Characterization of the Rosa roxburghii Tratt transcriptome and analysis of MYB genes

Chemical diversity, traditional uses, and bioactivities of Rosa roxburghii Tratt: A comprehensive review

Rosa roxburghii Tratt (RRT), known as chestnut rose, has been a subject of growing interest because of its diverse chemical composition and wide range of traditional uses. This comprehensive review aimed to thoroughly examine RRT, including its traditional applications, chemical diversity, and various bioactivities. The chemical profile of this plant is characterized by the presence of essential nutrients such as vitamin C (ascorbic acid), flavonoids, triterpenes, organic acids, tannins, phenolic compounds, polysaccharides, carotenoids, triterpenoids, volatile compounds, amino acids, and essential oils. These constituents contribute to the medicinal and nutritional value. Additionally, we explore the multifaceted bioactivities of RRT, including its potential as an anticancer agent, antioxidant, antiaging agent, antiatherogenic agent, hypoglycemic agent, immunoregulatory modulator, radioprotective agent, antimutagenic agent, digestive system regulator, anti-inflammatory agent, cardioprotective agent, and antibacterial agent, and its intriguing role in modulating the gut microbiota. Furthermore, we discuss the geographical distribution and genetic diversity of this plant species and shed light on its ecological significance. This comprehensive review provides a holistic understanding of RRT, bridges traditional knowledge with contemporary scientific research, and highlights its potential applications in medicine, nutrition, and pharmacology.

Simultaneous determination of choline, L-carnitine, betaine, trimethylamine, trimethylamine N-oxide, and creatinine in plasma, liver, and feces of hyperlipidemic rats by UHPLC-MS/MS

BACKGROUND

Due to the close correlation between choline, L-carnitine, betaine and their intestinal microbial metabolites, including trimethylamine (TMA) and trimethylamine N-oxide (TMAO), and creatinine, there has been an increasing interest in the study of these compounds in vivo.

METHODS

In this study, a rapid stable isotope dilution (SID)-UHPLC-MS/MS method was developed for the simultaneous determination of choline, L-carnitine, betaine, TMA, TMAO and creatinine in plasma, liver and feces of rats. The method was validated using quality control (QC) samples spiked at low, medium and high levels. Second, we applied the method to quantify the effects of Rosa Roxburghii Tratt juice (RRTJ) on plasma, liver, and fecal levels of choline, L-carnitine, betaine, TMA, TMAO, and creatinine in high-fat diet-induced hyperlipidemic rats, demonstrating the utility of the method.

RESULTS

The limits of detection (LOD) were 0.04-0.027 µM and the limits of quantification (LOQ) were 0.009-0.094 µM. The linear ranges for each metabolite in plasma were choline1.50-96 µM; L-carnitine: 2-128 µM; betaine: 3-192 µM; TMA: 0.01-40.96 µM; TMAO: 0.06-61.44 µM and creatinine: 1-64 µM (R2 ≥ 0.9954). The linear ranges for each metabolite in liver were Choline: 12-768 µM; L-carnitine: 1.5-96 µM; betaine: 10-640 µM; TMA: 0.5-32 µM; TMAO: 0.02-81.92 µM and creatinine: 0.2-204.8 µM (R2 ≥ 0.9938). The linear ranges for each metabolite in feces were choline: 1.5-96 µM; L-carnitine: 0.01-40.96 µM; Betaine: 1.5-96 µM; TMA: 1-64 µM; TMAO: 0.02-81.92 µM and Creatinine: 0.02-81.92 µM (R2 ≥ 0.998). The intra-day and inter-day coefficients of variation were < 8 % for all analytes. The samples were stabilized after multiple freeze-thaw cycles (3 freeze-thaw cycles), 24 h at room temperature, 24 h at 4 °C and 20 days at -80 °C. The samples were stable. The average recovery was 89 %-99 %. This method was used to quantify TMAO and its related metabolites and creatinine levels in hyperlipidemic rats. The results showed that high-fat diet led to the disorder of TMAO and its related metabolites and creatinine in rats, which was effectively improved after the intervention of Rosa Roxburghii Tratt juice（RRTJ）.

