Genomic insights into longan evolution from a chromosome-level genome assembly and population genomics of longan accessions

Longan (Dimocarpus longan) is a subtropical fruit tree best known for its nutritious fruit and regarded as a valuable tonic and traditional medicine since ancient times. A high-quality chromosome-scale genome assembly is valuable for functional genomic study and genetic improvement of longan. Here, we report a chromosome-level reference genome sequence for the longan cultivar JDB. The assembled genome is 455.5 Mb in size and anchored to fifteen chromosomes, representing a significant improvement in contiguity (contig N50 = 12.1 Mb, scaffold N50 = 29.5 Mb) over a previous draft assembly. A total of 40 420 protein-coding genes were predicted in the D. longan genome. Synteny analysis suggests that longan shares the widespread gamma event with core eudicots but has no other whole genome duplications. Comparative genomics showed that the D. longan genome experienced significant expansions of UDP-glucosyltransferase and phenylpropanoid biosynthesis-related gene families. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor to its genetic diversity and revealed clear population admixture and introgression among cultivars of different geographic origins, suggesting a likely migration trajectory of longan that is confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTLs) for six different fruit quality traits and revealed a shared QTL that contained three genes for total soluble solids and seed weight. The chromosome-level reference genome assembly, annotation, and population genetic resources for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.