Comparative analysis of carotenoid accumulation in two goji (Lycium barbarum L. and L. ruthenicum Murr.) fruits

Development and evaluation of suitable reference genes for qRT-PCR normalization of hybrids derived from Lycium barbarum and Lycium ruthenicum

BACKGROUND

A correct and stably expressing reference gene is prerequisite for successful quantitative real-time PCR (qRT-PCR). Investigating gene expression profiling during flower development could enhance our understanding of the molecular mechanisms of flower formation and fertility in Lycium.

METHODS AND RESULTS

In this study, 11 candidate reference genes in Lycium flower development were selected from transcriptome sequence data and evaluated with five traditional housekeeping genes from previous studies based on qRT-PCR amplification. Comparing the expression stability result of 16 candidate genes using GeNorm, NormFinder, BestKeeper, and Delta Ct algorithms, Lba04g01649 and Lba12g02820 were validated as the optimal reference genes for the flower development of Lycium.

CONCLUSIONS

The reference genes identified in this study would improve the accuracy of qRT-PCR quantification of target gene expression in Lycium flower development and facilitate future functional genomics studies on flower development. This research could lay the foundation for the study of the reproduction and development of the Lycium flower.

Fruit development and ripening orchestrating the biosynthesis and regulation of Lycium barbarum polysaccharides in goji berry

Lycium barbarum polysaccharides (LBPs) are the primary bioactive components in fruits of L. barbarum, commonly known as goji berry. Despite significant progress in understanding the chemical structures and health benefits of LBPs, the biosynthesis and regulation of LBPs in goji berry remains largely unknown. In this study, physiological indicators, including LBPs, were monitored in goji berry during fruit development and ripening (FDR), suggesting that pectin might be the major component of LBPs with increased content reaching 235.8 mg/g DW. Proteomic and transcriptomic analysis show that 6410 differentially expressed genes (DEGs) and 2052 differentially expressed proteins (DEPs) were identified with overrepresentation of flavonoids and polysaccharides-related gene ontology (GO) terms and KEGG pathways. Weighted gene co-expression network analysis (WGCNA) showed that LBPs coexpress with genes involved in pectin biosynthesis (LbGALS3, LbGATL5, LbQUA1, LbGAUT1/4/7, LbRGGAT1, LbRRT1/7, and LbRHM2), modification (LbSBT1.7), and regulation (LbAP2, LbGL2 LbTLP2, LbERF4, and LbTTG2), as well as with novel transcription factors (LbSPL9 and LbRIN homologs) and glycosyltransferases. Transgenic hairy roots overexpressing LbRIN validated that LbRIN modulate the expression of WGCNA-predicted regulators, including LbERF4, LbTTG2, and LbSPL9. These findings suggest that the biosynthesis and regulation of LBPs is conserved partially to those in Arabidopsis pectin. Taken together, this study provides valuable insights into the biosynthesis and regulation of LBPs, which can facilitate future studies on synthetic biology applications and genetic improvement of LBPs.

ERF5.1 modulates carotenoid accumulation by interacting with CCD4.1 in Lycium

Carotenoids are important natural pigments and have medical and health functions for humans. Carotenoid cleavage dioxygenase 4 (CCD4) and ethylene responsive factor (ERF) participate in carotenoid metabolism, but their roles in Lycium have not been discovered. Here, we annotated LbCCDs from the Lycium reference genome and found that LbCCD4.1 expression was significantly correlated with the carotenoid metabolites during Lycium five fruit developmental stages. Over-expression of LbCCD4.1 in NQ's leaves resulted in a series of significantly lower contents of carotenoid metabolites, including β-carotene and β-cryptoxanthin. Moreover, LbERF5.1, a transcription factor belonging to the ERF family that was located in the nucleus, was isolated. Significant reductions in the carotenoids, especially lutein, violaxanthin and their derivatives, were observed in over-expressing ERF5.1 transgenic NQ's leaves. Over-expression or virus-induced gene silencing of LbERF5.1 in NQ's leaves induced a consistent up- or down-expression, respectively, of LbCCD4.1. Furthermore, yeast one-hybrid and dual-luciferase reporter assays showed that ERF5.1 interacted with the promoter of CCD4.1 to increase its expression, and LbERF5.1 could bind to any one of the three predicted binding sites in the promoter of LbCCD4.1. A transcriptome analysis of LbERF5.1 and LbCCD4.1 over-expressed lines showed similar global transcript expression, and geranylgeranyl diphosphate synthase, phytoene synthase, lycopene δ-cyclase cytochrome, cytochrome P450-type monooxygenase 97A, cytochrome P450-type monooxygenase 97C, and zeaxanthin epoxidase in the carotenoid biosynthesis pathway were differentially expressed. In summary, we uncovered a novel molecular mechanism of carotenoid accumulation that involved an interaction between ERF5.1 and CCD4.1, which may be used to enhance carotenoid in Lycium.

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.

Comparative Analysis of the GATA Transcription Factors in Five Solanaceae Species and Their Responses to Salt Stress in Wolfberry (Lycium barbarum L.)

GATA proteins are a class of zinc-finger DNA-binding proteins that participate in diverse regulatory processes in plants, including the development processes and responses to environmental stresses. However, a comprehensive analysis of the GATA gene family has not been performed in a wolfberry (Lycium barbarum L.) or other Solanaceae species. There are 156 GATA genes identified in five Solanaceae species (Lycium barbarum L., Solanum lycopersicum L., Capsicum annuum L., Solanum tuberosum L., and Solanum melongena L.) in this study. Based on their phylogeny, they can be categorized into four subfamilies (I-IV). Noticeably, synteny analysis revealed that dispersed- and whole-genome duplication contributed to the expansion of the GATA gene family. Purifying selection was a major force driving the evolution of GATA genes. Moreover, the predicted cis-elements revealed the potential roles of wolfberry GATA genes in phytohormone, development, and stress responses. Furthermore, the RNA-seq analysis identified 31 LbaGATA genes with different transcript profiling under salt stress. Nine candidate genes were then selected for further verification using quantitative real-time PCR. The results revealed that four candidate LbaGATA genes (LbaGATA8, LbaGATA19, LbaGATA20, and LbaGATA24) are potentially involved in salt-stress responses. In conclusion, this study contributes significantly to our understanding of the evolution and function of GATA genes among the Solanaceae species, including wolfberry.

