moderately resistant cultivar) and B214 (a moderately susceptible cultivar). RNA-seq was performed on P. melonis-infected B488 and B214 12 hours post infection (hpi). Compared with the control, 680 and 988 DEGs were respectively detected in B488 and B214. A KEGG pathway analysis combined with a cluster analysis revealed that phenylpropanoid biosynthesis, plant-pathogen interaction, the MAPK signaling pathway-plant, and plant hormone signal transduction were the most relevant pathways during the response of both B488 and B214 to P. melonis infection, as well as the differentially expressed genes in the two cultivars. In addition, a cluster analysis of transcription factor genes in DEGs identified four genes upregulated in B488 but not in B214 at 6 hpi and 12 hpi, which was confirmed by qRT-PCR. These were candidate genes for elucidating the mechanism of the B. hispida response to P. melonis infection and laying the foundation for the improvement of B. hispida.

Keywords: Benincasa hispida; Phytophthora melonis; RNA-Seq; resistanceassociated gene; wilt disease.

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Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
P. melonis resistance of B488 and B214. (A) Two-leaf stage B488 and B214 seedlings were irrigated with 5 ml of a P. melonis zoospore suspension (103 zoospores per milliliter) for each seedling, pictures showed the state of B488 and B214 seedlings at 4 days post infection (dpi). (B) the survival rates of B488 and B214 were calculated daily for 5 days post infection.
Figure 2
Figure 2
DEGs and the validation of selected DEGs using qRT-PCR. (A) Venn diagrammatic analysis of DEGs in B488 and B214. (B) up- and downregulated DEGs in B488 (mock infection vs. PmI) and B214 (mock infection vs. PmI). (C) Randomly selected DEGs expression tendency of qRT-PCR data compared with RNA-seq FKPM data.
Figure 3
Figure 3
KEGG annotations analysis and GO annotations analysis of DEGs. (A) KEGG annotations analysis of the DEGs in B488 (mock infection vs. PmI) and B214 (mock infection vs. PmI), the number indicated the percent of gene enrichment in the pathway. (B) GO annotations analysis of DEGs in B488 (mock vs. PmI) and B214 (mock vs. PmI).
Figure 4
Figure 4
KEGG enrichment analysis of DEGs. (A) KEGG enrichment analysis of the DEGs in B488. (B) KEGG enrichment analysis of the DEGs in B214. The y-axis indicates the pathway names, and the x-axis indicates the rich factor. Rich factor refers to the ratio of the number of DEGs located in the KEGG pathway and the total number of genes in the KEGG pathway. The larger the rich factor the greater the degree of enrichment. The size of the dots indicates the number of genes in the pathway, while the color of the dots indicates the adjust p-value ranges.
Figure 5
Figure 5
Heatmap of DEGs. (A) Heatmap of the DEGs in the phenylpropanoid biosynthesis pathway. (B) Heatmap of the DEGs in the plant pathogen interaction pathway. (C) Heatmap of the DEGs in the MAPK signaling-plant pathway. (D) Heatmap of the DEGs in the plant hormone signal transduction pathway. Log10(FPKM+1) values were used in the heatmap, and the average values of FPKM from the three biological replicates were used for log10 (FPKM+1) calculation. Red indicates high expression, and blue indicates low expression.
Figure 6
Figure 6
TF family of DEGs. (A) Statistics for TF in B488 (mock infection vs. PmI). (B) Statistics of TF in B214 (mock infection vs. PmI). (C) Heatmap of differentially expressed TF genes between B488 (mock infection vs. PmI) and B214 (mock infection vs. PmI).
Figure 7
Figure 7
Expression pattern of TF genes. A P. melonis zoospore suspension (105 zoospores per milliliter) was sprayed on surface of B488 and B214 leaves, sterilized water was sprayed on surface of B488 and B214 leaves as the control; leaves were harvested at 6 h and 12h for RNA extraction and subsequent qRT-PCR analysis, six biological replicates were performed, p value was determined using Fisher’s protected LSD test.
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