Background: Leaves are the main organs involved in photosynthesis. They capture light energy and promote gas exchange, and their size and shape affect yield. Identifying the regulatory networks and key genes that control citrus leaf size is essential for increasing citrus crop yield. Methods: In this study, transcriptome sequencing was performed on three leaf materials: the ‘Cuimi’ kumquat (Nor) variety and its leaf variants, larger-leaf (VarB) and smaller-leaf (VarS) varieties. Results: Correlation and principal component analyses revealed a relatively close correlation between Nor and VarS. A total of 7264 differentially expressed genes (DEGs), including 2374 transcription factors (TFs), were identified, and 254 DEGs were common among the three materials. GO and KEGG enrichment analyses revealed significant enrichment in glucose metabolism, cell wall composition, starch biosynthesis, and photosynthesis pathways. WGCNA identified three specific modules related to the different leaf sizes of these three citrus materials. Fifteen candidate genes related to leaf size, including three transcription factors, Fh5g30470 (MYB), Fh7g07360 (AP2/ERF), and Fh5g02470 (SAP), were identified on the basis of connectivity and functional annotations. Conclusions: These findings provide a theoretical foundation for a deeper understanding of the molecular mechanisms underlying citrus leaf size and offer new genetic resources for the study of citrus leaf size.

Siraitia grosvenorii (monk fruit) is a cucurbitaceous plant endemic to China that serves as both food and medicine. Its fruit accumulates mogrosides, zero-calorie natural sweeteners approximately 300-fold sweeter than sucrose that are widely used in food and beverages. Whereas tissue-culture studies of S. grosvenorii have focused largely on regenerated plantlets, the metabolic events underlying tuber formation in vitro remain poorly characterized. Here, we combined morphological observation, quantification of starch and soluble sugars, time-series transcriptomics, and widely targeted metabolomics to dissect metabolic reprogramming during in vitro tuberization of S. grosvenorii. Visible tuber structures emerged at 45 days post-inoculation and accumulated starch continuously throughout development. Starch and sucrose metabolism and flavonoid biosynthesis acted as core pathways regulating the accumulation of carbohydrates and flavonoids. Candidate MYB, bHLH, and ERF transcription factors were screened to explore putative upstream regulation of these metabolic changes. Our results demonstrate that in vitro tuber formation of S. grosvenorii is a multi-stage, highly coordinated process, and provide a molecular basis for breeding high-quality propagation materials and for exploiting this species as a source of functional food ingredients and natural sweeteners.