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.