CONCLUSIONS

A method for the determination of choline, L-carnitine, betaine, TMA, TMAO and creatinine in plasma, liver and feces samples was established, which is simple, time-saving, high precision, accuracy and recovery.

The chromosome-level genome and functional database accelerate research about biosynthesis of secondary metabolites in Rosa roxburghii

Rosa roxburghii Tratt, a valuable plant in China with long history, is famous for its fruit. It possesses various secondary metabolites, such as L-ascorbic acid (vitamin C), alkaloids and poly saccharides, which make it a high nutritional and medicinal value. Here we characterized the chromosome-level genome sequence of R. roxburghii, comprising seven pseudo-chromosomes with a total size of 531 Mb and a heterozygosity of 0.25%. We also annotated 45,226 coding gene loci after masking repeat elements. Orthologs for 90.1% of the Complete Single-Copy BUSCOs were found in the R. roxburghii annotation. By aligning with protein sequences from public platform, we annotated 85.89% genes from R. roxburghii. Comparative genomic analysis revealed that R. roxburghii diverged from Rosa chinensis approximately 5.58 to 13.17 million years ago, and no whole-genome duplication event occurred after the divergence from eudicots. To fully utilize this genomic resource, we constructed a genomic database RroFGD with various analysis tools. Otherwise, 69 enzyme genes involved in L-ascorbate biosynthesis were identified and a key enzyme in the biosynthesis of vitamin C, GDH (L-Gal-1-dehydrogenase), is used as an example to introduce the functions of the database. This genome and database will facilitate the future investigations into gene function and molecular breeding in R. roxburghii.

Analysis of the Protective Effects of Rosa roxburghii-Fermented Juice on Lipopolysaccharide-Induced Acute Lung Injury in Mice through Network Pharmacology and Metabolomics

Acute lung injury, a fatal condition characterized by a high mortality rate, necessitates urgent exploration of treatment modalities. Utilizing UHPLS-Q-Exactive Orbitrap/MS, our study scrutinized the active constituents present in Rosa roxburghii-fermented juice (RRFJ) while also assessing its protective efficacy against LPS-induced ALI in mice through lung histopathological analysis, cytokine profiling, and oxidative stress assessment. The protective mechanism of RRFJ against ALI in mice was elucidated utilizing metabolomics, network pharmacology, and molecular docking methodologies. Our experimental findings demonstrate that RRFJ markedly ameliorates pathological injuries in ALI-afflicted mice, mitigates systemic inflammation and oxidative stress, enhances energy metabolism, and restores dysregulated amino acid and arachidonic acid metabolic pathways. This study indicates that RRFJ can serve as a functional food for adjuvant treatment of ALI.

Chromosomal-scale genomes of two Rosa species provide insights into genome evolution and ascorbate accumulation

Rosa roxburghii and Rosa sterilis, two species belonging to the Rosaceae family, are widespread in the southwest of China. These species have gained recognition for their remarkable abundance of ascorbate in their fresh fruits, making them an ideal vitamin C resource. In this study, we generated two high-quality chromosome-scale genome assemblies for R. roxburghii and R. sterilis, with genome sizes of 504 and 981.2 Mb, respectively. Notably, we present a haplotype-resolved, chromosome-scale assembly for diploid R. sterilis. Our results indicated that R. sterilis originated from the hybridization of R. roxburghii and R. longicuspis. Genome analysis revealed the absence of recent whole-genome duplications in both species and identified a series of duplicated genes that possibly contributing to the accumulation of flavonoids. We identified two genes in the ascorbate synthesis pathway, GGP and GalLDH, that show signs of positive selection, along with high expression levels of GDP-d-mannose 3', 5'-epimerase (GME) and GDP-l-galactose phosphorylase (GGP) during fruit development. Furthermore, through co-expression network analysis, we identified key hub genes (MYB5 and bZIP) that likely regulate genes in the ascorbate synthesis pathway, promoting ascorbate biosynthesis. Additionally, we observed the expansion of terpene synthase genes in these two species and tissue expression patterns, suggesting their involvement in terpenoid biosynthesis. Our research provides valuable insights into genome evolution and the molecular basis of the high concentration of ascorbate in these two Rosa species.

