Leaf and fruit size are the crucial fitness characters for plant evolution and the agronomic traits for crop yield and quality improvement in watermelon. However, the underlying genes and molecular mechanisms for regulating fruit size and biomass remain elusive. Here, we identified a Citrullus lanatus UDP-rhamnose (Rha)/UDP-galactose (Gal) transporter ClURGT4, which is localized in the Golgi apparatus and has the dual functions of transporting UDP-Gal and UDP-Rha. Loss-of-function clurgt4 mutants resulted in decreased biomass and reduced Gal, Rha, and galacturonic acid (GalA) in cell wall components. Microscopical analysis showed that ClURGT4 promoted leaf and fruit size by modulating cell expansion. Proteomic analysis revealed that several cell wall metabolism-related proteins were changed in clurgt4 mutants. Moreover, protein glycosylation was changed in the mutants, and several of the differentially glycosylated proteins were related to cell wall metabolism. These findings elucidated that ClURGT4 might control leaf and fruit size by affecting cell wall metabolism and provided a novel case for comprehensively revealing the regulatory network of watermelon biomass.

Watermelon (Citrullus lanatus), an important member of the Cucurbitaceae family, has become one of the most popular economic crops in the world, and understanding its fruit development and ripening has always been a hot topic. Although DNA methylation is known to play an essential role in fruit ripening, its contribution to watermelon ripening remains unknown. Here, we found a global and conspicuous hypermethylation pattern during watermelon fruit development and ripening, which is opposite to the hypomethylation found in tomato and strawberry. Application of the DNA methylation inhibitor 5-azacytidine (5-Aza) delayed fruit ripening, confirming that the positive role of hypermethylation in this process. The hypermethylation mainly occurred in CHG and CHH types, and gene-body hypermethylation strongly correlated with the expression of genes that related to sugar metabolism and ABA (abscisic acid) response. We also found an overall hypermethylation pattern in domesticated watermelon. ClROS1 (Repressor Of Silencing 1), a gene encoding the DNA demethylase, was under selection; its expression was negatively correlated with DNA methylation levels, suggesting that it contributes to the hypermethylation during ripening. Collectively, our research illuminates the genome-wide DNA methylation dynamics during watermelon ripening and provides an invaluable genetic resource that will greatly benefit the molecular breeding and quality improvement of this important crop.

Pangenomes are increasingly important for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here we present a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated genomes representing all seven species. This super-pangenome captures approximately 1 million structural variants (SVs), enabling accurate variant genotyping across 914 accessions. Broader sampling within the pangenome provides insights into watermelon genome evolution and the origin of cultivated watermelon. Incorporating SVs into genome-wide association studies improves mapping resolution and reveals a copy number variant upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, these findings and genomic resources establish a foundation for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crops.

Heterosis, characterized by enhanced resistance and yield, has been widely utilized in watermelon breeding. However, our understanding of the regulatory mechanisms underlying male-sterile phenotypes in watermelon remains limited. Here, we determined that the miR159a targets ClMYB33 to regulate anther dehiscence, leading to male sterility in watermelon. Both overexpression of Cl-miR159a (OE-miR159a) and knockout of ClMYB33 (clmyb33) in watermelon suppressed the degradation of septum and stomium tissues, thereby impairing anther dehiscence and preventing successful pollen release. Based on DNA affinity purification sequencing (DAP-seq), RNA-seq, and verified interaction assays, ClPG1 and ClQRT2 were identified as downstream target genes of ClMYB33; both were positively regulated by ClMYB33. Both ClPG1 and ClQRT2 exhibited polygalacturonase (PG) activity in vivo. The knockout of ClQRT2 led to reduced PG activity and a failure in anther dehiscence. Furthermore, the GST-ClQRT2 fusion protein was capable of rescuing the indehiscent anther phenotype observed in both OE-miR159a and clmyb33 plants. Our results reveal a new mechanism by which the miR159a-ClMYB33 module regulates anther dehiscence by mediating PG activity, and provide a new molecular tool to create male sterility in watermelon.

