Background: Long non-coding RNAs (lncRNAs) are a class of non-coding RNAs with more than 200 nucleotides in length, which play vital roles in a wide range of biological processes. Powdery mildew disease (PM) has become a major threat to the production of melon. To investigate the potential roles of lncRNAs in resisting to PM in melon, it is necessary to identify lncRNAs and uncover their molecular functions. In this study, we compared the lncRNAs between a resistant and a susceptible melon in response to PM infection. Results: It is reported that 11,612 lncRNAs were discovered, which were distributed across all 12 melon chromosomes, and > 85% were from intergenic regions. The melon lncRNAs have shorter transcript lengths and fewer exon numbers than protein-coding genes. In addition, a total of 407 and 611 lncRNAs were found to be differentially expressed after PM infection in PM-susceptible and PM-resistant melons, respectively. Furthermore, 1232 putative targets of differently expressed lncRNAs (DELs) were discovered and gene ontology enrichment (GO) analysis showed that these target genes were mainly enriched in stress-related terms. Consequently, co-expression patterns between LNC_018800 and CmWRKY21, LNC_018062 and MELO3C015771 (glutathione reductase coding gene), LNC_014937 and CmMLO5 were confirmed by qRT-PCR. Moreover, we also identified 24 lncRNAs that act as microRNA (miRNA) precursors, 43 lncRNAs as potential targets of 22 miRNA families and 13 lncRNAs as endogenous target mimics (eTMs) for 11 miRNAs. Conclusion: This study shows the first characterization of lncRNAs involved in PM resistance in melon and provides a starting point for further investigation into the functions and regulatory mechanisms of lncRNAs in the resistance to PM.

This study aimed to investigate the correlation between salt tolerance during the germination and seedling stages in melons by analyzing 10 melon varieties under NaCl stress during germination and seedling stages. We found that 200 mM is the appropriate concentration for screening salt-tolerant germplasm in melons. Salt stress led to a decline in germination and seedling growth parameters, while antioxidant enzyme activities and osmotic substance contents significantly increased. Specifically, the activities of CAT and SOD increased by up to 27.22-fold and 6.35-fold, respectively, and soluble protein and proline contents increased by up to 1.03-fold and 1.05-fold, respectively. Varietal differences in salt tolerance traits were observed. Correlation and principal component analyses revealed that 6 germination indicators could be consolidated into 1 comprehensive indicator, accounting for 79.225% of the variance, while 16 seedling-stage indicators were reduced to 3 comprehensive indicators, with a cumulative contribution rate of 75.089%. Membership function and cluster analyses categorized the 10 varieties into 3 groups at both stages, identifying ‘Xindongfangmi’ and ‘Jinyuliuxing’ as salt-tolerant varieties. Additionally, a significant positive correlation (r = 0.834) was found between the comprehensive membership function values of germination and seedling stages. These results provide a scientific basis for assessing melon salt tolerance, indicating that germination-stage salt tolerance may predict seedling-stage salt tolerance. By utilizing PCA, comprehensive evaluation, and cluster analysis of relevant indicators under salt stress during the germination period of melon, the salt tolerance of the seedling stage can be quickly identified. The implementation of rapid salt tolerance screening at the germination stage can facilitate the selection of salt-tolerant germplasm and the development of salt-tolerant melon varieties.

Salt stress, as a significant adverse consequence of global climate change, severely restricts the yield and quality of watermelon. In this study, salt-tolerant cultivar T23 and salt-sensitive cultivar B2 were subjected to a 200 mM NaCl treatment (0 h, 6 h, 24 h, 48 h, and 168 h) at the three-leaf stage, and the adaptation mechanisms of the watermelon roots to salt stress were systematically investigated at the phenotypic, physiological, and gene transcription levels. Phenotypic observations revealed that salt stress inhibited seedling growth, caused leaf curling, and induced root yellowing, with the damage being significantly more severe in B2 than in T23. Compared with B2, the activities of superoxide dismutase (SOD) were increased by −7.13%, 169.15%, 34.95%, 84.87%, and 39.87% under NaCl treatment at 0 h, 6 h, 24 h, 48 h, and 168 h, respectively. Compared to the 0 h NaCl treatment, the proline content in B2 increased by 4.25%, 14.39%, and 110.00% at 24 h, 48 h, and 168 h of NaCl treatment, respectively, while T23 showed increases of 93.74%, 177.55%, and 380.56% at the corresponding time points. The provided physiological data demonstrate that T23 exhibits superior antioxidant and osmoregulatory abilities relative to B2. The transcriptome analysis identified differentially expressed genes (DEGs) between the two cultivars under salt stress, with T23 showing the highest number of DEGs at 6 h, while B2 exhibited a significant increase in DEGs at 168 h. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed that metabolic pathways such as plant hormone signal transduction, terpenoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling pathways, transporter activity, and transcription regulator activity play important roles in the salt stress response. Furthermore, yeast overexpression experiments preliminarily validated the critical roles of the tonoplast dicarboxylate transporter gene ClCG01G010280 and the NAC transcription factor gene ClCG05G024110 in salt stress tolerance. This study provides new molecular insights into the salt tolerance mechanism of watermelon and offers potential genetic resources for breeding salt-tolerant varieties.

