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Hemerocallis citrina Baroni ( H. citrina ), a traditional medicinal and edible plant, is rich in bioactive flavonoids. This study investigated flavonoid metabolites in H. citrina flowers from ten accessions using UPLC-MS/MS-based metabolomics. A total of 642 flavonoids and 14 tannins were identified in the flowers. Among these, 375 flavonoids were classified as flavonols and flavone, representing for 39.33% and 17.53%, respectively. The identification of 309 differential flavonoid metabolites was achieved through analyses of nine pairwise comparison groups. These differential flavonoids in flowers of H. citrina could be distinctly categorized into two groups, clearly separating the 7 edible accessions from the 3 non-edible accessions . Significant variations in 14 flavonoid markers were observed among 10 H. citrina accessions originating from different regions, as determined by hierarchical clustering and ROC analyses. Transcriptomic analyses revealed that the majority of differentially expressed genes were enriched in the flavonoid metabolism pathway among these accessions. Integrated transcriptomic and metabolic analyses identified 14 differential flavonoid metabolites (DFMs) and 47 differentially expressed genes (DEGs) associated with flavonoid biosynthesis through Pearson’s correlation analysis and WGCNA analyses. qRT-PCR validation of 13 DEGs confirmed the consistency of transcriptomic data. A flavonoid-gene correlation network indicated that the 14 DFMs might be directly regulated by 17 DEGs, comprising 13 flavnoid metabolism-related genes and 4 transcript factors. These findings provide biological and chemical insights into flavonoid metabolic difference across H. citrina origins, offering a theoretical basis for food and medical applications, and enabling clear differentiation between edible and non-edible H. citrina flowers in the market.

Background Hemerocallis citrina Baroni (daylily) is a horticultural ornamental plant and vegetable with various applications as a raw material in traditional Chinese medicine and as a flavouring agent. Daylily contains many functional substances and is rich in lecithin, which is mostly composed of glycerophospholipids. To study the comprehensive dynamic changes in glycerophospholipid during daylily flowering and the underlying signalling mechanisms, we performed comprehensive, time-resolved lipidomic and transcriptomic analyses of ‘Datong Huanghua 6’ daylily. Results Labelling with PKH67 fluorescent antibodies clearly and effectively helped visualise lipid changes in daylily, while relative conductivity and malonaldehyde content detection revealed that the early stages of flowering were controllable processes; however, differences became non-significant after 18 h, indicating cellular damage. In addition, phospholipase D (PLD) and lipoxygenase (LOX) activities increased throughout the flowering process, suggesting that lipid hydrolysis and oxidation had intensified. Lipidomics identified 558 lipids that changed during flowering, with the most different lipids found 12 h before and 12 h after flowering. Transcriptome analysis identified 13 key functional genes and enzymes in the glycerophospholipid metabolic pathway. The two-way orthogonal partial least squares analysis showed that diacylglycerol diphosphate phosphatase correlated strongly and positively with phosphatidic acid (PA)(22:0/18:2), PA(34:2), PA(34:4), and diacylglycerol(18:2/21:0) but negatively with phospholipase C. In addition, ethanolamine phosphotransferase gene and phospholipid-N-methyltransferase gene correlated positively with phosphatidylethanolamine (PE)(16:0/18:2), PE(16:0/18:3), PE(33:2), and lysophosphatidylcholine (16:0) but negatively with PE(34:1). Conclusions Overall, this study elucidated changes in the glycerophospholipid metabolism pathway during the daylily flowering process, as well as characteristic genes, thus providing a basis for future studies of glycerophospholipids and signal transduction in daylilies.

SHORT VEGETATIVE PHASE (SVP) genes are members of the well-known MADS-box gene family that play a key role in regulating vital developmental processes in plants. Hemerocallis are perennial herbs that exhibit continuous flowering development and have been extensively used in landscaping. However, there are few reports on the regulatory mechanism of flowering in Hemerocallis. To better understand the molecular basis of floral formation of Hemerocallis, we identified and characterized the SVP-like gene HkSVP from the Hemerocallis cultivar ‘Kanai Sensei’. Quantitative RT-PCR (qRT-PCR) indicated that HkSVP transcript was mainly expressed in the vegetative growth stage and had the highest expression in leaves, low expression in petals, pedicels and fruits, and no expression in pistils. The HkSVP encoded protein was localized in the nucleus of Arabidopsis protoplasts and the nucleus of onion epidermal cells. Yeast two hybrid assay revealed that HKSVP interacted with Hemerocallis AP1 and TFL1. Moreover, overexpression of HkSVP in Arabidopsis resulted in delayed flowering and abnormal phenotypes, including enriched trichomes, increased basal inflorescence branches and inhibition of inflorescence formation. These observations suggest that the HkSVP gene may play an important role in maintaining vegetative growth by participating in the construction of inflorescence structure and the development of flower organs.

