Analysis of Differentially Expressed Genes in Transcriptome
Based on the gene expression profiles induced by trypsin treatment, the analysis of expression level differences was completed. First, the results of sample correlation analysis showed that there was a strong correlation between biological duplicate samples (Fig. 1A). PCA analysis showed that the samples were divided into two independent groups (Fig. 1B), with significant differences between the two groups (PC1= 55.58%), while the samples marked with the same color within the group were closely clustered together (PC2= 12.63%). A total of 9061 DEGs were screened from the expression difference analysis, among which 4416 were upregulated and 4645 were downregulated (Figure 1C).
These DEGs were further categorized based on their transcription factor families (Figure 1D), and it was found that they were mainly enriched in the ERF, MYB, bHLH, and WRKY families. Subsequently, we conducted KEGG pathway enrichment analysis on the 9061 significantly DEGs and found that they were distributed across 131 metabolic pathways (Table S2), with 83 genes enriched in the MAPK signaling pathway. We established a gene set for this pathway and conducted further analysis.
GSEA Analysis of MAPK Pathway-Related Genes
By conducting GSEA analysis on the 83 genes enriched in the MAPK signaling pathway, the results indicated that in addition to being annotated in the MAPK pathway itself (MAP04016), they were also annotated in the Plant-Pathogen Interaction pathway (MAP04626) and Plant Hormone Signal Transduction pathway (MAP04075) (Table 1).
Table 1:GSEA Analysis Statistical Table
gene set name
|
Description
|
Size
|
ES
|
NES
|
p_value
|
p adjust
|
Rank at MAX
|
Leading edge
|
MAP04016
|
MAPK signaling pathway - plant
|
83
|
1
|
1
|
0
|
0.146667
|
82
|
83
|
MAP04626
|
Plant-pathogen interaction
|
24
|
-0.26342
|
-0.79703
|
0.725191
|
0.738269
|
15
|
8
|
MAP04075
|
Plant hormone signal transduction
|
42
|
0.230415
|
0.965639
|
0.485915
|
0.9185
|
11
|
9
|
A total of 9 genes were enriched in the leading edge subset of the MAP04075 pathway, among which the screenedMYCtranscription factor (Table S3) has been previously reported by our laboratory [29]. Moreover, from the leading edge subset of the MAP04626 pathway, a total of 8 genes were screened (Table S4). Among these 8 genes, we identified CsaV3_4G006110 as a member of the WRKY transcription factor family, named WRKY33in the study by Chen et al [36]. As an essential transcription factor involved in the MAPK pathway, we hypothesized that CsWRKY33 might influence the synthesis and metabolism of relevant substances, thus enhancing the fruit's disease-resistance capacity.
Co-expression Network Analysis of WRKY33 and Metabolites
Through widely targeted metabolomic analysis, a total of 175 significantly different metabolites were identified (Table S5). We constructed a co-expression network by integrating the transcriptomic data with the metabolomic data to analyze the expression correlations between the selected 83 genes and the metabolites (Figure 3A). The co-expression network, created by using Cytoscape, consisted of 226 nodes and 811 edges.
Furthermore, we employed the "EPC" ranking method using cytoHubba to prioritize the associations between CsWRKY33and the 8 metabolites (Figure 3B). It's noticeable that CsWRKY33 displayed negative correlations with most metabolites from the relationship between genes and metabolites. Among them, the most significant negative correlations were observed with 2-hydroxy-3-phenylpropanoic acid and vanillin. Additionally, other metabolites, such as dihydrocharcone-4'-O-glucoside, were also negatively correlated with CsWRKY33.
Bioinformatics Analysis of the CsWRKY33 Gene
The CsWRKY33gene shares a high similarity of 95.22% with CmWRKY22(The sequences were provided in Table S6). CsWRKY33's open reading frame (ORF) spans a total length of 810 base pairs, encoding a polypeptide comprising 269 amino acids. The calculated molecular weight for this polypeptide was approximately 30.31 kDa, with a theoretical isoelectric point of 6.323. Notably, at its N-terminal region,CsWRKY33harbored a highly conserved WRKYGQK amino acid sequence, which constituted the distinctive WRKY domain characteristic of WRKY transcription factors. Additionally, CsWRKY33featured a putative zinc finger motif (C-X4-5-C-X22-23-H-X1-H) (Figure 4A). Through the utilization of the Blast online alignment tool on NCBI, we conducted multiple sequence alignment involving 11 highly homologous proteins, and subsequently, we constructed an evolutionary tree employing MEGA 6.0 software. The results conclusively indicated that CsWRKY33exhibited the highest homology with CmWRKY22(Figure 4B).
Cloning of CsWRKY33 partial sequence and vector construction
Utilizing C. sativus cDNA as the template, a 249-bp cDNA fragment was amplified with CsWRKY33-specific primers. The agarose gel electrophoresis of the PCR product is shown in Figure 5A. The amplified fragment was excised from the gel and then sent to Sangon Biotech (Shanghai) Co., Ltd. for sequencing. The alignment results confirmed that the fragment is specific to the CsWRKY33gene. The pTRV2-CsWRKY33 vector was constructed (Figure 5B). Subsequently, these plasmids were introduced into the Agrobacterium strainGV3101 for use in the subsequent VIGS validation experiment.
Fruit phenotypic changes and data measurement
During the initial storage period, C. sativus fruits from all groups exhibited good quality with vibrant color (Figure 6A). After 16 days of storage, the control group fruits showed evident yellowing, severe shriveling at the top and near the center, and signs of rot (Figure 6A). In contrast, the fruits treated with trypsin maintained the highest overall freshness, with the least yellowing and shriveling of the skin, and no signs of decay on the surface (Figure 6A). The freshness preservation effect of the silenced group was also superior to the control group, with only slight yellowing at the root and minimal overall yellowing and mild shriveling at the top. As the storage time extended, the weight loss rate of fruits in all groups significantly increased (Figure 6B). The control group exhibited the highest fruit weight loss rate (43.36%), while the trypsin-treated group had the lowest rate (22.55%) (Figure 6B). The weight loss rate of the silenced group's fruits was 30.33%, indicating that VIGS treatment and trypsin treatment slowed down the rate of fruit water loss. Furthermore, verification through RT-qPCR (Figure 6C) revealed thatWRKY33expression was suppressed by trypsin treatment compared to the control group. The silenced group also showed consistent downregulation of WRKY33expression, further confirming the potential role of trypsin in preservation through the inhibition of WRKY33expression.