Vegetables are crucial to human diet and health. To ensure sustainable vegetable production, regulatory measures are needed to enhance seed germination, plant growth, and resilience to extreme environmental conditions. Nanomaterials (NMs), owing to their high surface area, nanoscale dimensions, and unique photocatalytic properties, exhibit remarkable biological effects, such as promoting germination and growth, as well as improving stress resistance in crops, offering novel solutions to key challenges in vegetable cultivation. This review summarizes the absorption pathways of NMs in plants, specifically through the leaves and roots of vegetables. Their uptake and translocation occur via passive diffusion, active transport, and endocytosis, with key influencing factors including particle size, chemical composition, surface charge, and surface modifications. We further evaluate the advantages of nanofertilizers and nanopesticides, in vegetable production over their traditional counterparts, focusing on improvements in seed germination rates, seedling vigor, biotic and abiotic stress tolerance, and overall yield and quality. Through this review, we aim to offer comprehensive insights into the application of NMs in vegetable crop production.

N6-methyladenosine(m6A)is the most prevalent internal chem-ical modification found in eukaryotic mRNAs,playing a critical reg-ulatory role across various stages of mRNA metabolism[1].With the development of RNA immunoprecipitation using m6A-specific antibodies followed by sequencing(m6ARIP-seq),m6A modification has been widely reported in viral RNAs across a diverse range of viruses that replicate either in the nucleus or the cytoplasm[2].

Fruit size correlates with yield potential and serves as a vital agronomic trait. However, the key regulatory genes controlling fruit size in watermelon (Citrullus lanatus) remain poorly understood. In this study, we identified a NAC transcription factor gene ClNAC100 localized to selective sweep regions that positively regulated plant height and fruit size. CRISPR-Cas9-mediated knockout of ClNAC100 caused dramatic reductions in both plant height and fruit size, concomitant with decreased gibberellin (GA) levels in mutants. Exogenous GA4 application partially rescued the plant height and fruit size of the clnac100 mutant, while it could not restore these traits to wild-type levels. ClNAC100 directly upregulated expansin gene ClEXPA1 and GA biosynthetic genes ClGA3oxs, though DELLA protein interactions attenuated this transcriptional activation. A natural variant (-1087, T/C) of ClNAC100 enabled the Dof transcription factor ClDof4.6 to bind and activate ClNAC100 expression during watermelon domestication. Together, our results demonstrate that ClNAC100 mainly modulates the GA pathway to regulate fruit size and plant height, advancing mechanistic understanding of these agriculturally critical traits.

Oriental melon, a climacteric fruit prized for its superior quality, faces limited shelf life. Although knockout NON-RIPENING (CmNOR) prolongs storage duration at the expense of quality loss, the potential of its direct agricultural application to reconcile this conflict remains uninvestigated. Through crossing homozygotes Cmnor and wild-type (WT) plants, we created CmNOR/Cmnor heterozygotes. These heterozygotes exhibited a 6-day ripening delay accompanied by reduced sucrose and β-carotene levels, yet ultimately attained WT quality parameters. Exogenous ethylene treatment accelerated fruit softening but failed to restore key quality parameters in both heterozygotes and homozygotes to WT levels. Transcriptomic and quantitative polymerase chain reaction (qPCR) analysis revealed that homozygotes displayed >10-fold expression differences versus WT in quality-associated genes (e.g. involved in carotenoid biosynthesis and sucrose metabolism). These expression disparities diminished to approximately 2-fold in heterozygotes. Furthermore, heterozygotes extended shelf life by 3-5 days during storage at 20°C while maintaining fruit quality. Storage-phase differential genes clustered in water regulation and cell wall modification pathways, with heterozygous-WT expression disparities gradually decreasing over time. The CmNOR dosage effect dynamically modulates interconnected quality and preservation networks, proposing an editing-based solution to overcome the storability-quality dichotomy in climacteric fruits.