Transcriptomics and Metabolomics Reveal the Critical Genes of Carotenoid Biosynthesis and Color Formation of Goji (Lycium barbarum L.) Fruit Ripening

Carotenoids in goji (Lycium barbarum L.) have excellent health benefits, but the underlying mechanism of carotenoid synthesis and color formation in goji fruit ripening is still unclear. The present study uses transcriptomics and metabolomics to investigate carotenoid biosynthesis and color formation differences in N1 (red fruit) and N1Y (yellow fruit) at three stages of ripening. Twenty-seven carotenoids were identified in N1 and N1Y fruits during the M1, M2, and M3 periods, with the M2 and M3 periods being critical for the difference in carotenoid and color between N1 and N1Y fruit. Weighted gene co-expression network analysis (WGCNA), gene trend analysis, and correlation analysis suggest that PSY1 and ZDS16 may be important players in the synthesis of carotenoids during goji fruit ripening. Meanwhile, 63 transcription factors (TFs) were identified related to goji fruit carotenoid biosynthesis. Among them, four TFs (CMB1-1, WRKY22-1, WRKY22-3, and RAP2-13-like) may have potential regulatory relationships with PSY1 and ZDS16. This work sheds light on the molecular network of carotenoid synthesis and explains the differences in carotenoid accumulation in different colored goji fruits.

The health-promoting anthocyanin petanin in Lycium ruthenicum fruit: a promising natural colorant

Acylated anthocyanins derived from dietary sources have gained significant attention due to their health-promoting properties and potential as natural colorants with high stability. However, exploration of the functional food products using acylated anthocyanins enriched in fruits and vegetables remains largely delayed in food industries. The black goji (Lycium ruthencium) fruit (LRF) is a functional food that is extensively used due to its exceptionally high levels of acylated anthocyanins, including petanin. This review provides a comprehensive summary of the functional properties and anthocyanin components of LRF. The stability, bioaccessibility, bioavailability, and bioactivities of petanin, the major anthocyanin component, are compared with those of LRF anthocyanin extracts and other food sources. Furthermore, the biosynthetic pathway and regulatory network of petanin in LRF are proposed and constructed, respectively. The key genes that could be potentially used for metabolic engineering to produce petanin are predicted. Finally, the potential application of petanin derivatives in the food industry is also discussed. This review presents comprehensive and systematic information about the dual-function of petanin as a bioactive component and a promising natural colorant for future food industrial applications.

Genome-Wide Identification and Analysis of the BBX Gene Family and Its Role in Carotenoid Biosynthesis in Wolfberry (Lycium barbarum L.)

The B-box proteins (BBXs) are a family of zinc-finger transcription factors with one/two B-Box domain(s) and play important roles in plant growth and development as well as stress responses. Wolfberry (Lycium barbarum L.) is an important traditional medicinal and food supplement in China, and its genome has recently been released. However, comprehensive studies of BBX genes in Lycium species are lacking. In this study, 28 LbaBBX genes were identified and classified into five clades by a phylogeny analysis with BBX proteins from Arabidopsis thaliana and the LbaBBXs have similar protein motifs and gene structures. Promoter cis-regulatory element prediction revealed that LbaBBXs might be highly responsive to light, phytohormone, and stress conditions. A synteny analysis indicated that 23, 20, 8, and 5 LbaBBX genes were orthologous to Solanum lycopersicum, Solanum melongena, Capsicum annuum, and Arabidopsis thaliana, respectively. The gene pairs encoding LbaBBX proteins evolved under strong purifying selection. In addition, the carotenoid content and expression patterns of selected LbaBBX genes were analyzed. LbaBBX2 and LbaBBX4 might play key roles in the regulation of zeaxanthin and antheraxanthin biosynthesis. Overall, this study improves our understanding of LbaBBX gene family characteristics and identifies genes involved in the regulation of carotenoid biosynthesis in wolfberry.

Phylogeography and Population Genetics Analyses Reveal Evolutionary History of the Desert Resource Plant Lycium ruthenicum (Solanaceae)

Climactic oscillations during the Quaternary played a significant role in the formation of genetic diversity and historical demography of numerous plant species in northwestern China. In this study, we used 11 simple sequence repeats derived from expressed sequence tag (EST-SSR), two chloroplast DNA (cpDNA) fragments, and ecological niche modeling (ENM) to investigate the population structure and the phylogeographic history of Lycium ruthenicum, a plant species adapted to the climate in northwestern China. We identified 20 chloroplast haplotypes of which two were dominant and widely distributed in almost all populations. The species has high haplotype diversity and low nucleotide diversity based on the cpDNA data. The EST-SSR results showed a high percentage of total genetic variation within populations. Both the cpDNA and EST-SSR results indicated no significant differentiation among populations. By combining the evidence from ENM and demographic analysis, we confirmed that both the last interglacial (LIG) and late-glacial maximum (LGM) climatic fluctuations, aridification might have substantially narrowed the distribution range of this desert species, the southern parts of the Junggar Basin, the Tarim Basin, and the eastern Pamir Plateau were the potential glacial refugia for L. ruthenicum during the late middle Pleistocene to late Pleistocene Period. During the early Holocene, the warm, and humid climate promoted its demographic expansion in northwestern China. This work may provide new insights into the mechanism of formation of plant diversity in this arid region.

Discrimination of Geographical Origins of Wolfberry (Lycium barbarum L.) Fruits Using Stable Isotopes, Earth Elements, Free Amino Acids, and Saccharides

To develop sophisticated approaches for distinguishing goji origins, 325 wolfberry fruit samples of a certain cultivar, plant age, drying method, and collection season were gathered from 26 producing areas across Northwest China in 2017 and 2018. We employed 49 indices, including stable isotopes, earth elements, soluble amino acids, and saccharides, to identify the regions of origin of these goji fruits. Analysis of variance (ANOVA) and heritability analysis were used to assess the effects of the environment (producing areas), cultivar, plant age, drying process, and collection season. Samples from the same place can be classified and partially discriminated using principal component analysis (PCA). We were able to distinguish fruits produced in Zhongning County from those produced in the other five producing provinces using orthogonal projection to latent structure-discriminant analysis (OPLS-DA). Calcium (Ca), manganese (Mn), ornithine (Orn), cystine (Cys-Cys), glutamate (Glu), phenylalanine (Phe), phosphoserine (Ps), serine (Ser), lysine (Lys), taurine (Tau), proline (Pro), and tyrosine (Tyr) indices were chosen using S-plots and heritability analysis, and their repeatability was established with samples collected in 2018. The indices selected in this study can distinguish goji berries produced in Zhongning County from fruits originating from five other Provinces with high repeatability, which was validated with various cultivars, drying methods, harvest seasons, and plant ages and with heritability analysis.

