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.

Longan is an ancient and popular plant with highly nutritious fruit. The pulp is the main part of the fruit which is consumed. However, the potentials of other longan fruit parts such as the peel and the seed as reservoirs of important bioactive components have not yet fully been explored. This study aimed at exploring the diversity of primary and secondary metabolites in two commercial longan varieties, i.e., Shixia and Chuliang, concerning fruit, pulp, peel, and seed based on a widely targeted metabolomics approach. A total of 706 metabolites were identified grouped into eight diverse classes of metabolites, including flavonoids, amino acids and its derivatives, alkaloids, tannins, phenolic acids, organic acids, nucleotides and derivatives, lipids, and lignans. Chuliang peel showed a higher accumulation of metabolites viz. flavonoids, alkaloids, and tannins, while Shixia seeds showed abundance in amino acids, organic acid, nucleic acids and its derivatives. Chuliang pulp showed relatively higher accumulation of lipids when compared with other fruit parts. Differential metabolome profiling between fruit parts indicates the prevalence of key metabolites, i.e., O-Phosphocholine, betaine, piperidine, L-Arginine, and L-Phenylalanine, in seed and peel of the longan fruit. The findings in this research provide a new glance on the nutritional value and biochemical basis of longan fruit pharmaceutical value, with emphasis on valorization of longan peel and seed tissues for their pharmaceutical properties and nutritional values.

Background: Essential micronutrient Boron (B) plays crucial roles in plant survival and reproduction but becomes toxic in higher quantities. Although plant cells have different B transport systems, B homeostasis is mainly maintained by two transporter protein families: B exporters (BOR) and nodulin-26-like intrinsic proteins (NIP). Their diversity and differential expression are responsible for varied B tolerance among plant varieties and species. Longan is a highly admired subtropical fruit with a rising market in China and beyond. In the present study, we cultured Shixia (SX) and Yiduo (YD), two differently characterized Longan cultivars, with foliar B spray. We analyzed their leaf physiology, fruit setting, B content, and boron transporter gene expression of various tissue samples. We also traced some of these genes' subcellular localization and overexpression effects. Results: YD and SX foliage share similar microstructures, except the mesophyll cell wall thickness is double in YD. The B spray differently influenced their cellular constituents and growth regulators. Gene expression analysis showed reduced BOR genes expression and NIP genes differential spatiotemporal expression. Using green fluorescent protein, two high-expressing NIPs, NIP1 and NIP19, were found to translocate in the transformed tobacco leaves' cell membrane. NIPs transformation of SX pollen was confirmed using magnetic beads and quantified using a fluorescence microscope and polymerase chain reaction. An increased seed-setting rate was observed when YD was pollinated using these pollens. Between the DlNIP1 and DlNIP19 transformed SX pollen, the former germinated better with increasing B concentrations and, compared to naturally pollinated plants, had a better seed-setting rate in YD♀ × SX♂. Conclusion: SX and YD Longan have different cell wall structures and react differently to foliar B spray, indicating distinct B tolerance and management. Two B transporter NIP genes were traced to localize in the plasma membrane. However, under high B concentrations, their differential expression resulted in differences in Jasmonic acid content, leading to differences in germination rate. Pollination of YD using these NIPs transformed SX pollen also showed NIP1 overexpression might overcome the unilateral cross incompatibility between YD♀ × SX♂ and can be used to increase Longan production.

Longan (Dimocarpus longan Lour.) is an important tropical and subtropical fruit, and most of its cultivars bloom once a year (once-flowering, OF). Dimocarpus longan cv. ‘Sijimi’ (SJ) is a tropical ecotype variety that blooms several times a year (continuous-flowering, CF) without the need for low-temperature induction. Several studies have focused on the mechanism of continuous flowering in SJ longan; however, none used leaves as research material. As leaves are a key organ in sensing floral-induction signals, we compared gene-expression differences between mature leaves of CF (SJ) and OF (D. longan cv. ‘Shixia’ (SX) and D. longan cv. ‘Chuliang’ (CL)) longan by transcriptome sequencing. An average of 47,982,637, 43,833,340 and 54,441,291 clean reads were obtained for SJ, SX and CL respectively, and a total of 6745 differentially expressed genes (DEGs) were detected. Following Metabolic pathways, Plant-pathogen interaction and Biosynthesis of secondary metabolites, most of the other genes were assigned to the KEGG classifications of MAPK signaling pathway- plant, Plant hormone signal transduction, Amino sugar and nucleotide sugar metabolism and Starch and sucrose metabolism. WGCNA analysis clustered genes into 27 modules, among which bisque4 and darkorange2 module genes specifically were expressed at low and high levels in SJ, respectively. Different gene-expression patterns were detected between CF and OF longan in bisque4 and darkorange2 modules, especially the high levels of transcription factor (TF) expression and the large number of gibberellic acid (GA)-signaling-pathway-specific genes expressed at high levels in CF longan (SJ). Floral-induction-gene expression levels in CF longan, such as levels of GA-signaling-related and FT genes, were always high. In CF longan, after vegetative-growth accumulation, flowers could be directly induced, thereby eliminating the need for low-temperature induction.