The regulation of non-climacteric fruit ripening by the transcription factor NON-RIPENING (NOR) is poorly understood. Here, we identified that the NOR homolog in the non-climacteric fruit watermelon (Citrullus lanatus) was located within the selective sweep and sweetness quantitative trait locus that was selected during domestication from landraces to cultivars. ClNOR knockout substantially delayed fruit ripening, and the fruits of the knockout plants had lower abscisic acid (ABA) levels, lighter colored flesh, and were less sweet compared to wild type. Transcriptome analysis and DNA affinity purification sequencing revealed that ClNOR targeted the Basic Leucine Zipper gene ClbZIP1, which links ClNOR to genes that do not have a ClNOR-binding motif in their promoters, such as the ABA biosynthesis gene, 9-cis-epoxycarotenoid dioxygenase ClNCED1 and the chromoplast phosphate transporter gene ClPHT4;2. The double mutant Clnor Clbzip1 exhibited delayed fruit ripening, lower ABA level, and lighter colored flesh. Its delayed ripening phenotype was stronger than that of the Clbzip1 single mutant. Additionally, the ClNORT,T haplotype in cultivated watermelon resulted in higher ClbZIP1 expression, but ClNORC,T from landraces and ClNORC,G from ancestral watermelon did not. Heterologous ClNORT,T expression rescued the delayed ripening phenotype of the Slnor knockout in tomato (Solanum lycopersicum). This natural variant (564T/C) of ClNOR promoted fruit ripening by enhancing target genes transcription. Overall, these findings will help elucidate the evolutionary mechanisms of nonclimacteric fruit ripening.

Watermelon is one of the most important cucurbit crops, but its production is seriously affected by viral infections. Although eIF4E proteins have emerged as the major mediators of the resistance to viral infections, the mechanism underlying the contributions of eIF4E to watermelon disease resistance remains unclear. In this study, three CleIF4E genes and one CleIF(iso)4E gene were identified in the watermelon genome. Among these genes, CleIF4E1 was most similar to other known eIF4E genes. To investigate the role of CleIF4E1, CRISPR/Cas9 technology was used to knock out CleIF4E1 in watermelon. One selected mutant line had an 86 bp deletion that resulted in a frame-shift and the expression of a truncated protein. The homozygous mutant exhibits developmental defects in plant growth, leaf morphology and reduced yield. Furthermore, the mutant was protected against the zucchini yellow mosaic virus, but not the cucumber green mottled mosaic virus. In summary, this study preliminarily clarified the functions of eIF4E proteins in watermelon. The generated data will be useful for elucidating eIF4E-related disease resistance mechanisms in watermelon. The tissue-specific editing of CleIF4E1 in future studies may help to prevent adverse changes to watermelon fertility.

Watermelon (Citrullus lanatus) as non-climacteric fruit is domesticated from the ancestors with inedible fruits. We previously revealed that the abscisic acid (ABA) signaling pathway gene ClSnRK2.3 might influence watermelon fruit ripening. However, the molecular mechanisms are unclear. Here, we found that the selective variation of ClSnRK2.3 resulted in lower promoter activity and gene expression level in cultivated watermelons than ancestors, which indicated ClSnRK2.3 might be a negative regulator in fruit ripening. Overexpression (OE) of ClSnRK2.3 significantly delayed watermelon fruit ripening and suppressed the accumulation of sucrose, ABA and gibberellin GA(4). Furthermore, we determined that the pyrophosphate-dependent phosphofructokinase (ClPFP1) in sugar metabolism pathway and GA biosynthesis enzyme GA20 oxidase (ClGA20ox) could be phosphorylated by ClSnRK2.3 and thereby resulting in accelerated protein degradation in OE lines and finally led to low levels of sucrose and GA(4). Besides that, ClSnRK2.3 phosphorylated homeodomain-leucine zipper protein (ClHAT1) and protected it from degradation to suppress the expression of the ABA biosynthesis gene 9'-cis-epoxycarotenoid dioxygenase 3 (ClNCED3). These results indicated that ClSnRK2.3 negatively regulated watermelon fruit ripening by manipulating the biosynthesis of sucrose, ABA and GA(4). Altogether, these findings revealed a novel regulatory mechanism in non-climacteric fruit development and ripening.

Fruit ripening is a highly complicated process that is accompanied by the formation of fruit quality. In recent years, a series of studies have demonstrated post-transcriptional control play important roles in fruit ripening and fruit quality formation. Till now, the post-transcriptional mechanisms for watermelon fruit ripening have not been comprehensively studied. In this study, we conducted PacBio single-molecule long-read sequencing to identify genome-wide alternative splicing (AS), alternative polyadenylation (APA) and long non-coding RNAs (lncRNAs) in watermelon fruit. In total, 6,921,295 error-corrected and mapped full-length non-chimeric (FLNC) reads were obtained. Notably, more than 42,285 distinct splicing isoforms were derived from 5,891,183 intron-containing full-length FLNC reads, including a large number of AS events associated with fruit ripening. In addition, we characterized 21,506 polyadenylation sites from 11,611 genes, 8703 of which have APA sites. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that fructose and mannose metabolism, starch and sucrose metabolism and carotenoid biosynthesis were both enriched in genes undergoing AS and APA. These results suggest that post-transcriptional regulation might potentially have a key role in regulation of fruit ripening in watermelon. Taken together, our comprehensive PacBio long-read sequencing results offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of watermelon fruit ripening.