Genome-Wide Comparative Analysis of the R2R3-MYB Gene Family in Five Solanaceae Species and Identification of Members Regulating Carotenoid Biosynthesis in Wolfberry

The R2R3-MYB is a large gene family involved in various plant functions, including carotenoid biosynthesis. However, this gene family lacks a comprehensive analysis in wolfberry (Lycium barbarum L.) and other Solanaceae species. The recent sequencing of the wolfberry genome provides an opportunity for investigating the organization and evolutionary characteristics of R2R3-MYB genes in wolfberry and other Solanaceae species. A total of 610 R2R3-MYB genes were identified in five Solanaceae species, including 137 in wolfberry. The LbaR2R3-MYB genes were grouped into 31 subgroups based on phylogenetic analysis, conserved gene structures, and motif composition. Five groups only of Solanaceae R2R3-MYB genes were functionally divergent during evolution. Dispersed and whole duplication events are critical for expanding the R2R3-MYB gene family. There were 287 orthologous gene pairs between wolfberry and the other four selected Solanaceae species. RNA-seq analysis identified the expression level of LbaR2R3-MYB differential gene expression (DEGs) and carotenoid biosynthesis genes (CBGs) in fruit development stages. The highly expressed LbaR2R3-MYB genes are co-expressed with CBGs during fruit development. A quantitative Real-Time (qRT)-PCR verified seven selected candidate genes. Thus, Lba11g0183 and Lba02g01219 are candidate genes regulating carotenoid biosynthesis in wolfberry. This study elucidates the evolution and function of R2R3-MYB genes in wolfberry and the four Solanaceae species.

Current findings and future prospective of high-value trans Himalayan medicinal plant Lycium ruthenicum Murr: a systematic review

Background

The genus Lycium is commercially known for its nutrient dense goji-berries, among these berries, black goji-berries obtained from Lycium ruthenicum Murr are highly valued and widely used as traditional medicine in trans-himalayan cold desert Ladakh and as functional food in several countries.

Methods

The current collection of data and literature was done by exploring different scientific portals like SciFinder, Google scholar, PubMed, Dictonary of Natural Products, Institute for Scientific Information, Web of Science and Scopus by searching keywords like black goji berry, crystal pearl, and trans-Himalayan plant.

Results

Fruits of L. ruthenicum Murr, are overwhelmingly enriched in anthocyanins, proanthocyanidins, polysaccharides, spermine and spermidine alkaloids. The presence of these bioactive phyto-chemicals has been linked with reported anti-diabetic, anti-inflammatory, anti-fatigue, anti-atherosclerosis and neuro-protective properties of black goji berries. A unique color of these berries makes them exceptional as compared to other berries.

Conclusions

In this article, we have reviewed the variety of high value phytochemicals of Lycium ruthenicum Murr, with a special focus on health promoting anthocyanins which will provide an insight to the readers for exploring novel applications of L. ruthenicum Murr in field of medicine and food industries.

Prebiotic effects of goji berry in protection against inflammatory bowel disease

The prevalence of inflammatory bowel disease (IBD) is increasing, which is concerning because IBD is a known risk factor for the development of colorectal cancer. Emerging evidence highlights environmental factors, particularly dietary factors and gut microbiota dysbiosis, as pivotal inducers of IBD onset. Goji berry, an ancient tonic food and a nutraceutical supplement, contains a range of phytochemicals such as polysaccharides, carotenoids, and polyphenols. Among these phytochemicals, L. barbarum polysaccharides (LBPs) are the most important functional constituents, which have protective effects against oxidative stress, inflammation, and neurodegeneration. Recently, the beneficial effects of goji berry and associated LBPs consumption were linked to prebiotic effects, which can prevent dysbiosis associated with IBD. This review assessed pertinent literature on the protective effects of goji berry against IBD focusing on the gut microbiota and their metabolites in mediating the observed beneficial effects.

Unraveling the versatility of CCD4: Metabolic engineering, transcriptomic and computational approaches

Carotenoids are economically valuable isoprenoids synthesized by plants and microorganisms, which play a paramount role in their overall growth and development. Carotenoid cleavage dioxygenases are a vast group of enzymes that specifically cleave thecarotenoids to produce apocarotenoids. Recently, CCDs are a subject of talk because of their contributions to different aspects of plant growth and due to their significance in the production of economically valuable apocarotenoids. Among them, CCD4 stands unique because of its versatility in performing metabolic roles. This review focuses on the multiple functionalities of CCD4 like pigmentation, volatile apocarotenoid production, stress responses, etc. Interestingly, through our literature survey we arrived at a conclusion that CCD4 could perform functions of other carotenoid cleaving enzymes.The metabolic engineering, transcriptomic, and computational approaches adopted to reveal the contributions of CCD4 were also considered here for the study.Phylogenetic analysis was performed to delve into the evolutionary relationships of CCD4 in different plant groups. A tree of 81CCD genes from 64 plant species was constructed, signifying the presence of well-conserved families. Gene structures were illustrated and the difference in the number and position of exons could be considered as a factor behind functional versatility and substrate tolerance of CCD4 in different plants.

TCM-Blast for traditional Chinese medicine genome alignment with integrated resources

The traditional Chinese medicine (TCM) genome project aims to reveal the genetic information and regulatory network of herbal medicines, and to clarify their molecular mechanisms in the prevention and treatment of human diseases. Moreover, the TCM genome could provide the basis for the discovery of the functional genes of active ingredients in TCM, and for the breeding and improvement of TCM. The traditional Chinese Medicine Basic Local Alignment Search Tool (TCM-Blast) is a web interface for TCM protein and DNA sequence similarity searches. It contains approximately 40G of genome data on TCMs, including protein and DNA sequence for 36 TCMs with high medical value.The development of a publicly accessible TCM genome alignment database hosted on the TCM-Blast website ( http://viroblast.pungentdb.org.cn/TCM-Blast/viroblast.php ) has expanded to query multiple sequence databases to obtain TCM genome data, and provide user-friendly output for easy analysis and browsing of BLAST results. The genome sequencing of TCMs helps to elucidate the biosynthetic pathways of important secondary metabolites and provides an essential resource for gene discovery studies and molecular breeding. The TCMs genome provides a valuable resource for the investigation of novel bioactive compounds and drugs from these TCMs under the guidance of TCM clinical practice. Our database could be expanded to other TCMs after the determination of their genome data.

