Interspecies Developmental Differences in Metabonomic Phenotypes of Lycium ruthenicum and L. barbarum Fruits

Characterization of dicaffeoylspermidine derivatives related glucosyltransferases during fruit development of goji berry

The fruit of Lycium barbarum (Lb), known as red goji berry, is a "superfruit" due to its abundance of bioactive compounds. Among these compounds, dicaffeoylspermidine derivatives (DCSPDs) have anti-oxidant and anti-Alzheimer's Disease activity. This study employed ultra-high-performance liquid chromatography with tandem mass spectrometry to investigate metabolic changes during the development and ripening stages of red goji berries. Totally 97 compounds, including 51 DCSPDs, were tentatively identified. Correlation analysis of these DCSPDs revealed that glycosyltransferases (GTs) play an important role in the formation of glycosylated DCSPDs. In vitro experiments characterized 3 novel GTs could add a glucosyl moiety to N1-caffeoyl-N10-dihydrocaffeoyl spermidine. Homologous GTs from L. ruthenicum (Lr) exhibited similar activity, despite the absence of abundant glycosylated DCSPDs in Lr. These findings provide insights into the metabolic changes and interconnections among active compounds in red goji berries. The identified GTs hold potential for metabolic engineering of DCSPDs and functional food development.

Metabolite-based genome-wide association studies enable the dissection of the genetic bases of flavonoids, betaine and spermidine in wolfberry (Lycium)

Wolfberry is a plant with medicinal and food values. However, its bioactive ingredients and the corresponding genetic bases have not been determined. Here, we de novo generated a chromosome-level genome assembly for wolfberry, yielding a genome sequence of ~1.77 Gb with contig N50 of 50.55 Mb and 39 224 predicted gene models. A variation map, using 307 re-sequenced accessions, was called based on this genome assembly. Furthermore, the fruit metabolome of these accessions was profiled using 563 annotated metabolites, which separated Lycium barbarum L. and non-L. barbarum L. The flavonoids, coumarins, alkaloids and nicotinic acid contents were higher in the former than in the latter. A metabolite-based genome-wide association study mapped 156 164 significant single nucleotide polymorphisms corresponding to 340 metabolites. This included 19 219 unique lead single nucleotide polymorphisms in 1517 significant association loci, of which three metabolites, flavonoids, betaine and spermidine, were highlighted. Two candidate genes, LbUGT (evm.TU.chr07.2692) and LbCHS (evm.TU.chr07.2738), with non-synonymous mutations, were associated with the flavonoids content. LbCHS is a structural gene that interacts with a nearby MYB transcription factor (evm.TU.chr07.2726) both in L. barbarum and L. ruthenicum. Thus, these three genes might be involved in the biosynthesis/metabolism of flavonoids. LbSSADH (evm.TU.chr09.627) was identified as possibly participating in betaine biosynthesis/metabolism. Four lycibarbarspermidines (E-G and O) were identified, and only the lycibarbarspermidines O content was higher in L. barbarum varieties than in non-L. barbarum varieties. The evm.TU.chr07.2680 gene associated with lycibarbarspermidines O was annotated as an acetyl-CoA-benzylalcohol acetyltransferase, suggesting that it is a candidate gene for spermidine biosynthesis. These results provide novel insights into the specific metabolite profile of non-L. barbarum L. and the genetic bases of flavonoids, betaine and spermidine biosynthesis/metabolism.

