Identification of Sucrose Phosphate Synthase, Sucrose Synthase, and Invertase Gene Families of Longan in Relation to On-Tree Preservation

As a typical sucrose-accumulating fruit, longan commonly experiences sugar receding during on-tree preservation, leading to quality deterioration. To investigate the mechanism of sucrose degradation in longan fruit, we conducted genome-wide identification and analysis of key genes involved in sucrose synthesis and catabolism based on the ‘Shixia’ (SX) genome. The results revealed that longan contained 8 sucrose synthases (SUSs), 4 sucrose phosphate synthases (SPSs), and 26 invertases (INVs). Notably, members of the longan SUS, SPS, and cell wall invertase (CWINV) families all contained the motif 10 sequence, while cytoplasmic invertase (CINV) members exhibited diverse motif combinations. Similarity analysis revealed that sequence similarity was reliable only when the sequence lengths of the compared genes were comparable. Cis-acting elements and miRNA prediction showed that these genes were enriched in MYB elements and regulated by miR156/827/171. Additionally, the expansion of SUS, SPS, and INV genes was driven by segmental duplication events under purifying selection. Furthermore, the ‘Chuliang’ (CL) cultivar exhibited slower on-tree sucrose degradation than SX, with sucrose accounting for 72.2% of total sugars at maturity, which is 33.4% higher than SX. Enzyme activity assay during the sucrose decline stage revealed that SUS, SPS, and INV activities were generally higher in SX pulp than in CL. Furthermore, correlation analysis showed that the activities of AINV and A/N-INV were both significantly negatively correlated with TSS and sucrose content, respectively. Additionally, the expression of DlCWINV10 exhibited a negative correlation with TSS (p < 0.05) and sucrose content (r = −0.6, p = 0.07), suggesting that DlCWINV10 may play an important role in the sucrose degradation process. In summary, this study elucidates the characteristics of SUS, SPS, and INV gene families in longan and their potential roles in sucrose metabolism, providing a theoretical foundation for understanding the on-tree sucrose degradation mechanism.