Background Hemerocallis citrina Baroni is a traditional vegetable crop widely cultivated in eastern Asia for its high edible, medicinal, and ornamental value. The phenomenon of codon usage bias (CUB) is prevalent in various genomes and provides excellent clues for gaining insight into organism evolution and phylogeny. Comprehensive analysis of the CUB of mitochondrial (mt) genes can provide rich genetic information for improving the expression efficiency of exogenous genes and optimizing molecular-assisted breeding programmes in H. citrina . Results Here, the CUB patterns in the mt genome of H. citrina were systematically analyzed, and the possible factors shaping CUB were further evaluated. Composition analysis of codons revealed that the overall GC (GCall) and GC at the third codon position (GC3) contents of mt genes were lower than 50%, presenting a preference for A/T-rich nucleotides and A/T-ending codons in H. citrina . The high values of the effective number of codons (ENC) are indicative of fairly weak CUB. Significant correlations of ENC with the GC3 and codon counts were observed, suggesting that not only compositional constraints but also gene length contributed greatly to CUB. Combined ENC-plot, neutrality plot, and Parity rule 2 (PR2)-plot analyses augmented the inference that the CUB patterns of the H. citrina mitogenome can be attributed to multiple factors. Natural selection, mutation pressure, and other factors might play a major role in shaping the CUB of mt genes, although natural selection is the decisive factor. Moreover, we identified a total of 29 high-frequency codons and 22 optimal codons, which exhibited a consistent preference for ending in A/T. Subsequent relative synonymous codon usage (RSCU)-based cluster and mt protein coding gene (PCG)-based phylogenetic analyses suggested that H. citrina is close to Asparagus officinalis , Chlorophytum comosum , Allium cepa , and Allium fistulosum in evolutionary terms, reflecting a certain correlation between CUB and evolutionary relationships. Conclusions There is weak CUB in the H. citrina mitogenome that is subject to the combined effects of multiple factors, especially natural selection. H. citrina was found to be closely related to Asparagus officinalis , Chlorophytum comosum , Allium cepa , and Allium fistulosum in terms of their evolutionary relationships as well as the CUB patterns of their mitogenomes. Our findings provide a fundamental reference for further studies on genetic modification and phylogenetic evolution in H. citrina .

To trace the fate of individual pollen grains through pollination processes, we determined genotypes of single pollen grains deposited on Hemerocallis stigmas in an experimental mixed-species array. Hemerocallis fulva, pollinated by butterflies, has diurnal, reddish and unscented flowers, and H. citrina, pollinated by hawkmoths, has nocturnal, yellowish and sweet scent flowers. We observed pollinator visits to an experimental array of 24 H. fulva and 12 F2 hybrids between the two species (H. fulva and H. citrina) and collected stigmas after every trip bout of swallowtail butterflies or hawkmoths. We then measured selection by swallowtail butterflies or hawkmoths through male and female components of pollination success as determined by single pollen genotyping. As expected, swallowtail butterflies imposed selection on reddish color and weak scent: the number of outcross pollen grains acquired is a quadratic function of flower color with the maximum at reddish color, and the combined pollination success was maximal at weak scent (almost unrecognizable for human). This explains why H. fulva, with reddish flowers and no recognizable scent, is mainly pollinated by swallowtail butterflies. However, we found no evidence of hawkmoths-mediated selection on flower color or scent. Our findings do not support a hypothesis that yellow flower color and strong scent intensity, the distinctive floral characteristics of H. citrina, having evolved in adaptations to hawkmoths. We suggest that the key trait that triggers the evolution of nocturnal flowers is flowering time rather than flower color and scent.