Longan ( Dimocarpus longan ) is a subtropical fruit best known for its nutritious fruit and regarded as a precious tonic and traditional medicine since ancient times. 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 longan cultivar JDB with an assembled genome of 455.5 Mb in size anchored to fifteen chromosomes, representing a significant improvement of 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 D. longan genome. Synteny analysis suggests longan shares the widespread gamma event with core eudicots, but has no other whole genome duplications. Comparative genomics showed that D. longan genome experienced significant expansions of gene families related to phenylpropanoid biosynthesis and UDP-glucosyltransferase. Deep genome sequencing analysis of longan cultivars identified longan biogeography as a major contributing factor for genetic diversity, and revealed a clear population admixture and introgression among cultivars of different geographic origins, postulating a likely migration trajectory of longan overall confirmed by existing historical records. Finally, genome-wide association studies (GWAS) of longan cultivars identified quantitative trait loci (QTL) for six different fruit quality traits and revealed a shared QTL containing three genes for total soluble solid and seed weight. The chromosome-level reference genome assembly, annotation and population genetic resource for D. longan will facilitate the molecular studies and breeding of desirable longan cultivars in the future.

The HB (homeobox) transcription factor family plays important roles in plant growth, development, morphogenesis, and stress responses; however, its involvement in longan (Dimocarpus longan Lour.) fruit energy metabolism remains unclear. In this study, 32 DlHB family members were identified in the longan genome, and their physicochemical properties, phylogenetic relationships, gene structures, conserved motifs, conserved domains, tissue-specific expression patterns, promoter cis-acting elements, and collinearity relationships were systematically analyzed. The DlHB family was classified into four subfamilies, HD-ZIP I–IV, with substantial divergence in structural composition, expression patterns, and putative regulatory features. Our previous work showed that 1.5% chitosan (CTS) treatment improved postharvest longan fruit quality through modulation of energy metabolism, and the corresponding CTS-treatment transcriptome was therefore used here to screen energy-metabolism-associated DlHB candidates. DlHB22 was selected as a representative candidate, and its CTS-responsive expression was independently confirmed by qRT-PCR. Exogenous ATP treatment was then used as an independent physiological validation of the relationship between energy metabolism and postharvest storability; ATP-treated fruit showed reduced deterioration together with higher ATP, ADP, and AMP contents and higher activities of H+-ATPase, Ca²+-ATPase, cytochrome c oxidase (CCO), and succinate dehydrogenase (SDH) at 15 d, although adenylate energy charge (AEC) was lower than in the control. DlHB22 localized predominantly to the nucleus. Heterologous overexpression of DlHB22 in tomato accelerated fruit color transition and ripening progression and altered ATP, ADP, and AMP contents, AEC, and the activities of H+-ATPase, Ca²+-ATPase, CCO, and SDH. Transcriptome analysis of DlHB22-overexpressing tomato fruit revealed broad transcriptional changes in pathways associated with central carbon metabolism, energy metabolism, glutathione metabolism, hormone signaling, and MAPK signaling, and qRT-PCR validation of six representative DEGs was consistent with the RNA-seq trends. Because tomato is climacteric whereas longan is non-climacteric, the heterologous tomato results demonstrate the regulatory potential of DlHB22 but do not establish an identical native ripening pathway in longan. Overall, DlHB22 is best regarded as a candidate transcription factor associated with longan fruit energy metabolism, whose native regulatory mechanism requires direct validation in longan.