Wolfberry genomes and the evolution of Lycium (Solanaceae)

Wolfberry Lycium, an economically important genus of the Solanaceae family, contains approximately 80 species and shows a fragmented distribution pattern among the Northern and Southern Hemispheres. Although several herbaceous species of Solanaceae have been subjected to genome sequencing, thus far, no genome sequences of woody representatives have been available. Here, we sequenced the genomes of 13 perennial woody species of Lycium, with a focus on Lycium barbarum. Integration with other genomes provides clear evidence supporting a whole-genome triplication (WGT) event shared by all hitherto sequenced solanaceous plants, which occurred shortly after the divergence of Solanaceae and Convolvulaceae. We identified new gene families and gene family expansions and contractions that first appeared in Solanaceae. Based on the identification of self-incompatibility related-gene families, we inferred that hybridization hotspots are enriched for genes that might be functioning in gametophytic self-incompatibility pathways in wolfberry. Extremely low expression of LOCULE NUBER (LC) and COLORLESS NON-RIPENING (CNR) orthologous genes during Lycium fruit development and ripening processes suggests functional diversification of these two genes between Lycium and tomato. The existence of additional flowering locus C-like MADS-box genes might correlate with the perennial flowering cycle of Lycium. Differential gene expression involved in the lignin biosynthetic pathway between Lycium and tomato likely illustrates woody and herbaceous differentiation. We also provide evidence that Lycium migrated from Africa into Asia, and subsequently from Asia into North America. Our results provide functional insights into Solanaceae origins, evolution and diversification.

Integrative Analysis of Transcriptome and Metabolome Reveals Salt Stress Orchestrating the Accumulation of Specialized Metabolites in Lycium barbarum L. Fruit

Salt stress seriously affects yield and quality of crops. The fruit of Lycium barbarum (LBF) is extensively used as functional food due to its rich nutrient components. It remains unclear how salt stress influences the quality of LBF. In this study, we identified 71 differentially accumulated metabolites (DAMs) and 1396 differentially expressed genes (DEGs) among ripe LBF with and without 300 mM of NaCl treatment. Pearson correlation analysis indicated that the metabolomic changes caused by salt stress were strongly related to oxidoreductases; hydrolases; and modifying enzymes, in particular, acyltransferases, methyltransferases and glycosyltransferases. Further analysis revealed that salt stress facilitated flavonoid glycosylation and carotenoid esterification by boosting the expression of structural genes in the biosynthetic pathways. These results suggested that salt stress prompts the modification of flavonoids and carotenoids to alleviate ROS damage, which in turn improves the quality of LBF. Our results lay a solid foundation for uncovering the underlying molecular mechanism of salt stress orchestrating LBF quality, and the candidate genes identified will be a valuable gene resource for genetic improvement of L. barbarum.

Biochemical characterization of fruits of Lycium spp. in Ukraine

Fruits of Lycium possess therapeutic properties due to which they are used in traditional and folk medicine and can be used as a kind of functional food. The objective of this study was to evaluate the biochemical characterization of Lycium L. (L. barbarum L., L. chinense Mill. and L. truncatum Y. C. Wang) fruits for 16 cultivars and varieties from the collections in the M. M. Gryshko National Botanical Garden of NAS of Ukraine (Kyiv). This study was aimed at determining the concentration of nutrients in the Lycium fruits. Individual genotypes of three Lycium species: L. barbarum, L.chinense, and L. truncatum, differed in such features as the content of dry matter, sugars, vitamin C, β-carotene, acidity, and tannins in the fruit. Fruits of Lycium spp. are a valuable source of nutrients such as vitamin C (4.38–121.0 mg 100g–1 FW), β-carotene content (1.45–5.52%), and tannin (0.12–1.34%). The sugar content (13.83–20.87%) and acidity of the fruit (0.23–4.62%) meet the consumers' requirements for fresh fruit. The cultivar Amber Sweet (L. chinense) had fruits of which the similarities between biochemical characteristics of different studies genotypes were the lowest. The cv. Amber Sweet was characterized by fruit with high sugar content, very high vitamin C content, average acid content, low tannins and β-carotene content, and the lowest dry matter content. Furthermore, a distinctive feature of the other tested genotypes was the yellow colour of the fruit. The data obtained can be used for further selective work.

Goji berry (Lycium spp.) extracts exhibit antiproliferative activity via modulating cell cycle arrest, cell apoptosis, and the p53 signaling pathway

The phytochemical profiles, antioxidant activity and antiproliferative mechanism of two goji berry varieties were investigated in the present study. In contrast to Lycium barbarum L. (LB), Lycium ruthenicum Murr. (LRM) showed stronger antioxidant activity evaluated by ORAC, PSC and CAA assays, which might be attributed to its higher total phenolics and total flavonoids. However, LB contains greater contents of VE and carotenoids compared to LRM, which may endow LB with other unique functions instead of antioxidant activity. Additionally, high dose LRM showed a stronger capability in terms of cell cycle arrest and cell apoptosis induction of MDA cells with increments of 17.85% cells blocked at the G1 phase and 50.49% cells achieving early apoptosis compared with the control group. Although supplementation with LB increased the number of cells in the G1 phase by 10%, its effect on inducing cell apoptosis was not ideal. Furthermore, both LRM and LB activated the proliferation-related p53 signaling pathway including p53, p21, CDK4, Cyclin E, Bax and Caspase3, but LB failed to downregulate bcl-2 and CDK2 levels, indicating the weaker antiproliferative effect of LB. The present findings indicated LRM and LB as potential candidates for managing the proliferation of cancer cells and improving human health.