Key message Saline-alkali stress induces oxidative damage and photosynthesis inhibition in H. citrina , with a significant downregulation of the expression of photosynthesis- and antioxidant-related genes at high concentration. Soil salinization is a severe abiotic stress that impacts the growth and development of plants. In this study, Hemerocallis citrina Baroni was used to investigate its responsive mechanism to complex saline-alkali stress (NaCl:Na 2 SO 4 :NaHCO 3 :Na 2 CO 3  = 1:9:9:1) for the first time. The growth phenotype, photoprotective mechanism, and antioxidant system of H. citrina were studied combining physiological and transcriptomic techniques. KEGG enrichment and GO analyses revealed significant enrichments of genes related to photosynthesis, chlorophyll degradation and antioxidant enzyme activities, respectively. Moreover, weighted gene co-expression network analysis (WGCNA) found that saline-alkali stress remarkably affected the photosynthetic characteristics and antioxidant system. A total of 29 key genes related to photosynthesis and 29 key genes related to antioxidant enzymes were discovered. High-concentration (250 mmol L −1 ) stress notably inhibited the expression levels of genes related to light-harvesting complex proteins, photosystem reaction center activity, electron transfer, chlorophyll synthesis, and Calvin cycle in H. citrina leaves. However, most of them were insignificantly changed under low-concentration (100 mmol L −1 ) stress. In addition, H. citrina leaves under saline-alkali stress exhibited yellow–brown necrotic spots, increased cell membrane permeability and accumulation of reactive oxygen species (ROS) as well as osmolytes. Under 100 mmol L −1 stress, ROS was eliminate by enhancing the activities of antioxidant enzymes. Nevertheless, 250 mmol L −1 stress down-regulated the expression levels of genes encoding antioxidant enzymes, and key enzymes in ascorbate–glutathione (AsA-GSH) cycle as well as thioredoxin-peroxiredoxin (Trx-Prx) pathway, thus inhibiting the activities of these enzymes. In conclusion, 250 mmol L −1 saline-alkali stress caused severe damage to H. citrina mainly by inhibiting photosynthesis and ROS scavenging capacity.

Key message Cd induces photosynthetic inhibition and oxidative stress damage in H. citrina , which mobilizes the antioxidant system and regulates the expression of corresponding genes to adapt to Cd and Pb stress. Cd and Pb are heavy metals that cause severe pollution and are highly hazardous to organisms. Physiological measurements and transcriptomic analysis were combined to investigate the effect of 5 mM Cd or Pb on Hemerocallis citrina Baroni. Cd significantly inhibited H. citrina growth, while Pb had a minimal impact. Both Cd and Pb suppressed the expression levels of key chlorophyll synthesis genes, resulting in decreased chlorophyll content. At the same time, Cd accelerated chlorophyll degradation. It reduced the maximum photochemical efficiency of photosystem (PS) II, damaging the oxygen-evolving complex and leading to thylakoid dissociation. In contrast, no such phenomena were observed under Pb stress. Cd also inhibited the Calvin cycle by down-regulating the expression of Rubisco and SBPase genes, ultimately disrupting the photosynthetic process. Cd impacted the light reaction processes by damaging the antenna proteins, PS II and PS I activities, and electron transfer rate, while the impact of Pb was weaker. Cd significantly increased reactive oxygen species and malondialdehyde accumulation, and inhibited the activities of antioxidant enzymes and the expression levels of the corresponding genes. However, H. citrina adapted to Pb stress by the recruitment of antioxidant enzymes and the up-regulation of their corresponding genes. In summary, Cd and Pb inhibited chlorophyll synthesis and hindered the light capture and electron transfer processes, with Cd exerting great toxicity than Pb. These results elucidate the physiological and molecular mechanisms by which H. citrina responds to Cd and Pb stress and provide a solid basis for the potential utilization of H. citrina in the greening of heavy metal-polluted lands.

Background  Hemerocallis middendorffii is a kind of high quality ornamental plant with strong cold resistance, pleasant aroma, and gorgeous floral color. Hemerocallis is one of the three internationally recognized perennial flowers that has huge demand in the flower market. However, little is known about the floral scent and color biosynthesis in daylily due to the large genome size. Results We reported here a high-quality chromosome-scale genome of H. middendorffii which was a native daylily in China. Using PacBio HiFi and Hi-C sequencing technologies, we assembled a chromosome-level genome of 4.10 Gb with a contig N50 of 12.81 Mb. We identified 65,536 protein-coding genes across the 11 chromosomes. We employed a combination of genomic, transcriptomic, and metabolomic approaches to investigate mechanisms behind the floral scent and color biosynthesis in daylily. The main terpenoids contributing to floral fragrance were linalool, 3-carene, nerolidol, and α-farnesene, while carotenoids and anthocyanidins were the main components of floral color. These traits could be stably inherited by their hybrid progenies, and some of them exhibited heterosis. Through Weighted Gene Co-expression Network Analysis (WGCNA) analysis, we identified two modules MEblueviolet and MEgreenyellow related to terpenoids (floral scents) and carotenoids (floral colors) biosynthesis. The 10 hub genes including DXS , MVD , MVK , DXR , LCYBs , Z-ISO , CYPs , and JAS were screened by network construction. The results of qRT-PCR analysis showed that these hub genes were significant differentially expressed in daylily samples, and these results were basically consistent with the relative transcript levels of RNA-seq. Conclusions This study not only provides new insights into the molecular mechanisms of floral scent and color, but also lays a foundation for subsequent research on key gene functions and molecular breeding in Hemerocallis .

