Genomic Resources and Gene Family Studies in Longan (Dimocarpus longan Lour.): Progress, Limitations, and Prospects

The rapid accumulation of genome-scale data has transformed plant biology from descriptive genetics to predictive and increasingly mechanistic genomics. Longan (Dimocarpus longan Lour.) is an economically important subtropical fruit tree in China and Southeast Asia, but compared with model plants and major temperate fruit crops, its genomic resources and functional studies have developed relatively late. Here, we review recent progress in longan genomics with emphasis on three interrelated areas: genome assembly and annotation, transcriptomic resources, and representative gene family studies associated with flowering, somatic embryogenesis, and transporter-mediated stress tolerance. The progression from the first draft genome of ‘Honghezi’ to the chromosome-scale assemblies of ‘Jidanben’ and ‘Shixia’ has substantially improved contiguity and gene annotation, thereby enabling population-genomic analysis, genome-wide gene family identification, and candidate-gene discovery. Available transcriptomic datasets further support studies of reproductive development, stress responses, and embryogenic competence, although cross-study integration remains limited. We also summarize how gene family analyses have advanced the current understanding of floral induction, continuous flowering, somatic embryogenesis, mineral transport, and sugar transport in longan. Importantly, the field is still dominated by cataloguing and expression-based inference, whereas causal validation, pan-genomic analysis, and multi-omics integration remain insufficient. We therefore argue that future progress in longan molecular breeding will depend on integrating high-quality genomic resources with functional validation, standardized comparative annotation, and improved transformation or regeneration systems.