甜瓜是我国重要的蔬菜作物,海南是我国重要的甜瓜产区,而病毒病的发生严重影响了海南甜瓜的生产.综述了近几年在海南发生的较为严重的几种病毒病害,并在此基础上分析了病毒病的流行原因,并提出了相应的防控措施.及时了解病毒病害发生的种类、有效使用化学药剂防控田间传播介体、培育抗病品种是当前防控病毒病害的重要举措,旨在为甜瓜的安全生产、病毒病害防治提供科学依据和参考.

Watermelon (Citrullus lanatus, 2n = 2x = 22) is an economically important Cucurbitaceae species that is widely cultivated worldwide. Commercial watermelon cultivars are usually F1 hybrids due to harness heterosis, which used pure lines as parents. However, obtaining pure inbred lines requires at least eight generations of self-pollinating, which is time-consuming, resource-intensive and cost-prohibitive. By contrast, doubled haploid (DH) technology provides homozygous lines within two generations. Parthenogenesis is the best-known method to obtain DHs in cucurbits, but this method in cucurbits presents many limiting factors which impede efficient production of haploids, especially in watermelon (Sari and Solmaz, 2021). New approach for producing DH efficiently in Cucurbitaceae is urgent for their application in breeding programs. Significant advances have been made in DH production in dicots, with the application of a haploid-inducing (HI) gene, Domain of unknown function 679 membrane protein (DMP) (Zhong et al., 2019), whose homologues have been identified in both monocots and dicots (Zhong et al., 2020). Importantly, mutations in DMP homologues trigger HI and produced DHs in Fabaceae (Wang et al., 2022), Solanaceae (Zhong et al., 2022a,b) and Brassicaceae (Li et al., 2022; Zhong et al., 2022b). However, this approach has not yet been applied in Cucurbitaceae. Here, we identified six putative DMP-like genes in the watermelon genome. In accordance with the pipeline proposed for selection of DMP candidate genes for HI (Zhong et al., 2020), we selected ClDMP4 (Cla97C06G121370; the most similar gene to ZmDMP) (Figure S1), which is specifically expressed in male flower buds and pollen (Figure S2). To introduce mutations in ClDMP4, we designed a construct for genome editing via clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated nuclease 9 (Cas9), targeting the first exon of ClDMP4; the binary construct also included a cassette (Figure 1a) driving the expression of enhanced fluorescence protein (Venus) under the control of the cauliflower mosaic virus (CaMV) 35S promoter for the later identification of haploid seeds. After Agrobacterium (Agrobacterium tumefaciens)-mediated transformation (Tian et al., 2017), two homozygous cldmp4 mutants with insertion (1 bp) or deletion (2 bp) that resulted in translational frame shifts and premature stop codons were generated in the watermelon inbred line PI179878 background (Figure 1b). Compared with wild type, cldmp4 mutants reduced the number of filled seeds and increased the percentage of aborted seeds, as previously reported. To investigate whether Cldmp4 mutants can induce maternal haploids when used as the male parent, we used pollen from Cldmp4 mutants to pollinate the F1 hybrid ‘yellow JingXin No.1 (YJX1)’. YJX1 is a yellow-rind hybrid derived from a cross of a dark green female parent and a yellow-rind male parent, whose offspring display a variety of rind colours. To identify haploid plants among the F1 offspring of the YJX1 9 Cldmp4 cross, we looked for green fluorescence in peeled seeds as an indicator of diploid hybrid seeds (Figure 1c). We then grew seeds devoid of fluorescence and genotyped the resulting seedlings with a pair of kompetitive allele-specific PCR (KASP) markers. KASP markers can distinguish the difference of one nucleotide between two parents, seedlings with the same genotyping as YJX1 are considered as possible haploids. Finally, we confirmed the haploids by flow cytometry (Figure 1e), chromosome counting (Figure 1f) and plant phenotyping (Figure 1g). To further test the maternal origin of these haploids, we analysed 42 single nucleotide polymorphisms (SNPs) that differ between Cldmp4 (generated in the watermelon inbred line GS24, whose rind is striped dark green) and YJX1 using the KASP platform (Yang et al., 2022). We established that none of these haploid seedlings carries SNPs from the paternal parent, as we only detected maternally-derived SNPs. Compared to diploid controls, haploid watermelon seedlings were smaller (Figure 1g,h) and produced smaller leaf and reproductive organs than the diploids (Figure 1i–l). In addition, the haploid watermelon plants were male sterile, similar to previously described haploids (Zhong et al., 2020). Haploid plants are typically sterile and their chromosome number needs to double to develop into fertile diploid homozygous plants. We thus applied 25 mg/L oryzalin directly to the shoot apex of haploid watermelon seedlings (Bae et al., 2020). We observed the successful conversion of three haploid seedlings into DH plants, with restoration of fertility. The offspring of these three DHs have stable rind colours, like the dark green or yellow rind parents of YJX1. The F2 offspring of the YJX1 9 Cldmp4 cross display a variety of rind colours (Figure 1m). We further crossed Cldmp4 mutants (as male parents) to two other F1 hybrid watermelon plants (JM2K and YXF3). The average haploid induction rate (HIR) ranged from 0.55% to 1.08% (Figure 1n). These results indicate that dmp mutants can be used for efficient and genotype-independent maternal DH production in watermelon.

