Integrated transcriptomic and metabolomic analysis of Jinggang honey pomelo yellow spot disease to reveal the disease resistance mechanism

Abstract

Jinggangshan honey pomelo is a specialty fruit grown in Jiangxi Province, China. Pomelo yellow spot disease, also known as greasy spot disease, is a fungal pathology primarily affecting pomelo (Citrus maxima) leaves and fruits. The causative agent is the ascomycete fungus Phyllosticta citricarpa, taxonomically classified within the phylum Ascomycota.This study performed integrated metabolomic and transcriptomic analysis to identify key differentially accumulated metabolites (DAMs) and differentially expressed genes (DEGs) between the control (CK) and diseased groups (HB) of the Jinlan pomelo (af) and Jinsha pomelo (js) varieties. We identified 1,681 DAMs in the af variety and 1,233 DAMs in the jsCK_vs_jsHB variety. Flavonoid compounds were the most upregulated class of DAMs in both the af and js diseased varieties. Transcriptome analysis identified 1,714 common DEGs between the af and js diseased varieties. KEGG pathway enrichment analysis demonstrated that these common DEGs were significantly enriched in pathways such as plant hormone signal transduction, plant-pathogen interaction, phenylpropanoid biosynthesis, MAPK signaling pathway in plants, and flavonoid biosynthesis. The integrated metabolome and transcriptome analysis showed that the metabolic pathways associated with the common DEGs and DAMs in both the af and js varieties were significantly enriched in phenylpropanoid biosynthesis pathway. Our data showed that differential expression of key enzymes in the flavonoid biosynthesis and phenylpropanoid biosynthesis pathways led to the accumulation of flavonoid metabolites, which play a crucial role in the plant defense mechanisms against external stresses, including pathogen infection. The results suggest that the flavonoid compounds play a key role in the disease resistance mechanism of Jinggangshan honey pomelo against yellow spot disease.

Fig 1. Jinggang honey pomelo metabolome changes in response to Phyllosticta citricarpa.

(A) PCA score plot. (B) Select the top 20 Metabolite classification summary based on the HMDB database. (C-D) Volcano plots of differentially expressed metabolites between the afCK _vs_afHB and jsCK_vs_jsHB groups (p-value < 0.05 and Fold Change > 1).

Fig 2. Analysis of the metabolome changes in Jinggang honey pomelo in response to infection by Phyllosticta citricarpa.

(A) The Venn diagram shows common DAMs between the afCK_vs_afHB and jsCK_vs_jsHB groups. (B) Classification diagram shows common DAMs in the afCK_vs_afHB and jsCK_vs_jsHB groups. (C) Classification diagram shows DAMs that are co-upregulated in the afCK_vs_afHB and jsCK_vs_jsHB groups. (D) KEGG pathway enrichment map for the common DAMs. (E) Heat map of the 16 flavonoid DAMs.

Fig 3. Analysis of the transcriptome changes in the Jinggang honey pomelo varieties in response to infection by Phyllosticta citricarpa.

(A) The number of DEGs in the afCK_vs_afHB and jsCK_vs_jsHB groups. (B) Venn diagram shows the number of common DEGs between afCK_vs_afHB and jsCK_vs_jsHB groups. (C) GO analysis of the 1741 common DEGs. (D) KEGG pathway analysis of the 1741 common DEGs. (E-G) Classification diagrams of transcription factors associated with enriched DEGs in the afCK_vs_afHB and jsCK_vs_jsHB groups.

Fig 4. Integrated analysis of the metabolome and transcriptome in Jinggang honey pomelo.

(A-B) Venn diagram shows the number of common metabolic pathways represented by the DEGs and DAMs between the afCK_vs_afHB and jsCK_vs_jsHB groups. (C-D) Bar charts show the top 10 pathways with the most DAMs and DEGs in the afCK_vs_afHB and jsCK_vs_jsHB groups.

Fig 5. Heat maps of DAMs and DEGs related to the phenylpropanoid biosynthesis and flavonoid biosynthesis pathways.

In the metabolic pathways, red represents upregulated expression; green represents downregulated expression. In the heatmaps, colors indicate upregulation or downregulation of DAMs and DEGs; red represents upregulation and blue represents downregulation; darker color indicates higher expression level.

Fig 6. Spearman correlation network diagram.

(A-B) Correlation between DAMs and DEGs in the afCK_vs_afHB and jsCK_vs_jsHB groups.