The World Health Organization predicts that over the next several years, depression will become the most important mental health issue globally. Growing evidence shows that the flower buds of Hemerocallis citrina Baroni (H. citrina) possess antidepressant properties. In the search for new anti-depression drugs, a total of 15 phenylpropanoids and 22 flavonoids were isolated and identified based on spectral data (1D and 2D NMR, HR-ESI-MS, UV) from H. citrina. Among them, compound 8 was a novel compound, while compounds 1–4, 6, 9, 10, 15, 17, 24–26, 28, and 37 were isolated for the first time from Hemerocallis genus. To study the antidepressant activity of phenylpropanoids and flavonoids fractions from H. citrina, macroporous resin was used to enrich them under the guidance of UV characteristics. UHPLC-MS/MS was applied to identify the constituents of the enriched fractions. According to behavioral tests and biochemical analyses, it showed that phenylpropanoid and flavonoid fractions from H. citrina can improve the depressive-like mental state of chronic unpredictable mild stress (CUMS) rats. This might be accomplished by controlling the amounts of the inflammatory proteins IL-6, IL-1β, and TNF-α in the hippocampus as well as corticosterone in the serum. Thus, the monomer compounds were tested for their anti-neuroinflammatory activity and their structure–activity relationship was discussed in further detail.

Background Hemerocallis citrina  Baroni is a traditional medical and edible plant. It is rich in flavonoid compounds, which are a kind of important bioactive components with various health benefits and pharmaceutical value. However, the flavonoid metabolomics profile and the comparison of flavonoid compounds from different parts of H. citrina is scarce. Results In this study, flavonoid metabolites were investigated from roots, stems, leaves and flowers of H. citrina . A total of 364 flavonoid metabolites were identified by UPLC-MS/MS based widely targeted metabolomics, and the four plant parts showed huge differences at flavonoid metabolic level. Compared to roots, 185, 234, and 119 metabolites accounted for upregulated differential flavonoid metabolites (DFMs) in stems, leaves, and flowers, respectively. Compared to stems, 168 and 29 flavonoid metabolites accounted for upregulated DFMs in leaves and flowers, respectively. Compared to leaves, only 29 flavonoid metabolites accounted for upregulated DFMs in flowers. A number of 35 common flavonoid metabolites were observed among six comparison groups, and each comparison group had its unique differential metabolites. The most abundant flavonoid metabolites in the four parts are flavonols and flavones, followed by flavanones, chalcones, flavanols, flavanonols, anthocyanidins, tannin, and proanthocyanidins. 6,7,8-Tetrahydroxy-5-methoxyflavone, 7,8,3’,4’-tetrahydroxyflavone, 1-Hydroxy-2,3,8-trimethoxyxanthone, Farrerol-7- O -glucoside, 3’,7-dihydroxy-4’-methoxyflavone, 3,3’- O -Dimethylellagic Acid, 5-Hydroxy-6,7-dimethoxyflavone, Nepetin (5,7,3’,4’-Tetrahydroxy-6-methoxyflavone), (2s)-4,8,10-trihydroxy-2-methoxy-1 h,2 h-furo[3,2-a]xanthen-11-one are dominant in roots. Isorhamnetin-3- O -(6’’-malonyl)glucoside-7- O -rhamnoside, 7-Benzyloxy-5-hydroxy-3’,4’-methylenedioxyflavonoid, 3-Hydroxyphloretin-4’- O -glucoside are dominant in stems. Chrysoeriol-7- O -glucoside, Epicatechin glucoside, Kaempferol-3- O -rhamnoside (Afzelin)(Kaempferin)*, Azaleatin (5- O -Methylquercetin), Chrysoeriol-5- O -glucoside, Nepetin-7- O -glucoside(Nepitrin), 3,5,7,2’-Tetrahydroxyflavone; Datiscetin, Procyanidin B2*, Procyanidin B3*, Procyanidin B1, Isorhamnetin-3- O -(6’’-acetylglucoside) are dominant in leaves. kaempferol-3-p-coumaroyldiglucoside, Delphinidin-3- O -sophoroside-5- O -glucoside, Limocitrin-3- O -sophoroside, Kaempferol-3- O -rutinoside(Nicotiflorin), Luteolin-7- O -(6’’-malonyl)glucoside-5- O -rhamnoside are dominant in flowers. Conclusion There was significant difference in flavonoid metabolites among different parts of H. citrina . Leaves had relative higher metabolites contents than other parts. This study provided biological and chemical evidence for the different uses of various plant parts of H. citrina , and these informations are important theoretical basis for the food industry, and medical treatment.