Chemical Characterization, Antioxidant and Antimicrobial Properties of Goji Berries Cultivated in Serbia

Since the fruits of Lycium L. species (Fructus lycii, goji berries) are promoted as a “superfood” with plenty of health benefits, there is extensive research interest in their nutritional and phytochemical composition. In the present study, the nutritional value, minerals, fatty acid composition, and bioactive compounds of L. barbarum L., red, yellow, and black goji berry (L. ruthenicum Murray.) cultivated in Serbia were investigated. Antioxidant and antimicrobial properties of their methanol extracts were assessed. Red goji berry had the highest content of fats, dietary fiber, iron, total carotenoids, and 2-O-β-d-glucopyranosyl-l-ascorbic acid (AA-2βG). The yellow goji berry extract showed the highest level of flavonoids and the most prominent antimicrobial (especially against Gram-negative bacteria) properties. The highest total phenolic content and the most potent antioxidant activity were observed for the extract of black goji berry. Therefore, all goji berries could be a valuable source of bioactive compounds in the food and pharmaceutical industry.

The major zeaxanthin dipalmitate derivatives from wolfberry

Zeaxanthin dipalmitate (3) and two zeaxanthin dipalmitate derivatives, including one new compound (1), were obtained from wolfberry [the fruit of Lycium barbarum L. (Solanaceae)]. Their structures were unambiguously elucidated by spectroscopic analyses. Compound 2 is isolated from the genus Lycium for the first time, and its 1D/2D NMR data are firstly reported. All the compounds belong to carotenoids which are a kind of major bioactive constituents in wolfberry and are also responsible for wolfberry's red color.

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.

Chromosome doubling mediates superior drought tolerance in Lycium ruthenicum via abscisic acid signaling

Plants are continuously affected by unfavorable external stimuli, which influences their productivity and growth. Differences in gene composition and expression patterns lead homologous polyploid plants to exhibit different physiological phenomena, among which enhanced environmental adaptability is a powerful phenotype conferred by polyploidization. The mechanisms underlying the differences in stress tolerance between diploids and autotetraploids at the molecular level remain unclear. In this research, a full-length transcription profile obtained via the single-molecule real-time (SMRT) sequencing of high-quality single RNA molecules for use as background was combined with next-generation transcriptome and proteome technologies to probe the variation in the molecular mechanisms of autotetraploids. Tetraploids exhibited an increase in ABA content of 78.4% under natural conditions and a superior stress-resistance phenotype under severe drought stress compared with diploids. The substantial differences in the transcriptome profiles observed between diploids and autotetraploids under normal growth conditions were mainly related to ABA biosynthesis and signal transduction pathways, and 9-cis-epoxycarotenoid dioxygenase 1 (NCED1) and NCED2, which encode key synthetic enzymes, were significantly upregulated. The increased expression of the ABRE-binding factor 5-like (ABF5-like) gene was a pivotal factor in promoting the activation of the ABA signaling pathway and downstream target genes. In addition, ABA strongly induced the expression of osmotic proteins to increase the stress tolerance of the plants at the translational level. We consider the intrinsic mechanisms by which ABA affects drought resistance in tetraploids and diploids to understand the physiological and molecular mechanisms that enhance abiotic stress tolerance in polyploid plants.

Ultrasonic-assisted extraction and high-speed counter-current chromatography purification of zeaxanthin dipalmitate from the fruits of Lycium barbarum L

Zeaxanthin dipalmitate (ZDP) is a major non-saponified carotenoid in fully ripe fruits of Lycium barbarum L. In the present study, response surface methodology was used to optimize the ultrasonic-assisted extraction (UAE) conditions of carotenoids from the fruits of L. barbarum, and the optimal extraction conditions were determined as follows: ultrasonic power of 360 W, ultrasonic time of 40 min and the ratio of extraction solvent to sample of 30 mL/g. An actual value of ZDP content of 5.40 mg/g and short extraction time indicated the efficiency of UAE. Furthermore, a promising high-speed counter-current chromatography (HSCCC) method was established for the purification of ZDP from the fruits of L. barbarum. With a developed two-phase solvent system composed of n-hexane/dichloromethane/acetonitrile (10/3/7, v/v/v), ZDP with a purity of higher than 95% was successfully isolated from the crude extract. This is the first report on the purification of ZDP by using HSCCC.

Impact of Nitrogen Fertilizer Levels on Metabolite Profiling of the Lycium barbarum L. Fruit

The yield and quality of goji (Lycium barbarum L.) fruit are heavily dependent on fertilizer, especially the availability of nitrogen, phosphorus, and potassium (N, P, and K, respectively). In this study, we performed a metabolomic analysis of the response of goji berry to nitrogen fertilizer levels using an Ultra Performance Liquid Chromatography-Electrospray Ionization-Tandem Mass Spectrometry (UPLC-ESI-MS/MS) method. There was no significant difference in the fruit yield or the commodity grade between N0 (42.5 g/plant), N1 (85 g/plant), and N2 (127.5 g/plant). The primary nutrients of the goji berry changed with an increasing nitrogen fertilization. Comparative metabolomic profiling of three nitrogen levels resulted in the identification of 612 metabolites, including amino acids, flavonoids, carbohydrates, organic acids, and lipids/alcohols, among others, of which 53 metabolites (lipids, fatty acids, organic acids, and phenolamides) demonstrated significant changes. These results provide new insights into the molecular mechanisms of the relationship between yield and quality of goji berry and nitrogen fertilizer.

Zeaxanthin Dipalmitate in the Treatment of Liver Disease

Goji berry, Lycium barbarum, has been widely used in traditional Chinese medicine (TCM), but its properties have not been studied until recently. The fruit is a major source of zeaxanthin dipalmitate (ZD), a xanthophyll carotenoid shown to benefit the liver. Liver disease is one of the most prevalent diseases in the world. Some conditions, such as chronic hepatitis B virus, liver cirrhosis, and hepatocellular carcinoma, remain incurable. Managing them can constitute an economic burden for patients and healthcare systems. Hence, development of more effective pharmacological drugs is warranted. Studies have shown the hepatoprotective, antifibrotic, antioxidant, anti-inflammatory, antiapoptotic, antitumor, and chemopreventive properties of ZD. These findings suggest that ZD-based drugs could hold promise for many liver disorders. In this paper, we reviewed the current literature regarding the therapeutic effects of ZD in the treatment of liver disease.

