The NBS-LRR (NLR) gene family plays a pivotal role in regulating disease defense response in plants. Cucumber is one of the most important vegetable crops in the world, and various plant diseases, including powdery mildew (PM), cause severe losses in both cucumber productivity and quality annually. To characterize and understand the role of the CC-NBS-LRR(CNL) family of genes in disease defense response in cucumber plants, we performed bioinformatical analysis to characterize these genes systematically. We identified 33 members of the CNL gene family in cucumber plants, and they are distributed on each chromosome with chromosome 4 harboring the largest cluster of five different genes. The corresponding CNL family member varies in the number of amino acids and exons, molecular weight, theoretical isoelectric point (pI) and subcellular localization. Cis-acting element analysis of the CNL genes reveals the presence of multiple phytohormone, abiotic and biotic responsive elements in their promoters, suggesting that these genes might be responsive to plant hormones and stress. Phylogenetic and synteny analysis indicated that the CNL proteins are conserved evolutionarily in different plant species, and they can be divided into four subfamilies based on their conserved domains. MEME analysis and multiple sequence alignment showed that conserved motifs exist in the sequence of CNLs. Further DNA sequence analysis suggests that CsCNL genes might be subject to the regulation of different miRNAs upon PM infection. By mining available RNA-seq data followed by real-time quantitative PCR (qRT-PCR) analysis, we characterized expression patterns of the CNL genes, and found that those genes exhibit a temporospatial expression pattern, and their expression is also responsive to PM infection, ethylene, salicylic acid, and methyl jasmonate treatment in cucumber plants. Finally, the CNL genes targeted by miRNAs were predicted in cucumber plants. Our results in this study provided some basic information for further study of the functions of the CNL gene family in cucumber plants.

Watermelon (Citrullus lanatus), a vital economic crop, is severely threatened by Fusarium wilt (FW), which is caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. niveum (Fon). To elucidate the molecular mechanisms underlying FW resistance in watermelon, we tracked the infection process via microscopy, identifying three critical time points (1, 6, and 8 days post-inoculation) corresponding to spore germination, hyphal invasion of the xylem vascular system, and symptom onset, respectively. Transcriptional profiling at these stages revealed six disease-resistance-associated gene modules through differential expression analysis, expression pattern clustering, weighted gene co-expression network analysis, and functional enrichment. These modules exhibited strong correlations with distinct infection phases. Protein–protein interaction networks identified 35 hub genes, including receptor-like kinases; WRKY and ethylene-responsive factor transcription factors; and genes involved in cell wall reinforcement, hormone signaling, defense metabolism/detoxification, programmed cell death regulation, and antimicrobial compound biosynthesis. Differential expressions of these genes across infection stages likely underpin the observed phenotypic disparities. Five hub regulatory genes were identified by quantitative real-time PCR in the SRgreen and SRblack modules, namely, Cla97C01G014990 (WRKY transcription factor 42), Cla97C02G042360 (calcium-transporting ATPase), Cla97C08G155710 (AIG2), Cla97C09G170380 (ethylene-responsive factor 1B-like), and Cla97C06G121810 (receptor kinase, putative). These genes mediate early rapid defense responses via SRgreen and sustain long-term resistance through SRblack. By validating the expression patterns of hub genes, the study elucidated the watermelon resistance response and provided insights into transcriptional regulation during different stages of Fon–watermelon interactions. Additionally, it identified candidate genes that could enhance watermelon resistance to wilt disease.