Lycium RIN negatively modulate the biosynthesis of kukoamine A in hairy roots through decreasing thermospermine synthase expression

Root bark (Lycii cortex) of Lycium contains high contents of characteristic bioactive compounds, including kukoamine A (KuA) and kukoamine B (KuB). RIPENING INHIBITOR (RIN) is well known as a master regulator of Solanaceaous fruit ripening. However, the role of RIN in the biosynthetic pathway of KuA in Lycium remains unclear. In this study, integrated transcriptomic, metabolomic analyses and hairy root system are used to characterize the role of RIN in KuA biosynthesis in Lycium. The ultra performance liquid chromatography electrospray ionization tandem mass spectrometry analysis revealed that KuA was significantly induced in LrRIN1 RNAi lines and not detected in overexpression lines. A total of 20,913 differentially expressed genes (DEGs) and 60 differentially accumulated metabolites (DAMs) were detected in LrRIN1 transgenic hairy roots, which were used for weighted gene co-expression network analysis. Our result reveals a high association between KuA and structural genes in the phenolamide pathway, which shows a negative correlation with LrRIN1. In addition, overexpression of the polyamine pathway gene thermospermine synthase LcTSPMS, a potential target gene of Lycium RIN, increased the contents of both KuA and KuB in L. chinense hairy root, indicating that TSPMS is responsible for KuA biosynthesis and is also the common upstream biosynthetic gene for both KuA and KuB. Our results lay a solid foundation for uncovering the biosynthetic pathway of KuA, which will facilitate the molecular breeding and genetic improvement of Lycium species.

Integrated Metabolome and Transcriptome during Fruit Development Reveal Metabolic Differences and Molecular Basis between Lycium barbarum and Lycium ruthenicum

Wolfberry (Lycium barbarum) is a traditional cash crop in China and is well-known worldwide for its outstanding nutritional and medicinal value. Lycium ruthenicum is a close relative of Lycium barbarum but differs significantly in size, color, flavor and nutritional composition. To date, the metabolic differences between the fruits of the two wolfberry varieties and the genetic basis behind them are unclear. Here, we compared metabolome and transcriptome data of two kinds of wolfberry fruits at five stages of development. Metabolome results show that amino acids, vitamins and flavonoids had the same accumulation pattern in various developmental stages of fruit but that Lycium ruthenicum accumulated more metabolites than Lycium barbarum during the same developmental stage, including L-glutamate, L-proline, L-serine, abscisic acid (ABA), sucrose, thiamine, naringenin and quercetin. Based on the metabolite and gene networks, many key genes that may be involved in the flavonoid synthesis pathway in wolfberry were identified, including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H and FLS. The expression of these genes was significantly higher in Lycium ruthenicum than in Lycium barbarum, indicating that the difference in the expression of these genes was the main reason for the variation in flavonoid accumulation between Lycium barbarum and Lycium ruthenicum. Taken together, our results reveal the genetic basis of the difference in metabolomics between Lycium barbarum and Lycium ruthenicum and provide new insights into the flavonoid synthesis of wolfberry.

Effect of hot water, ultrasound, microwave, and pectinase-assisted extraction of anthocyanins from black goji berry for food application

Lycium ruthenicum, commonly known as black goji berry, is a rich anthocyanin source containing a high amount of monoacylated anthocyanins. This study investigates the effect of different extraction methods to extract anthocyanins from black goji berry for food application. Different hot water extraction conditions were applied to investigate the effect of specific substrate: solvent ratio (1:15 and 1:20 (w/v)), extraction time (30 and 60 min) and extraction temperature (40, 50 and 60 °C) on the extraction yield, total anthocyanin content (TAC) and the total phenolic content (TPC) of the anthocyanin extracts. Best hot water extraction conditions for obtaining an anthocyanin extract with high TAC (13.8 ± 1.14 mg CGE/g), TPC (69.7 ± 2.50 mg of GAE/g), and extraction yield (48.3 ± 3.25%) consuming less solvent, time and heat were substrate: solvent ratio of 1: 15 (w/v), extraction temperature of 50 °C, and extraction time of 30 min. The effect of pectinase, ultrasound, and microwave on hot water extraction of anthocyanins from black goji berry was investigated using the best conditions for hot water extraction. Pectinase-assisted extraction [1.5% (w/v) pectinase, substrate: solvent ratio of 1:15 (w/v) at 50 °C for 30 min] was the best extraction method to extract black goji berry anthocyanins demonstrating higher extraction yield, TAC, TPC, and the highest percentage of petunidin-3-O-(trans-p-coumaroyl)-rutinoside-5-O-glucoside.