ABA mediates development-dependent anthocyanin biosynthesis and fruit coloration in Lycium plants

BACKGROUND

Anthocyanins, which are colored pigments, have long been used as food and pharmaceutical ingredients due to their potential health benefits, but the intermediate signals through which environmental or developmental cues regulate anthocyanin biosynthesis remains poorly understood. Fleshy fruits have become a good system for studying the regulation of anthocyanin biosynthesis, and exploring the mechanism underlying pigment metabolism is valuable for controlling fruit ripening.

RESULTS

The present study revealed that ABA accumulated during Lycium fruit ripening, and this accumulation was positively correlated with the anthocyanin contents and the LbNCED1 transcript levels. The application of exogenous ABA and of the ABA biosynthesis inhibitor fluridon increased and decreased the content of anthocyanins in Lycium fruit, respectively. This is the first report to show that ABA promotes the accumulation of anthocyanins in Lycium fruits. The variations in the anthocyanin content were consistent with the variations in the expression of the genes encoding the MYB-bHLH-WD40 transcription factor complex or anthocyanin biosynthesis-related enzymes. Virus-induced LbNCED1 gene silencing significantly slowed fruit coloration and decreased both anthocyanin and ABA accumulation during Lycium fruit ripening. An qRT-PCR analysis showed that LbNCED1 gene silencing clearly reduced the transcript levels of both structural and regulatory genes in the flavonoid biosynthetic pathway.

CONCLUSIONS

Based on the results, a model of ABA-mediated development-dependent anthocyanin biosynthesis and fruit coloration during Lycium fruit maturation was proposed. In this model, the developmental cues transcriptionally activates LbNCED1 and thus enhances accumulation of the phytohormone ABA, and the accumulated ABA stimulates transcription of the MYB-bHLH-WD40 transcription factor complex to upregulate the expression of structural genes in the flavonoid biosynthetic pathway and thereby promoting anthocyanin production and fruit coloration. Our results provide a valuable strategy that could be used in practice to regulate the ripening and quality of fresh fruit in medicinal and edible plants by modifying the phytohormone ABA.

Comparison of Functional Components and Antioxidant Activity of Lycium barbarum L. Fruits from Different Regions in China

The fruit of Lycium barbarum L. (FLB) has been used as medicines and functional foods for more than 2000 years in East Asia. In this study, carotenoid, phenolic, flavonoid, and polysaccharide contents as well as the antioxidant activities of FLB from 13 different regions in China from a total of 78 samples were analyzed. The results showed that total carotenoid contents ranged from 12.93 to 25.35 mg β-carotene equivalents/g DW. Zeaxanthin dipalmitate was the predominant carotenoid (4.260–10.07 mg/g DW) in FLB. The total phenolic, total flavonoid, and total polysaccharide contents ranged from 6.899 to 8.253 mg gallic acid equivalents/g DW, 3.177 to 6.144 mg rutin equivalents/g DW, and 23.62 to 42.45 mg/g DW, respectively. Rutin content ranged from 0.1812 to 0.4391 mg/g DW, and ferulic acid content ranged from 0.0994 to 0.1726 mg/g DW. All of these FLB could be divided into two clusters with PCA analysis, and both individual carotenoids and total carotenoid contents could be used as markers for regional characterization. The phenolic components were the main substance for the antioxidant activity of FLB. Considering the functional component and antioxidant activities, FLB produced in Guyuan of Ningxia was the closest to Daodi herbs (Zhongwei of Ningxia), which is commercially available high quality FLB. The results of this study could provide guidance for comprehensive applications of FLB production in different regions.

Physiological characterization, transcriptomic profiling, and microsatellite marker mining of Lycium ruthenicum

Lycium ruthenicum is a perennial shrub species that has attracted considerable interest in recent years owing to its nutritional value and ability to thrive in a harsh environment. However, only extremely limited transcriptomic and genomic data related to this species can be found in public databases, thereby limiting breeding research and molecular function analysis. In this study, we characterized the physiological and biochemical responses to saline-alkaline mixed stress by measuring photochemical efficiency, chlorophyll content, and protective enzyme activity. We performed global transcriptomic profiling analysis using the Illumina platform. After optimizing the assembly, a total of 68 063 unique transcript sequences with an average length of 877 bp were obtained. Among these sequences, 4096 unigenes were upregulated and 4381 unigenes were down-regulated after saline-alkaline mixed treatment. The most abundant transcripts and over-represented items were assigned to gene ontology (GO) terms or Kyoto Encyclopedia of Genes and the Genomes (KEGG) categories for overall unigenes, and differentially expressed unigenes were analyzed in detail. Based on this set of RNA-sequencing data, a total of 9216 perfect potential simple sequence repeats (SSRs) were identified within 7940 unigenes with a frequency of 1/6.48 kb. A total of 77 primer pairs were synthesized and examined in wet-laboratory experiments, of which 68 loci (88.3%) were successfully amplified with specific products. Eleven pairs of polymorphic primers were verified in 225 individuals from nine populations. The inbreeding coefficient and the polymorphism information content value ranged from 0.011 to 0.179 and from 0.1112 to 0.6750, respectively. The observed and expected heterozygosities ranged from 0.064 to 0.840 and from 0.115 to 0.726, respectively. Nine populations were clustered into three groups based on a genetic diversity study using these novel markers. Our data will be useful for functional genomic investigations of L. ruthenicum and could be used as a basis for further research on the genetic diversity, genetic differentiation, and gene flow of L. ruthenicum and other closely related species.

Isolation and characterization of a salt stress-responsive betaine aldehyde dehydrogenase in Lycium ruthenicum Murr

As compatible solute, glycine betaine (GB) plays a significant role in salinity tolerance in GB accumulating plants. Solanaceous crops such as tomato (Solanum lycopersicum) and tobacco (Nicotiana tabacum) are salt sensitive and naturally GB non-accumulators. In Solanaceae, only the Lycium genus has been recorded as halophytes in China, and several Lycium species have been reported as GB accumulators. The last biosynthetic step of GB is catalyzed by aminoaldehyde dehydrogenase (AMADH) with betaine aldehyde dehydrogenase (BADH) activities. Failure of GB synthesis in tomato and tobacco was attributed to lack of BADH activity. Here, by comparing the BADH functional residues of AMADHs between the Lycium genus and solanaceous crops, we predict that all studied AMADH1s have low BADH activities while only LbAMADH2 from L. barbarum has high BADH activity. For two AMADHs in L. ruthenicum, results from substrate enzyme assays confirmed low BADH activity of LrAMADH1 and no BADH activity of LrAMADH2. Despite the very low GB contents in L. ruthenicum seedlings (< 0.5 μmol g^-1 fresh weight), GB contents in fruits are up to 150 μmol g^-1 FW, inferring fruits of L. ruthenicum as good GB sources. In NaCl treated seedlings, accompanied by elevated GB accumulation, expression of LrAMADH1 was up-regulated, indicating response of LrAMADH1 to salt stress in L. ruthenicum. Virus-induced silence of LrAMADH1 leads to less GB accumulation than control, revealing that LrAMADH1 participates in GB synthesis in planta. Collectively, our results show that LrAMADH1 is the bona fide BADH, which responds to salt stress in L. ruthenicum.