Genome-Wide Identification and Expression Analysis of Rosa roxburghii Autophagy-Related Genes in Response to Top-Rot Disease

Autophagy is a highly conserved process in eukaryotes that degrades and recycles damaged cells in plants and is involved in plant growth, development, senescence, and resistance to external stress. Top-rot disease (TRD) in Rosa roxburghii fruits caused by Colletotrichum fructicola often leads to huge yield losses. However, little information is available about the autophagy underlying the defense response to TRD. Here, we identified a total of 40 R. roxburghii autophagy-related genes (RrATGs), which were highly homologous to Arabidopsis thaliana ATGs. Transcriptomic data show that RrATGs were involved in the development and ripening processes of R. roxburghii fruits. Gene expression patterns in fruits with different degrees of TRD occurrence suggest that several members of the RrATGs family responded to TRD, of which RrATG18e was significantly up-regulated at the initial infection stage of C. fructicola. Furthermore, exogenous calcium (Ca²⁺) significantly promoted the mRNA accumulation of RrATG18e and fruit resistance to TRD, suggesting that this gene might be involved in the calcium-mediated TRD defense response. This study provided a better understanding of R. roxburghii autophagy-related genes and their potential roles in disease resistance.

Association of Physcion and Chitosan Can Efficiently Control Powdery Mildew in Rosa roxburghii

Powdery mildew is an extremely serious disease of all Rosa roxburghii production regions in China and frequently causes 30~40% of economic losses. Natural products are considered excellent alternatives to chemical fungicides. In this work, we investigated the efficacy of physcion used together with chitosan controls R. roxburghii powdery mildew and impacts its resistance, growth, yield, and quality. The results reveal that the foliar application of 12.5 mg L−1 0.5% physcion aqueous solutions (AS) + 250 mg L−1 chitosan efficiently controlled powdery mildew with the efficacies of 92.65% and 90.68% after 7 d and 14 d, respectively, which conspicuously (p < 0.05) higher than 83.62% and 80.43% of 25 mg L−1 0.5% physcion AS, as well as 70.75% and 77.80% of 500 mg L−1 chitosan. Meanwhile, this association prominently ameliorated the resistant and photosynthetic capabilities of R. roxburghii. Simultaneously, this association was more efficient than physcion or chitosan alone for ameliorating the yield and quality of R. roxburghii. This work emphasizes that the association of physcion and chitosan can be nominated as a natural, efficient and environmental-friendly alternative ingredient in controlling R. roxburghii powdery mildew and ameliorating its resistant, photosynthesis, yield, and quality.

Transcriptome Analysis Revealed Hormone Pathways and bZIP Genes Responsive to Decapitation in Sunflower

Decapitation is an essential agricultural practice and is a typical method for analyzing shoot branching. However, it is unclear exactly how decapitation controls branching. In this study, the decapitation of sunflower plants led to the development of lateral buds, accompanied by a decrease in indole-3-acetic acid (IAA) and abscisic acid (ABA) levels and an increase in cytokinin (CK) levels. Additionally, 82 members of the HabZIP family were discovered and categorized into 9 groups, using phylogenetic and conservative domain analysis. The intron/exon structure and motif compositions of HabZIP members were also investigated. Based on tissue-specific expression and expression analysis following decapitation derived from the transcriptome, several HabZIP members may be involved in controlling decapitation-induced bud outgrowth. Therefore, it is hypothesized that the dynamic variations in hormone levels, in conjunction with particular HabZIP genes, led to the development of axillary buds in sunflowers following decapitation.

Chitosan as an Adjuvant to Enhance the Control Efficacy of Low-Dosage Pyraclostrobin against Powdery Mildew of Rosa roxburghii and Improve Its Photosynthesis, Yield, and Quality