The WRKY proteins constitute a large family of transcription factors that have been known to play a wide range of regulatory roles in multiple biological processes. Over the past few years, many reports have focused on analysis of evolution and biological function of WRKY genes at the whole genome level in different plant species. However, little information is known about WRKY genes in melon ( Cucumis melo L.). In the present study, a total of 56 putative WRKY genes were identified in melon, which were randomly distributed on their respective chromosomes. A multiple sequence alignment and phylogenetic analysis using melon, cucumber and watermelon predicted WRKY domains indicated that melon WRKY proteins could be classified into three main groups (I-III). Our analysis indicated that no recent duplication events of WRKY genes were detected in melon, and strong purifying selection was observed among the 85 orthologous pairs of Cucurbitaceae species. Expression profiles of CmWRKY derived from RNA-seq data and quantitative RT-PCR (qRT-PCR) analyses showed distinct expression patterns in various tissues, and the expression of 16 CmWRKY were altered following powdery mildew infection in melon. Besides, we also found that a total of 24 WRKY genes were co-expressed with 11 VQ family genes in melon. Our comparative genomic analysis provides a foundation for future functional dissection and understanding the evolution of WRKY genes in cucurbitaceae species, and will promote powdery mildew resistance study in melon.

Leaf color mutants are key resources for uncovering the molecular mechanisms of chloroplast development and photosynthesis. Here, we identified a novel yellow-green melon mutant, ‘ygp2’, which displays yellow-green leaves and dwarfism throughout development. Genetic analysis indicated that the trait is controlled by a single recessive nuclear gene. Map-based cloning delimited the candidate region to an 805 kb interval on chromosome 11, within which only one missense mutation was identified in MELO13C_11G242690, encoding a triosephosphate isomerase (CmpdTPI). Phylogenetic analysis suggested its plastid localization, which was confirmed by transient expression of CmpdTPI-GFP in tobacco. The ‘ygp2’ mutant exhibited significantly reduced TPI enzyme activity and net photosynthetic rate. Transcriptome analysis revealed downregulation of genes related to light-harvesting complexes, cell division, and the cell cycle. These results demonstrate that the point mutation in CmpdTPI impairs chloroplast function and photosynthesis, leading to the yellow-green phenotype in melon. This study provides insight into the role of plastidial TPI in chlorophyll metabolism and chloroplast development.

To identify microRNAs (miRNAs) responsive to powdery mildew (PM) infection and elucidate their regulatory roles in melon PM resistance, thereby laying a foundation for deciphering the underlying molecular mechanisms, we combined high-throughput sequencing with bioinformatics analysis to screen PM-responsive miRNAs and their target genes using PM-resistant and PM-susceptible melon genotypes. In total, 113 non-redundant miRNAs were identified in both genotypes, including 70 known and 43 novel miRNAs. Subsequent differential expression analysis revealed distinct miRNA responses to PM infection between resistant and susceptible genotypes. Upon PM inoculation, 13 miRNAs showed significant differential expression in both susceptible and resistant genotypes. In addition, four miRNAs, including miR164c, miR396a, miR398a and miRn39, displayed differential expression specifically in the susceptible genotype. Conversely, five miRNAs (miR167c, miR398b, miR399g, miR530a and miRn8) showed differential expression exclusively in the resistant genotype upon PM infection. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses demonstrated that these miRNAs mediate melon’s susceptibility or resistance to PM by modulating plant immune homeostasis, antioxidant metabolism, and pathogen-triggered cell death. Quantitative real-time PCR (qRT-PCR) validation confirmed a negative regulatory relationship between the expression of PM-responsive miRNAs and their predicted target genes. Collectively, our findings provide novel insights and candidate targets for further investigations into miRNA functions and regulatory mechanisms underlying melon PM resistance.