Environmentally-driven metabolite and lipid variations correspond to altered bioactivities of black wolfberry fruit

Black wolfberry is a commonly cultivated woody plant in China, and is rich in nutrients that are beneficial for human. To characterize the endogenous metabolite differences among black wolfberry fruits grown in different geographical regions, mass spectrometry-based metabolomic and lipidomic analyses were performed in black wolfberry grown in nine locations throughout five provinces in China, from which 204 primary and specialized metabolites, and 267 lipids were identified in their fruits. Three samples from Alxa Left Banner, Jinta, and Minqin showed dramatically altered metabolite profiles, displaying higher levels of phenolic acids, soluble sugars and flavonoids, but lower levels of tricarboxylic acid cycle intermediates and aromatic amino acids. Moreover, the lipid profile of the Alxa Left Banner sample was strikingly distinct from all other samples, with high levels of monogalactosyl diacylglycerol and sulfoquinovosyl diacylglycerol, which are positively correlated with their anti-inflammatory capacities. These findings thus prompt for further studies on black wolfberry fruit for their health benefits.

Fruit ripening in Lycium barbarum and Lycium ruthenicum is associated with distinct gene expression patterns

Goji berries have been used as food and medicine for millennia. Due to their high morphological similarity, fruits of two distinct species belonging to the family Solanaceae, Lycium barbarum (LB) and Lycium chinense (Chinese boxthorn), are usually marketed together as goji berries, but nearly 90% of all commercially available goji berries belong to the former species. A third closely related species, a wild perennial thorny shrub native to north‐western China, Lycium ruthenicum (LR; known as Russian box thorn, and its fruit as black wolfberry), has become a popular choice for combating soil desertification and for alleviating soil salinity/alkalinity due to its high resistance to the harsh environment of saline deserts. Despite the phylogenetic closeness of LB and LR, their fruits are very different. To identify the genes involved in these distinct phenotypes, here we studied expression patterns of 22 transcriptional regulators that may be crucial drivers of these differences during five developmental stages. BAM1 may contribute to higher sugar content in LB. High expression of BFRUCT in ripe LR is likely to be an evolutionary adaptation to fruit ripening in an arid environment. Two arogenate dehydratase paralogues, CHS and LDOX, are probably crucial elements of the mechanism by which LR accumulates much higher levels of anthocyanin. DXS2 (carotenoid accumulation in LB) and CCD4 (carotenoid degradation in ripe LR fruit) may be crucial drivers behind the much higher content of carotenoids in LB. EIL3 and ERF5 are two transcription factors that may contribute to the higher abiotic stress resilience of LR. GATA22‐like appears to have more important roles in growth than ripening in LB fruit and vice versa in LR. HAT5‐like exhibited opposite temporal patterns in two fruits: high in the 1st stage in LB and high in the 5th stage in LR. PED1 was expressed at a much lower level in LR. Finally, we hypothesise that the poorly functionally characterised SCL32 gene may play a part in the increased resistance to environmental stress of LR. We suggest that BAM1, BFRUCT, EIL3, ERF5, ADT paralogues (for functional redundancy), PED1, GATA22‐like, HAT5‐like and SCL32 warrant further functional studies.

