3.3 Identification and functional enrichment analysis of DEGs
Both the growth of fungi and accumulation of H2O2 and O2- indicated that 24 hpi is the key point to differentiate the defense responses of susceptible and resistant accessions to GSB pathogen infection. Therefore, the samples at 24 hpi were selected for full-length transcriptome sequencing. A total of 118.2 Gb clean data with an average read length of 1229.3 bp were obtained (Supplementary Table 1). The ONT reads were mapped onto the reference genome. The expression abundance of the annotated genes was quantified using Ballgown and then DEGs were determined using DESeq2 (Figure 2A). Compared with their respective controls, 958 DEGs (457 up-regulated and 501 down-regulated) were identified for Payzawat, and 380 DEGs (344 up-regulated and 36 down-regulated) were identified for PI511890 after GSB pathogen infection. Additionally, a total of 663 DEGs were identified between Payzawat and PI511890 after GSB pathogen infection.
GO enrichment analysis showed that four terms of biological process were specifically enriched in PI511890 after infection relative to Payzawat, including hydrogen peroxide catabolic process, cell wall organization, response to wounding, and defense response (Figure 2B, Supplementary Figure2). KEGG enrichment analysis showed that three pathways (pyruvate metabolism, phenylpropanoid biosynthesis, and nitrogen metabolism) were enriched in both PI511890 and Payzawat after infection, demonstrating that these pathways are the common defense responses of melon to GSB (Figure 2C). Moreover, there were five pathways specifically enriched in PI511890 after infection, including biosynthesis of other secondary metabolites (flavonoid biosynthesis, stilbenoid, diarylheptanoid and gingerol biosynthesis, flavone and flavonol biosynthesis), MAPK signaling pathway-plant, and galactose metabolism. The DEGs enriched in the pathway of secondary metabolite synthesis were all up-regulated in GSB pathogen infected PI511890. On the other hand, 18 pathways were specifically enriched in Payzawat after infection, which included carbohydrate metabolism (glyoxylate and dicarboxylate metabolism, citrate cycle, pentose phosphate pathway, and glycolysis/gluconeogenesis), amino acid metabolism (glycine, serine and threonine metabolism, alanine, aspartate and glutamate metabolism, glutathione metabolism, arginine biosynthesis, phenylalanine metabolism, phenylalanine, tyrosine and tryptophan biosynthesis), and HIF-1 signaling pathway. These results indicated that PI511890 and Payzawat exhibit contrasting defense responses to GSB by regulating different pathways. PI511890 coped with GSB by regulating biosynthesis of secondary metabolites and MAPK signaling pathway. However, the defense response of Payzawat to GSB mainly involved carbohydrate metabolism and amino acid metabolism.