Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragmental duplications within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon’s ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue- or stage-specific. We analyzed the ALDH gene’s expression patterns under six stress types, namely salt, cold, waterlogged, powdery mildew, Fusarium wilt, and gummy stem blight. The results showed differential expression of CmALDH2C4 and CmALDH11A3 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR (quantitative reverse transcription PCR) analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Pigments in plants not only determine their visual characteristics but also play crucial roles in photosynthesis, pollinator attraction, and disease resistance. The diverse colors of chili peppers arise from various pigments. However, detailed reports on the genetic and metabolic changes of these pigments in the developmental stages of colorful chili peppers are limited. In this study, we analyzed the content of anthocyanins and carotenoids in the fruits of the cultivated pepper variety H18 at different growth and development stages. Our findings revealed that, as the fruits mature, the anthocyanin content gradually decreases while the carotenoid content increases. Using the transcriptomic and metabolomic sequencing of pepper fruits at various developmental stages, we identified four types of anthocyanins: pelargonidin, cyanidin, delphinidin, and peonidin, as well as a small amount of proanthocyanidins. The concentrations of these anthocyanins generally showed a decreasing trend, and the expression patterns of anthocyanin biosynthesis genes were consistent with the metabolic data. In the analysis of carotenoids, we found that, apart from Lutein, the concentrations of all other detected carotenoids increased during fruit development. Most carotenoids began to accumulate significantly at the orange fruit stage (H18-O) and peaked at the red fruit stage (H18-R). Transcriptomic and RT-qPCR data indicated that the expression of carotenoid biosynthesis genes also increased progressively. Furthermore, we investigated the degradation of anthocyanins and identified potential degradation genes, including BGLU, POD, and PPO. This study provides deep insights into the mechanisms underlying pigment changes in colorful peppers, which may contribute to the improvement of pepper varieties and future research on pigment regulatory mechanisms.

Through the integration of genomic information, transcriptome sequencing data, and bioinformatics methods, we conducted a comprehensive identification of the ALDH gene family in melon. We explored the impact of this gene family on melon growth, development, and their expression patterns in various tissues and under different stress conditions. Our study discovered a total of 17 ALDH genes spread across chromosomes 1, 2, 3, 4, 5, 7, 8, 11, and 12 in the melon genome. Through a phylogenetic analysis, these genes were classified into 10 distinct subfamilies. Notably, genes within the same subfamily exhibited consistent gene structures and conserved motifs. Our study discovered a pair of fragment repeats within the melon ALDH gene. Furthermore, there was a noticeable collinearity relationship between the melon's ALDH gene and that of Arabidopsis (12 times), and rice (3 times). Transcriptome data reanalysis revealed that some ALDH genes consistently expressed highly across all tissues and developmental stages, while others were tissue or stage-specific. We analysed the ALDH gene's expression patterns under six stress types, namely salt, chilling, waterlogged, powdery mildew, fusarium wilt, and gummy stem blight. The results showed differential expression of MELO3C024328 and MELO3C004430 under all stress conditions, signifying their crucial roles in melon growth and stress response. RT-qPCR analysis further corroborated these findings. This study paves the way for future genetic improvements in melon molecular breeding.

Golden2-like (GLK) genes positively regulate chloroplast development, increase crop yields, and improve fruit quality. However, there has been no comprehensive identification and characterization of GLKs in watermelon. In this study, a total of 48 ClGLKs were identified in the watermelon genome. Based on phylogenetic analysis, they were divided into five groups. ClGLKs within the same group showed a similar gene structure and conserved motif compositions. Promoter analysis indicated that cis-elements responsive to light were the most abundant, though cis-elements associated with hormones, stress, and developmental regulation were also identified in ClGLKs promoters. Expression analysis indicated significant responses of some ClGLKs to drought and CGMMV stress, suggesting that these genes may participate in responses to biotic and abiotic stresses. Phenotypic analyses revealed enhanced chloroplast development and increased thylakoid density and chlorophyll content in the pericarp of a “dark green” watermelon cultivar. ClGLK8 was identified as the homolog of GLK1-2, the genes that promote chloroplast development and chlorophyll biosynthesis in fruits, and showed significantly increased expression in accordance with chloroplast development and chlorophyll accumulation. Our results provide detailed knowledge of the ClGLKs, which will enhance efforts to further improve the fruit quality of watermelon.

Dirigent proteins (DIR) are involved in lignan biosynthesis, stress responses, and disease resistance in plants. However, systematic characterization of the DIR gene family in watermelon (Citrullus lanatus) remains limited. Here, we identified 22 ClDIR genes in watermelon using bioinformatics methods, designated ClDIR1 to ClDIR22, which were unevenly distributed across eight chromosomes and classified into three subfamilies (DIR-a, DIR-b/d, DIR-e) based on phylogenetic analysis, with DIR-b/d being the largest. Synteny analysis revealed that tandem duplication primarily drove ClDIR family expansion, and collinear relationships with Arabidopsis, rice, and cucurbit species indicated evolutionary conservation. Cis-acting element analysis showed abundant stress- and hormone-responsive elements in ClDIR promoters, suggesting roles in stress regulation. Tissue-specific expression analysis demonstrated distinct patterns, with most genes highly expressed in roots. Expression profiling under 16 abiotic and biotic stresses showed 18 ClDIR genes responded to stress, with ClDIR8 differentially expressed across all conditions. qRT-PCR validation of six key genes (ClDIR5, ClDIR8, ClDIR9, ClDIR12, ClDIR16, ClDIR22) confirmed their expression patterns under high-temperature, drought, salt, and low-temperature stresses, showing a high degree of consistency with transcriptome data. Subcellular localization indicated ClDIR8 is peroxisome-localized. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays validated two ClDIR8-interacting proteins, Cla97C02G049920 (encoding peroxidase) and Cla97C08G152180 (encoding catalase). These findings provide insights into ClDIR genes in watermelon, highlighting ClDIR8 as a key stress-responsive candidate for further functional studies and breeding.