A chromosome-scale genome assembly of watermelon (Citrullus lanatus cv. 'Mimei') integrates multi-omics data to decipher fruit quality development.

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conclusionA high-quality chromosome-level genome assembly (366.66 Mb, BUSCO completeness 94.8%, HOGs completeness 93.93%) of the classic watermelon cultivar 'Mimei' was generated using Illumina, PacBio HiFi, and Hi-C sequencing. The annotated genome contains 25,271 protein-coding genes and 2504 non-coding RNAs, providing a valuable genomic reference for watermelon research and breeding. Integrated metabolomic and transcriptomic analyses revealed dynamic accumulation patterns of fructose, glucose, sucrose, and carotenoids during fruit development. Differential expression and KEGG enrichment analyses identified key pathways-starch and sucrose metabolism, fructose and mannose metabolism, and carotenoid biosynthesis-as central to fruit quality formation. Dynamic expression profiling and transient overexpression of ClaSHY2 (Cla02MM07830) revealed its role in enhancing chlorophyll accumulation (especially increase in chlorophyll b) and coordinating photosynthetic capacity with carbohydrate metabolism. The key gene ClLCYB (Cla04MM09400) was experimentally confirmed to catalyze the conversion of lycopene to β-carotene, elucidating the molecular mechanism of carotenoid metabolism. This study provides a comprehensive multiomics resource and theoretical framework for genomics-assisted breeding and quality improvement in watermelon. Watermelon (Citrullus lanatus) is one of the most important fruit crops worldwide. Its fruit is prized for sweetness, rich nutritional composition, and distinct flavor variation among cultivars. However, owing to the species' complex genetic background, the molecular mechanisms underlying fruit quality formation remain insufficiently understood, and the application of modern molecular breeding approaches in watermelon is still limited. In this study, we present the first high-quality chromosome-level genome of the classic cultivar 'Mimei' (MM), with a total size of 366.66 Mb. The assembly was anchored to 11 chromosomes and annotated with 25271 protein-coding genes. By integrating spectrophotometric colorimetry, liquid chromatography-mass spectrometry, and transcriptome sequencing, we investigated the dynamic changes in soluble sugars and carotenoid metabolism during MM fruit development and ripening. Transcriptomic profiling revealed extensive differential gene expression across developmental stages, with significant enrichment in pathways related to starch and sucrose metabolism, fructose and mannose metabolism, carotenoid biosynthesis, and plant hormone signal transduction. Key genes, including sucrose synthase, beta-amylase, and phytoene synthase, exhibited expression patterns consistent with the accumulation of sugars and carotenoids during fruit maturation. Notably, auxin signaling components displayed dynamic regulation, with ClaSHY2 (Cla02MM07830) showing potential roles in coordinating photosynthetic efficiency and carbohydrate partitioning. Transient overexpression of ClaSHY2 in watermelon leaves resulted in a more than 50% increase in chlorophyll b content, suggesting its involvement in chloroplast development and sugar metabolism. Moreover, heterologous expression assays confirmed that ClLCYB (Cla04MM09400) catalyzes the conversion of lycopene into β-carotene. Collectively, these results provide comprehensive genomic, metabolomic, and transcriptomic resources for elucidating the molecular basis of fruit quality formation in MM watermelon and establish a valuable foundation for genomics-assisted breeding of this classic cultivar.