Powdery mildew is the most serious fungal disease of Rosa roxburghii in Guizhou Province, China. In this study, the control role of chitosan-assisted pyraclostrobin against powdery mildew of R. roxburghii and its influences on the resistance, photosynthesis, yield, quality and amino acids of R. roxburghii were evaluated. The results indicate that the foliar application of 30% pyraclostrobin suspension concentrate (SC) 100 mg L−1 + chitosan 500 mg L−1 displayed a superior control potential against powdery mildew, with a control efficacy of 89.30% and 94.58% after 7 d and 14 d of spraying, respectively, which significantly (p < 0.01) exceeded those of 30% pyraclostrobin SC 150 mg L−1, 30% pyraclostrobin SC 100 mg L−1, and chitosan 500 mg L−1. Simultaneously, their co-application could effectively enhance their effect on the resistance and photosynthesis of R. roxburghii leaves compared to their application alone. Meanwhile, their co-application could also more effectively enhance the yield, quality, and amino acids of R. roxburghii fruits compared to their application alone. This work highlights that chitosan can be applied as an effective adjuvant to promote the efficacy of low-dosage pyraclostrobin against powdery mildew in R. roxburghii and improve its resistance, photosynthesis, yield, quality, and amino acids.

Metabolomics Combined with Transcriptomics Analysis Revealed the Amino Acids, Phenolic Acids, and Flavonol Derivatives Biosynthesis Network in Developing Rosa roxburghii Fruit

Rosa roxburghii Tratt. is a specific fruit with high nutritional value and antioxidative activities. However, the key metabolites and their biosynthesis are still unknown. Herein, a main cultivated variety, ‘Guinong 5’ (Rr5), was chosen to analyze the metabolomics of the three developmental stages of R. roxburghii fruit by liquid chromatography–tandem mass spectrometry (LC-MS/MS). A total of 533 metabolites were identified, of which 339 were significantly altered. Total phenols, flavonoids, and amino acids were significantly correlated to at least one in vitro antioxidant activity. The conjoint Kyoto Encyclopedia of Genes and Genomes (KEGG) co-enrichment analysis of metabolome and transcriptome was focused on amino acid, phenylpropanoid, and flavonoid biosynthesis pathways. The amino acid, phenolic acid, and flavonol biosynthesis networks were constructed with 32 structural genes, 48 RrMYBs, and 23 metabolites. Of these, six RrMYBs correlated to 9–15 metabolites in the network were selected to detect the gene expression in six different R. roxburghii genotypes fruits. Subsequently, 21 key metabolites were identified in the in vitro antioxidant activities in the fruits at various developmental stages or in fruits of different R. roxburghii genotypes. We found that four key RrMYBs were related to the significantly varied amino acids, phenolic acids, and flavonol derivatives in the network during fruit development and the key metabolites in the in vitro antioxidative activities in the fruits of six R. roxburghii genotypes. This finding provided novel insights into the flavonoid, polyphenol, and amino acid synthesis in R. roxburghii.

Cotton genes GhMML1 and GhMML2 control trichome branching when ectopically expressed in tobacco

Trichomes exhibit extraordinary diversity in shape, ultrastructure, distribution, secretion capability, biological functions, and morphological differences, which are strongly associated with their multifunction. Previous researches showed MIXTA-like transcription factors involved in regulating trichome initiation and patterning via forming MYB-bHLH-WD40 transcriptional activator complex to induce the expression of downstream genes. Here, we report the characteristics and role of GhMML1 and GhMML2, members of subgroup 9 of the R2R3-type MYB TFs. GhMML1 and GhMML2 were preferentially targeted to the nucleus and prominently expressed in the early stage during fiber development. Ectopic expression of GhMML1 and GhMML2 respectively in the transgenic tobacco plants changed the morphological characteristics of leaf trichomes; that is, the unbranched trichomes turned into multiple branched, and in the meantime, the density of trichomes was reduced on the surface of the leaf. Y2H and LCI assay revealed that both GhMML1 and GhMML2 could physically interact with a bZIP transcription factor family protein (GhbZIP) in vivo and in vitro. It has been reported that GhbZIP's homolog TAG3 in Arabidopsis is involved in the asymmetric growth of leaves and flowers via direct interaction with BOP1. Taken together, our results demonstrated that two MYB MIXTA-like proteins, GhMML1 and GhMML2, together with GhbZIP might form a multimeric complex to involve in trichome development. This study highlights the importance of MIXTA-like genes from TF subgroup 9 and will help to uncover the molecular mechanism underlying differential trichomes and their development.