Streptomyces alfalfa strain 11F has inhibitory effects on many phytopathogenic fungi and improves the establishment and biomass yield of switchgrass. However, the antagonistic effects of strain 11F on Fusarium wilt of watermelon and its secondary metabolites that contribute to its biocontrol activity are poorly understood. We evaluated the antagonistic and growth-promoting effects of strain 11F and conducted a transcriptome analysis to identify the metabolites contributing to antifungal activity. Strain 11F had marked inhibitory effects on six fungal pathogens. The incidence of Fusarium wilt of watermelon seedlings was decreased by 46.02%, while watermelon seedling growth was promoted, as indicated by plant height (8.7%), fresh weight (23.1%), and dry weight (60.0%). Clean RNA-sequencing data were annotated with 7553 functional genes. The 2582 differentially expressed genes (DEGs) detected in the Control vs. Case 2 comparison were divided into 42 subcategories of the biological process, cellular component, and molecular function Gene Ontology categories. Seven hundred and forty functional genes (55.47% of the DEGs) were assigned to Kyoto Encyclopedia of Genes and Genomes metabolic pathways, reflecting the complexity of the strain 11F metabolic regulatory system. The expression level of the gene phzF, which encodes an enzyme essential for phenazine-1-carboxylic acid (PCA) synthesis, was downregulated 3.7-fold between the 24 h and 48 h fermentation time points, suggesting that strain 11F can produce phenazine compounds. A phenazine compound from 11F was isolated and identified as phenazine-1-carboxamide (PCN), which contributed to the antagonistic activity against Fusarium oxysporum f. sp. niveum. PCA was speculated to be the synthetic precursor of PCN. The downregulation in phzF expression might be associated with the decrease in PCA accumulation and the increase in PCN synthesis in strain 11F from 24 to 48 h. Streptomyces alfalfae 11F protects watermelon seedlings from Fusarium wilt of watermelon and promotes seedling growth. The transcriptome analysis of strain 11F provides insights into the synthesis of PCN, which has antifungal activity against F. oxysporum f. sp. niveum of watermelon.

