Improved Longan Genome Assembly Reveals Insights Into Flowering Mechanisms

Longan is an exotic tropical fruit crop and exhibits off-season flowering induced by potassium chlorate (KClO₃), though the molecular mechanisms remain unclear. We assembled a high-quality, 441.5 Mb genome of variety 'Shixia', with a contig N50 at 28.1 Mb, 29, 325 protein-coding genes, 26 telomeres and 15 centromeres. Comparative genomic analysis with lychee revealed structural variations potentially driving gene family expansions related to flavone biosynthesis and disease resistance. Transcriptomic profiling showed that natural flowering appears to be primarily regulated by photoperiod, vernalisation and autonomous pathways, while KClO₃-induced flowering may preferentially activate the gibberellin pathway at 5 days after treatment (DAT) and autonomous pathways at 10 DAT, involving putative repression of DlDDF1, DlFLCs and DlSVPs, and up-regulation of DlWRKY75_2. In the perpetual-flowering variety 'Sijimi', elevated expression of photoperiod genes, such as DlCOR28, DlCOR27, DlADO3, DlPRR5, DlGI and DlJMJ30, may explain its perpetual blooming. Overexpression of DlDDF1 in Arabidopsis delayed flowering, partially reversed by KClO₃ through an increase in bioactive GA₄. Together, KClO₃-induced flowering likely involves oxidative stress response and gibberellin signalling via DlDDF1 repression, while natural flowering relies on seasonal cues. These results lay the foundation for longan genetic improvement.