Antioxidants Distribution in Pulp and Seeds of Black and Red Goji Berries as Affected by Boiling Processing

Pulp and seeds from four varieties of black goji and two varieties of red goji with different geographical origins were examined for their total phenolic content (TPC), total flavonoid content (TFC), condensed tannin content (CTT), monomeric anthocyanin content (MAC), 2,2-diphenyl-1-picrylhydrazyl (DPPH) scavenging capacity, and ferric reducing antioxidant power (FRAP) using colorimetric methods. Contribution rates of pulp and seed to phytochemical contents and overall antioxidant capacities of whole fruits were calculated for each parameter. It was observed that most of the phytochemicals and antioxidant activities were predominantly contributed by the pulp in all six varieties. Boiling led to significant (p< 0.05) losses in the phytochemical content and antioxidant capacity. The average MAC value in black goji was significantly (p< 0.05) higher than that observed for red goji.

Zeaxanthin dipalmitate alleviates hepatic injury induced by superimposed chronic hepatitis B and non-alcoholic steatohepatitis in non-obese mice

A hepatitis B virus (HBV) transgenic mice model was used to establish the fatty liver superimposed model by feeding the methionine choline-deficient (MCD) diet for 8 weeks, with or without the gavage of 2 mg/kg zeaxanthin dipalmitate (ZD) three times per week. Both wild-type and HBV transgenic mice, with MCD diet, gained typical non-obese non-alcoholic steatohepatitis (NASH) and HBV symptoms. Coadministration with ZD exhibited evident therapeutic effects through alleviating those pathological events. Moreover, long-term vehicle-ZD treatment was found to be safe. Thus, ZD is a promising and safe hepato-protective agent against hepatic injury induced by superimposed HBV and NASH in non-obese mice.

Comparative studies on phenolic profiles, antioxidant capacities and carotenoid contents of red goji berry (Lycium barbarum) and black goji berry (Lycium ruthenicum)

Background

The study on phytochemical difference between red and black goji berry is limited.

Methods

Antioxidant activities and phenolic profiles in terms of total phenol content, total flavonoid contents, condensed tannin content, monomeric anthocyanin content, and total carotenoid content of red goji berry (Lycium barbarum) and black goji berry (L. ruthenicum) were compared using colorimetric assays.

Results

All goji berries were rich in phenolics. Black goji berry had the highest phenolic, condensed tannin content and monomeric anthocyanin content. Black goji berry samples possessed higher antioxidant capacities than red goji berry, while the red goji berry had the highest carotenoid content. Goji berries exhibited a positive linear correlation between phenolic compounds and antioxidant capacities. The average value of carotenoid content in red goji berry was 233.04 µg/g.

Conclusion

The phenolics and antioxidant capacities are much higher in black goji berry than red goji berry, while carotenoid content is much higher in red than black.

LbCML38 and LbRH52, two reference genes derived from RNA-Seq data suitable for assessing gene expression in Lycium barbarum L

For quantitative real-time PCR (qRT-PCR) analysis, the key prerequisite that determines result accuracy is the selection of appropriate reference gene(s). Goji (Lycium barbarum L.) is a multi-branched shrub belonging to the Solanaceae family. To date, no systematic screening or evaluation of reference gene(s) in Goji has been performed. In this work, we identified 18 candidate reference genes from the transcriptomic sequencing data of 14 samples of Goji at different developmental stages and under drought stress condition. The expression stability of these candidate genes was rigorously analyzed using qRT-PCR and four different statistical algorithms: geNorm, BestKeeper, NormFinder and RefFinder. Two novel reference genes LbCML38 and LbRH52 showed the most stable expression, whereas the traditionally used reference genes such as LbGAPDH, LbHSP90 and LbTUB showed unstable expression in the tested samples. Expression of a target gene LbMYB1 was also tested and compared using optimal reference genes LbCML38 and LbRH52, mediocre reference gene LbActin7, and poor reference gene LbHSP90 as normalization standards, respectively. As expected, calculation of the target gene expression by normalization against LbCML38, LbActin7 or LbHSP90 showed significant differences. Our findings suggest that LbCML38 and LbRH52 can be used as reference genes for gene expression analysis in Goji.

Carotenoid Cleavage Oxygenases from Microbes and Photosynthetic Organisms: Features and Functions

Apocarotenoids are carotenoid-derived compounds widespread in all major taxonomic groups, where they play important roles in different physiological processes. In addition, apocarotenoids include compounds with high economic value in food and cosmetics industries. Apocarotenoid biosynthesis starts with the action of carotenoid cleavage dioxygenases (CCDs), a family of non-heme iron enzymes that catalyze the oxidative cleavage of carbon-carbon double bonds in carotenoid backbones through a similar molecular mechanism, generating aldehyde or ketone groups in the cleaving ends. From the identification of the first CCD enzyme in plants, an increasing number of CCDs have been identified in many other species, including microorganisms, proving to be a ubiquitously distributed and evolutionarily conserved enzymatic family. This review focuses on CCDs from plants, algae, fungi, and bacteria, describing recent progress in their functions and regulatory mechanisms in relation to the different roles played by the apocarotenoids in these organisms.

Anti-inflammatory Activity of Berry Fruits in Mice Model of Inflammation is Based on Oxidative Stress Modulation

BACKGROUND

Many fruits have been used as nutraceuticals because the presence of bioactive molecules that play biological activities.

OBJECTIVE

The present study was designed to compare the anti-inflammatory and antioxidant effects of methanolic extracts of Lycium barbarum (GOJI), Vaccinium macrocarpon (CRAN) and Vaccinium myrtillus (BLUE).