Co-Application of Allicin and Chitosan Increases Resistance of Rosa roxburghii against Powdery Mildew and Enhances Its Yield and Quality

Powdery mildew, caused by Sphaerotheca sp., annually causes severe losses in yield and quality in Rosa roxburghii production areas of southwest China. In this study, the role of the co-application of allicin and chitosan in the resistance of R. roxburghii against powdery mildew and its effects on growth, yield and quality of R. roxburghii were investigated. The laboratory toxicity test results show that allicin exhibited a superior antifungal activity against Sphaerotheca sp. with EC₅₀ value of 148.65 mg kg⁻¹. In the field, the foliar application of allicin could effectively enhance chitosan against powdery mildew with control efficacy of 85.97% by spraying 5% allicin microemulsion (ME) 100–time liquid + chitosan 100–time liquid, which was significantly (p < 0.01) higher than 76.70% of allicin, 70.93% of chitosan and 60.23% of polyoxin. The co-application of allicin and chitosan effectively enhanced the photosynthetic rate and chlorophyll of R. roxburghii compared with allicin, chitosan or polyoxin alone. Moreover, allicin used together with chitosan was more effective than allicin or chitosan alone in enhancing R. roxburghii plant growth and fruit yield as well as improving R. roxburghii fruit quality. This work highlights that the co-application of allicin and chitosan can be used as a green, cost-effective and environmentally friendly alternative strategy to conventional antibiotics for controlling powdery mildew of R. roxburghii.

Transcriptome and de novo analysis of Rosa xanthina f. spontanea in response to cold stress

BACKGROUND

Rose is one of most popular ornamental plants worldwide and is of high economic value and great cultural importance. However, cold damage restricts its planting application in cold areas. To elucidate the metabolic response of rose under low temperature stress, we conducted transcriptome and de novo analysis of Rosa xanthina f. spontanea.

RESULTS

A total of 124,106 unigenes from 9 libraries were generated by de novo assembly, with N50 length was 1470 bp, under 4 °C and - 20 °C stress (23 °C was used as a control). Functional annotation and prediction analyses identified 55,084 unigenes, and 67.72% of these unigenes had significant similarity (BLAST, E ≤ 10^- 5) to those in the public databases. A total of 3031 genes were upregulated and 3891 were downregulated at 4 °C compared with 23 °C, and 867 genes were upregulated and 1763 were downregulated at - 20 °C compared with 23 °C. A total of 468 common DEGs were detected under cold stress, and the matched DEGs were involved in three functional categories: biological process (58.45%), cellular component (11.27%) and molecular function (30.28%). Based on KEGG functional annotations, four pathways were significantly enriched: metabolic pathway, response to plant pathogen interaction (32 genes); starch and sucrose metabolism (21 genes); circadian rhythm plant (8 genes); and photosynthesis antenna proteins (7 genes).

CONCLUSIONS

Our study is the first to report the response to cold stress at the transcriptome level in R. xanthina f. spontanea. The results can help to elucidate the molecular mechanism of cold resistance in rose and provide new insights and candidate genes for genetically enhancing cold stress tolerance.

Ultra-high Pressure Treatment Controls In Vitro Fecal Fermentation Rate of Insoluble Dietary Fiber from Rosa Roxburghii Tratt Pomace and Induces Butyrogenic Shifts in Microbiota Composition

Dietary fiber has been considered a key element in shaping the beneficial host-microbe symbiosis. In the present study, we identified Rosa roxburghii Tratt fruits as a promising dietary fiber source. The physicochemical properties and in vitro fermentability by human fecal microbes of R. roxburghii pomace water insoluble dietary fiber (RIDF) obtained from ultrasonic extraction and ultrahigh pressure (90 MPa)-treated RIDF (RIDF-90) were compared to those of R. roxburghii Tratt pomace (R). Ultrahigh pressure modification significantly increased the water holding, oil holding, and swelling capacity of RIDF-90 in comparison to R and RIDF. RIDF-90 displayed the slowest fermentation rate yet yielded the highest butyrate production. The superior butyrogenic properties of both RIDF-90 and, in part, RIDF were reflected by increased Coprococcus and Ruminococcus levels, demonstrating that ultrasonic extraction and/or further ultrahigh pressure treatment of insoluble fibers promotes the prebiotic value of R. roxburghii Tratt.

