Comparative metabolomics reveals differences in primary and secondary metabolites between "Shixia" and "Chuliang" longan (Dimocarpus longan Lour.) pulp.

Longan was a characteristic fruit for both medicine and food in China, which was rich in primary and secondary metabolites. Comprehensive high-throughput identification and comparison of metabolites in longan pulp among different varieties were still lacked. "Shixia" (SX) and "Chuliang" (CL) were the biggest major cultivars of longan in China. In this study, the content of total soluble solid, total flavonoid, and total phenolics indicated the difference of sweetness and bioactive compound content between the SX and CL pulp. Through a widely targeted metabolome, a total of 514 metabolites were identified and categorized into 23 groups mainly including flavonoids, amino acids & derivatives, lipids, phenolic acids, nucleotides & derivatives, alkaloids, organic acids and sugars & derivatives. A total of 89 metabolites with significantly differential accumulation (variable importance in projection (VIP) value ≧1, p-value <.05) over 1.2 fold were found between SX and CL, which were mainly enriched into pathways including flavone and flavonol biosynthesis, glycolysis/gluconeogenesis, and arginine and proline metabolism. Higher leveled hexose and hexose-phosphate (i.e., ß-D-glucose, D(+)-glucose, glucose-1-phosphate and glucose-6-phosphate), dominant organic acids (i.e., citric acid, succinic acid, D-malic acid, and citramalate), and essential amino acids (L-threonine, L-valine, L-isoleucine, L-leucine, L-phenylalanine and L-lysine) in SX pulp might be contributed to the taste and flavor difference between SX and CL. Moreover, the greatly differential accumulated secondary metabolites especially flavonoids and phenolic acids might result in different medicinal and nutritional characteristic between SX and CL. In conclusion, this study provided a systemic metabolic basis for understanding the nutritional differences between SX and CL and would help deepen the molecular biology and pharmacology research on characteristic metabolites in longan pulp.

Free Amino Acids Profile and Expression Analysis of Core Genes Involved in Branched-Chain Amino Acids Metabolism during Fruit Development of Longan (Dimocarpus longan Lour.) Cultivars with Different Aroma Types.

Amino acids are important component of fruit nutrition and quality. In this study, three longan cultivars, including non-aroma types 'Shixia' (SX), 'Lidongben' (LDB), and strong aroma type 'Xiangcui' (XC), were selected to analyze free amino acids (FAAs) variations at six distinct growth stages (S1-S6). The genome-wide identification and expression analysis of genes related to the branched-chain amino acids (BCAA) synthesis pathway were carried out. Results showed that 36 FAAs were identified, and the total FAAs content ranged from 2601.0 to 9073.5 mg/kg, which increased drastically with fruit development until ripening. L-glutamic acid (Glu), L-alanine (Ala), L-arginine (Arg), γ-Aminobutyric acid (GABA), L-aspartic acid (Asp), L-leucine (Leu), hydroxyl-proline (Hypro), and L-serine (Ser) were the predominant FAAs (1619.9-7213.9 mg/kg) in pulp, accounting for 62.28-92.05% of the total amino acids. During the period of rapid fruit expansion (S2-S4), the aroma of XC changed from light to strong, and the contents of L-alanine (Ala) and L-leucine (Leu) were significantly higher than those of SX and LDB. Furthermore, a total of two 2-isopropyl malate synthase (IPMS), two 3-isopropyl malate dehydrogenase (IPMD), and 16 BCAA transferase (BCAT) genes were identified. The expression levels of DilBCAT1, -6, and -9 genes in XC were significantly higher than those in SX and LDB, while DilBCAT16 in XC was lower. The content of Leu was negatively correlated with the expression of DilBCAT1, -6, and -9 in three varieties, but positively correlated with DilBCAT16, indicating that these four genes may be responsible for the different synthesis and degradation of Leu among cultivars.

Comparative Analysis of the MADS-Box Genes Revealed Their Potential Functions for Flower and Fruit Development in Longan (Dimocarpus longan).

Longan (Dimocarpus longan Lour.) is an important economic crop widely planted in tropical and subtropical regions, and flower and fruit development play decisive effects on the longan yield and fruit quality formation. MCM1, AGAMOUS, DEFICIENS, Serum Response Factor (MADS)-box transcription factor family plays important roles for the flowering time, floral organ identity, and fruit development in plants. However, there is no systematic information of MADS-box family in longan. In this study, 114 MADS-box genes were identified from the longan genome, phylogenetic analysis divided them into type I (Mα, Mß, Mγ) and type II (MIKC*, MIKC C ) groups, and MIKC C genes were further clustered into 12 subfamilies. Comparative genomic analysis of 12 representative plant species revealed the conservation of type II in Sapindaceae and analysis of cis-elements revealed that Dof transcription factors might directly regulate the MIKC C genes. An ABCDE model was proposed for longan based on the phylogenetic analysis and expression patterns of MADS-box genes. Transcriptome analysis revealed that MIKC C genes showed wide expression spectrums, particularly in reproductive organs. From 35 days after KClO3 treatment, 11 MIKC genes were up-regulated, suggesting a crucial role in off-season flower induction, while DlFLC, DlSOC1, DlSVP, and DlSVP-LIKE may act as the inhibitors. The gene expression patterns of longan fruit development indicated that DlSTK, DlSEP1/2, and DlMADS53 could be involved in fruit growth and ripening. This paper carried out the whole genome identification and analysis of the longan MADS-box family for the first time, which provides new insights for further understanding its function in flowers and fruit.

Identification of differentially expressed genes implicated in peel color (red and green) of Dimocarpus confinis.

Nowadays, there are few reports about regulatory genes implicated in peel color of longan. The basic genetic research of longan has been in stagnation for a long time as a lack of transcriptomic and genetic information. To predict candidate genes associated with peel color, Gene Functional Annotation and Coding Sequence prediction were used to perform functional annotation for our assembled unigenes and investigate differentially expressed genes (DEGs) of fruitlet peels from Longli (Dimocarpus confinis). Finally, a total of 24,044 (44.19 %) unigenes were annotated at least in one database after BLAST search to NCBI non-redundant protein sequence, NCBI non-redundant nucleotide sequences, Kyoto Encyclopedia of Genes and Genomes (KEGG) Ortholog, manually annotated and reviewed protein sequence database (Swiss-Prot), Protein family, Gene Ontology, euKaryotic Ortholog Groups databases. After searching against the KEGG-GENE protein database, a result of 6228 (11.45 %) unigenes were assigned to 245 KEGG pathways. Via comparing the distributions of expression value of all corresponding unigenes from red peel and green peel fruit, it could be intuitively concluded that high similarity was existed in the two distributions; however, on the whole, between two distributions of log RPKM expression value, some differences indicated that expression level in green-peel fruit group is slightly higher than values in red-peel fruit group. Finally, a total of 1349 unigenes were identified as DEGs after blasting the DEGs to public sequence databases, and 32 peel-color-related genes were identified in longan. Our results suggest that a number of unigenes involved in longan metabolic process, including anthocyanin biosynthesis. In addition, DRF, F3H, ANS, CYP75A1 and C1 may be the key ones. The study on key genes related to peel color will be contributed to revealing the molecular mechanisms of regulating peel color in woody plants.