Quantitative Metabonomic Analysis Reveals the Germination-Associated Dynamic and Systemic Biochemical Changes for Mung-Bean (Vigna radiata) Seeds

Seed germination is essential for plant survival, germplasm resource preservation, and worldwide food supplies, although the germination-associated seed biochemical variations are not fully understood. With the NMR-based metabonomics, we quantitatively analyzed the comprehensive metabolite composition (metabonome) of mung-bean (Vigna radiata) seeds at eight time points of germination covering all three phases. We found that mung-bean seed metabonomes were dominated by 63 metabolites including lipids, amino acids, oligo-/monosaccharides, cyclitols, cholines, organic acids, nucleotides/-sides, nicotinates, and the shikimate pathway-mediated secondary metabolites. During germination, metabolic changes included mainly the degradation of proteins and raffinose family oligosaccharides, glycolysis, tricarboxylic acid (TCA) cycle, anaerobic respiration, biosynthesis of osmolytes and antioxidants together with the metabolisms of nucleotides/-sides, nicotinates, and amino acids. Oligosaccharide degradation was the primary energy source for germination, which coupled with the mobilization of starch and protein storages to produce sugars and amino acids for biomaterial and energy generations. Osmotic and redox regulations were prerequisites for seed germination together with mitochondrial reparations and generations to enable TCA cycle. During the postgermination growth stage (phase-3), the use of small molecules including amino acids and saccharides was switched to meet the growth demands of radicle cells. Small metabolites passed freely through seed testa leaking into the culture media during early germination but were reabsorbed by seed cells around the postgermination growth stage. Extra after-ripening accelerated these metabolic processes of seeds in phase-1, especially the biosynthesis of cyclitols, choline, and nicotinates, increasing the germination uniformity in terms of speed and percentage. Germination-resistant seeds were incapable of activating the germination-associated metabolic processes.

Transcriptomic and metabolomic analyses of Lycium ruthenicum and Lycium barbarum fruits during ripening

Red wolfberry (or goji berry, Lycium barbarum; LB) is an important agricultural product with a high content of pharmacologically important secondary metabolites such as phenylpropanoids. A close relative, black wolfberry (L. ruthenicum; LR), endemic to the salinized deserts of northwestern China, is used only locally. The two fruits exhibit many morphological and phytochemical differences, but genetic mechanisms underlying them remain poorly explored. In order to identify the genes of interest for further studies, we studied transcriptomic (Illumina HiSeq) and metabolomic (LC-MS) profiles of the two fruits during five developmental stages (young to ripe). As expected, we identified much higher numbers of significantly differentially regulated genes (DEGs) than metabolites. The highest numbers were identified in pairwise comparisons including the first stage for both species, but total numbers were consistently somewhat lower for the LR. The number of differentially regulated metabolites in pairwise comparisons of developmental stages varied from 66 (stages 3 vs 4) to 133 (stages 2 vs 5) in both species. We identified a number of genes (e.g. AAT1, metE, pip) and metabolites (e.g. rutin, raffinose, galactinol, trehalose, citrulline and DL-arginine) that may be of interest to future functional studies of stress adaptation in plants. As LB is also highly suitable for combating soil desertification and alleviating soil salinity/alkalinity/pollution, its potential for human use may be much wider than its current, highly localized, relevance.

Induction, identification and characterization of tetraploidy in Lycium ruthenicum

Lycium ruthenicum of Solanaceae was widely used as healthy vegetables and natural medicine foods for containing numerous functional components in leaves, roots and fruits. In the present study, tetraploid plants of L. ruthenicum were obtained efficiently by treating their leaves with colchicine in vitro. The highest induction frequency of the tetraploids was 31.4%, which was obtained by preculturing the leaves for 10 days and then treating them with 100 mg/L of colchicine concentration for 48 h. The ploidy levels of the regenerated plants were determined by flow cytometry and chromosome counting methods. Cytological, morphological, and histological characterization validated the results of flow cytometry, revealing the differences between the two kinds of ploidy plants in their tissue culture stage and field production stages. Morphological indexes also provide a simple and intuitionistic method for distinguishing tetraploid from diploid plants. As the chromosome number increased, the stomatal size and number of the chloroplasts in the stomata also increased, but the stomatal density decreased. The results indicate that the chromosome number is correlated with the stomatal index. The generated tetraploid is a potentially useful cultivated variety and will be beneficial for producing triploid progeny in the future.