Chitosan Can Induce Rosa roxburghii Tratt. against Sphaerotheca sp. and Enhance Its Resistance, Photosynthesis, Yield, and Quality

Powdery mildew caused by Sphaerotheca sp. is the most serious disease of Rosa roxburghii cultivation. In this study, the foliar application of chitosan induced Rosa roxburghii Tratt. against Sphaerotheca sp. and its effects on the disease resistance, growth, yield, and quality of R. roxburghii were investigated. The results show that the foliar application of 1.0%~1.5% chitosan could effectively control Sphaerotheca sp. of R. roxburghii with the inducing control efficacy of 69.30%~72.87%. The foliar application of 1.0%~1.5% chitosan significantly (p < 0.01) increased proline, soluble sugar, flavonoids, superoxide dismutase (SOD), and polyphenoloxidase (POD) activities of the R. roxburghii leaf and decreased its malonaldehyde (MDA), as well as reliably enhanced its photosynthetic rate and chlorophyll. Moreover, the foliar application of 1.0%~1.5% chitosan notably improved single fruit weight, yield, vitamin C, soluble solid, soluble sugar, total acidity, soluble protein, flavonoids, and SOD activity of R. roxburghii fruits. This study highlights that chitosan can be used as an ideal, efficient, safe, and economical inductor for controlling powdery mildew of R. Roxburgh and enhancing its resistance, growth, yield, and quality.

Assessing the potential value of Rosa Roxburghii Tratt in arsenic-induced liver damage based on elemental imbalance and oxidative damage

Environmental exposure to arsenic is a major public health challenge worldwide. Growing evidence indicates that coal-burning arsenic can cause hepatic oxidative damage. However, the value of Rosa roxburghii Tratt (RRT) with antioxidant properties on arsenic-caused hepatic oxidative damage has never been elucidated yet. In this study, the animals were exposed to coal-burning arsenic (10 mg/kg bw) for 90 days and the result showed a loss of body weight, impaired liver function and liver diseases, increased hepatic oxidative damage and metabolic disorder of multiple elements including selenium, copper, zinc which were related to synthesis of antioxidant enzymes. Another finding is that RRT restored the abnormal liver function and alleviated the procedures of liver diseases of arsenic poisoning rats. In addition, it could also effectively reduce the degree of oxidative damage in serum and liver, and restore the activity of some antioxidant enzymes. Importantly, RRT reversed the content of most disordered elements caused by arsenic in liver and reduced the excretion of several essential elements in urine, including selenium, copper and zinc. Our study provides some limited evidence that RRT can alleviate coal-burning arsenic-induced liver damage induced by regulating elemental metabolic disorders and liver oxidation and antioxidant balance. The study provides a scientific basis for further studies of the causes of the arsenic-induced liver damage, and effective intervention strategies.

Polysaccharide from Rosa roxburghii Tratt Fruit Attenuates Hyperglycemia and Hyperlipidemia and Regulates Colon Microbiota in Diabetic db/db Mice

This study was aimed at investigating the hypoglycemic and hypolipidemic effects of a polysaccharide (RTFP) isolated from Rosa roxburghii Tratt fruit on type-2 diabetic db/db mice. The results indicated that the oral administration of RTFP could significantly decrease the body weight, fat, and liver hypertrophy and the levels of fasting blood glucose, serum insulin, and serum lipids of the db/db mice. Histopathological observation showed that RTFP could effectively protect the pancreas, liver, and epididymal fat against damage and dysfunction. Real-time quantitative polymerase chain reaction analysis confirmed that the gene expression levels of peroxisome proliferator-activated receptors-γ (PPAR-γ), sterol regulatory element-binding protein-1 (SREBP-1c), acetyl-CoA carboxylase-1 (ACC-1), fatty acid synthase (FAS), and glucose-6-phosphatase (G6 Pase) were significantly down-regulated in the liver of db/db mice after treatment with RTFP. Moreover, RTFP treatment reversed gut dysbiosis by lowering the Firmicutes-to-Bacteroidetes ratio and enhancing the relative abundances of beneficial bacteria including Bacteroidaceae, Bacteroidaceae S24-7 group, and Lactobacillaceae. These findings suggest that RTFP can be used as a promising functional supplement for the prevention and treatment of type-2 diabetes mellitus.