Fruit ripening is a highly complicated process, which is modulated by phytohormones, signal regulators and environmental factors playing in an intricate network that regulates ripening-related genes expression. Although transcriptomics is an effective tool to predict protein levels, protein abundances are also extensively affected by post-transcriptional and post-translational regulations. Here, we used RNA sequencing (RNA-seq) and tandem mass tag (TMT)-based quantitative proteomics to study the comprehensive mRNA and protein expression changes during fruit development and ripening in watermelon, a non-climacteric fruit. A total of 6,226 proteins were quantified, and the large number of quantitative proteins is comparable to proteomic studies in model organisms such as Oryza sativa L. and Arabidopsis. Base on our proteome methodology, integrative analysis of the transcriptome and proteome showed that the mRNA and protein levels were poorly correlated, and the correlation coefficients decreased during fruit ripening. Proteomic results showed that proteins involved in alternative splicing and the ubiquitin proteasome pathway were dynamically expressed during ripening. Furthermore, the spliceosome and proteasome were significantly enriched by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis, suggesting that post-transcriptional and post-translational mechanisms might play important roles in regulation of fruit ripening-associated genes expression, which might account for the poor correlation between mRNAs and proteins during fruit ripening. Our comprehensive transcriptomic and proteomic data offer a valuable resource for watermelon research, and provide new insights into the molecular mechanisms underlying the complex regulatory networks of fruit ripening.

The mutation of ClZISO identified in EMS-induced watermelon leads to photosensitive flesh in watermelon. Watermelon (Citrullus lanatus) has a colorful flesh that attracts consumers and benefits human health. We developed an ethyl-methanesulfonate mutation library in red-fleshed line ‘302’ to create new flesh color lines and found a yellow-fleshed mutant which accumulated ζ-carotene. The initial yellow color of this mutant can be photobleached within 10 min under intense sunlight. A long-term light-emitting diode (LED) light treatment turned flesh color from yellow to pink. We identified this unique variation as photosensitive flesh mutant (‘psf’). Using bulked segregant analysis, we fine-mapped an EMS-induced G-A transversion in ‘psf’ which leads to a premature stop codon in 15-cis-ζ-carotene isomerase (ClZISO) gene. We detected that wild-type ClZISO is expressed in chromoplasts to catalyze the conversion of 9,15,9’-tri-cis-ζ-carotene to 9,9’-di-cis-ζ-carotene. The truncated ClZISOmu protein in psf lost this catalytic function. Light treatment can partially compensate ClZISOmu isomerase activity via photoisomerization in vitro and in vivo. Transcriptome analysis showed that most carotenoid biosynthesis genes in psf were downregulated. The dramatic increase of ABA content in flesh with fruit development was blocked in psf. This study explores the molecular mechanism of carotenoid biosynthesis in watermelon and provides a theoretical and technical basis for breeding different flesh color lines in watermelon.

为了探明低温弱光环境对西瓜果实糖分积累的调节机制,本试验通过分析棉籽糖水解酶碱性α-半乳糖苷酶基因aga2突变体转录组数据发现低温弱光下aga2突变体西瓜果实中有686个基因上调表达,990个基因下调表达,进一步通过GO和KEGG分析发现MYB、NAC、WRKY等转录因子上调表达抵御低温弱光;而肌醇半乳糖苷合酶(Cla009222)、α-半乳糖苷酶(Cla022883、Cla019238)等与糖分代谢相关的基因在低温弱光下下调表达可能是导致aga2突变体果实糖含量下降的主要原因.本试验通过分析转录组数据,挖掘响应低温弱光的西瓜糖分积累相关基因,为西瓜果实响应低温弱光的糖代谢调控网络奠定了基础.

Grafting cultivation is implemented worldwide mainly to resist abiotic and biotic stresses and is an effective method to improve watermelon production. However, grafting may affect fruit development and quality. In our experiment, pumpkin-grafted (PG) watermelon fruits developed slower and the ripening period was extended compared to self-grafted (SG) fruits. We found that the concentrations of abscisic acid (ABA) among endogenous phytohormones were dramatically reduced by pumpkin grafting. In order to understand these changes at the gene expression level, we performed a comprehensive analysis of the fruit flesh transcriptomes between PG and SG during fruit development and ripening. A total of 1,675 and 4,102 differentially expressed genes (DEGs) were identified between PG and SG. Further functional enrichment analysis revealed that these DEGs were associated with carbohydrate biosynthesis, phytohormone signaling transmission, and cell wall metabolism categories. ABA centric phytohormone signaling and fruit quality-related genes including ABA receptor, PP2C proteins, AP2-EREBP transcription factors, sucrose transporter, and carotenoid isomerase were co-expressed with fruit ripening. These results provide the valuable resource for understanding the mechanism of pumpkin grafting effect on watermelon fruit ripening and quality development.