MATERIALS AND METHODS

Mices were treated with extracts (50 and 200 mg/kg, p.o.), twice a day through 10 days. Phytochemical analysis was performed by high-performance liquid chromatography. Antioxidant activity was determine by 2,2-diphenyl-1-picrylhydrazyl (DPPH) assay, reducing power, lipid peroxidation thiobarbituric acid reactive substances (TBARS), reduced glutathione (GSH) and catalase (CAT) activity. Anti-inflammatory activity was evaluated by paw edema followed by determination of myeloperoxidase (MPO) and TBARS.

RESULTS

High amount of phenolic compounds, including rutin, were identified in all berries extracts. However, quercetin was observed only in BLUE and CRAN. GOJI presents higher scavenging activity of DPPH radical and reducing power than BLUE and CRAN. The extracts improved antioxidant status in liver; BLUE showed the largest reduction (75.3%) in TBARS when compared to CRAN (70.7%) and GOJI (65.3%). Nonetheless, CAT activity was lower in BLUE group. However, hepatic concentrations of GSH were higher in animals treated with GOJI rather than CRAN and BLUE. Despite all fruits caused a remarkable reduction in paw edema and TBARS, only BLUE and CRAN were able to reduce MPO.

CONCLUSION

These results suggest that quercetin, rutin, or other phenolic compound found in these berry fruits extracts could produce an anti-inflammatory response based on modulation of oxidative stress in paw edema model.

SUMMARY

Within fruits broadly consumed because of its nutraceuticals properties include, Lycium barbarum (Goji berry), Vaccinium myrtillus (Blueberry or Bilberry) and Vaccinium macrocarpon (Cranberry)The objectives of this study were the investigation and comparison of chemical composition, antioxidant activity "in vitro" and "in vivo" and anti inflammatory property of berry fruits bought dry form.In summary, two main findings can be addressed with this study: (1) Berry fruits presented antioxidant and anti inflammatory activities "in vitro" and "in vivo"; (2) the extracts of GOJI, CRAN, and BLUE modulate the inflammatory process by different mechanisms.

Transcriptome Analysis of Differentially Expressed Genes Involved in Proanthocyanidin Accumulation in the Rhizomes of Fagopyrum dibotrys and an Irradiation-Induced Mutant

The rhizome of Fagopyrum dibotrys is a traditional Chinese medicine that has recently gained attention due to substantial findings regarding its bioactive proanthocyanidin (PA) compounds. However, the molecular mechanism underlying PA accumulation in F. dibotrys remains elusive. We previously obtained an irradiation-induced mutant (RM_R) of F. dibotrys that had a higher PA content compared to that of the wild-type (CK_R). The present study aimed to elucidate the molecular mechanism underlying PA accumulation in F. dibotrys by comparing the rhizome transcriptomes of the irradiation-induced mutant and wild-type using RNA-seq analysis. A total of 53,540 unigenes were obtained, of which 29,901 (55.84%) were annotated based on BLAST searches against public databases, and 501 unique sequences were differentially expressed between the two samples, which consisted of 204 up-regulated and 297 down-regulated unigenes. Further analysis showed that the expression patterns of some unigenes encoding enzymes involved in PAs biosynthesis in F. dibotrys rhizomes differed between RM_R and CK_R. In addition, we identified transcription factor families and several cytochrome P450s that may be involved in PA regulation in F. dibotrys. Finally, 12 unigenes that encode PA biosynthetic enzymes were confirmed by qRT-PCR analysis. This study sheds light on the molecular mechanism underlying radiation-mediated flavonoid accumulation and regulation in F. dibotrys rhizomes. These results will also provide a platform for further functional genomic research on this particular species.

Carotenoid metabolism and regulation in horticultural crops

Carotenoids are a diverse group of pigments widely distributed in nature. The vivid yellow, orange, and red colors of many horticultural crops are attributed to the overaccumulation of carotenoids, which contribute to a critical agronomic trait for flowers and an important quality trait for fruits and vegetables. Not only do carotenoids give horticultural crops their visual appeal, they also enhance nutritional value and health benefits for humans. As a result, carotenoid research in horticultural crops has grown exponentially over the last decade. These investigations have advanced our fundamental understanding of carotenoid metabolism and regulation in plants. In this review, we provide an overview of carotenoid biosynthesis, degradation, and accumulation in horticultural crops and highlight recent achievements in our understanding of carotenoid metabolic regulation in vegetables, fruits, and flowers.

Identification and characterization of miRNAs in ripening fruit of Lycium barbarum L. using high-throughput sequencing

MicroRNAs (miRNAs) are master regulators of gene activity documented to play central roles in fruit ripening in model plant species, yet little is known of their roles in Lycium barbarum L. fruits. In this study, miRNA levels in L. barbarum fruit samples at four developmental stages, were assayed using Illumina HiSeqTM2000. This revealed the presence of 50 novel miRNAs and 38 known miRNAs in L. barbarum fruits. Of the novel miRNAs, 36 were specific to L. barbarum fruits compared with L. chinense. A number of stage-specific miRNAs were identified and GO terms were assigned to 194 unigenes targeted by miRNAs. The majority of GO terms of unigenes targeted by differentially expressed miRNAs are "intracellular organelle," "binding," "metabolic process," "pigmentation," and "biological regulation." Enriched KEGG analysis indicated that nucleotide excision repair and ubiquitin mediated proteolysis were over-represented during the initial stage of ripening, with ABC transporters and sulfur metabolism pathways active during the middle stages and ABC transporters and spliceosome enriched in the final stages of ripening. Several miRNAs and their targets serving as potential regulators in L. barbarum fruit ripening were identified using quantitative reverse transcription polymerase chain reaction. The miRNA-target interactions were predicted for L. barbarum ripening regulators including miR156/157 with LbCNR and LbWRKY8, and miR171 with LbGRAS. Additionally, regulatory interactions potentially controlling fruit quality and nutritional value via sugar and secondary metabolite accumulation were identified. These include miR156 targeting of fructokinase and 1-deoxy-D-xylulose-5-phosphate synthase and miR164 targeting of beta-fructofuranosidase. In sum, valuable information revealed by small RNA sequencing in this study will provide a solid foundation for uncovering the miRNA-mediated mechanism of fruit ripening and quality in this nutritional food.