Genome sequencing provides insights into the evolution and antioxidant activity of Chinese bayberry

Effects of Low-Allergen Wheat and Bayberry Leaf on Wheat Bread: A Comparison with Commercial Wheat

Gliadin and glutenin wheat proteins are major food allergens. The allergenicity of various wheat products, such as bread, can be reduced by substituting flour with plant-derived tannins. Here, we investigated a technique for reducing the allergenicity of wheat by utilizing the properties of proanthocyanidins (PAs), which strongly bind to proteins. We compared commercial bread wheat (BW), low-allergen wheat (1BS-18 "Minamino Kaori"; 1BS-18M), and bayberry leaves (BBLs). Allergenicity was investigated through enzyme-linked immunosorbent assays (ELISAs) and Western blotting (WB). The immunoreactivity of wheat allergens in both BW and 1BS-18M decreased in a concentration-dependent manner with BBL substitution, and the effect was greatest at 10%. The antioxidative properties also increased with BBL substitution, and the highest antioxidative property was observed at 10%. The specific volumes of both BW and 1BS-18M decreased while the a* value (green to red) increased with increasing BBL substitution. In contrast, no significant differences were observed in the texture of breads with 0% (control), 3%, or 5% BBL substitution. However, 10% BBL substitution led to a significant (p < 0.05) reduction in the texture of the bread. Therefore, 5% BBL substitution is optimal for achieving low allergenicity and improved antioxidative properties while maintaining quality.

Therapeutic effect of targeted antioxidant natural products

The exploration of targeted therapy has proven to be a highly promising avenue in the realm of drug development research. The human body generates a substantial amount of free radicals during metabolic processes, and if not promptly eliminated, these free radicals can lead to oxidative stress, disrupting homeostasis and potentially contributing to chronic diseases and cancers. Before the development of contemporary medicine with synthetic pharmaceuticals and antioxidants, there was a long-standing practice of employing raw, natural ingredients to cure a variety of illnesses. This practice persisted even after the active antioxidant molecules were known. The ability of natural antioxidants to neutralise excess free radicals in the human body and so prevent and cure a wide range of illnesses. The term "natural antioxidant" refers to compounds derived from plants or other living organisms that have the ability to control the production of free radicals, scavenge them, stop free radical-mediated chain reactions, and prevent lipid peroxidation. These compounds have a strong potential to inhibit oxidative stress. Phytochemicals (antioxidants) derived from plants, such as polyphenols, carotenoids, vitamins, and others, are central to the discussion of natural antioxidants. Not only may these chemicals increase endogenous antioxidant defenses, affect communication cascades, and control gene expression, but they have also shown strong free radical scavenging properties. This study comprehensively summarizes the primary classes of natural antioxidants found in different plant and animal source that contribute to the prevention and treatment of diseases. Additionally, it outlines the research progress and outlines future development prospects. These discoveries not only establish a theoretical groundwork for pharmacological development but also present inventive ideas for addressing challenges in medical treatment.

T2T reference genome assembly and genome-wide association study reveal the genetic basis of Chinese bayberry fruit quality

Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar 'Zaojia' using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.

Ancient bayberry increased stress resistance by enriching tissue-specific microbiome and metabolites

The ancient bayberry demonstrates superior resistance to both biotic and abiotic stresses compared to cultivated bayberry, yet the underlying mechanisms remain largely unexplored. This study investigates whether long-term bayberry cultivation enhances stress resistance through modulation of tissue-specific microbes and metabolites. Employing microbiome amplicon sequencing alongside untargeted mass spectrometry analysis, we scrutinize the role of endosphere and rhizosphere microbial communities and metabolites in shaping the differential resistance observed between ancient and cultivated bayberry trees. Our findings highlight the presence of core microbiome and metabolites across various bayberry tissues, suggesting that the heightened resistance of ancient bayberry may stem from alterations in rhizosphere and endosphere microbial communities and secondary metabolites. Specifically, enrichment of Bacillus in roots and stems, Pseudomonas in leaves, and Mortierella in rhizosphere soil of ancient bayberry was noted. Furthermore, correlation analysis underscores the significance of enriched microbial species in enhancing ancient bayberry's resistance to stresses, with elevated levels of resistance-associated metabolites such as beta-myrcene, benzothiazole, L-glutamic acid, and gamma-aminobutyric acid identified through GC-MS metabolomics analysis. The beneficial role of these resistance-associated metabolites was further elucidated through assessment of their promotive and allelopathic effects, as well as their phytostatic and antioxidant functions in lettuce plants. Ultimately, our study delves into the intrinsic reasons behind the greater resistance of ancient bayberry to biotic and abiotic stresses by evaluating the impact of long-term planting on the microbial community and metabolites in the bayberry endosphere and rhizosphere, shedding light on the complex dynamics of host-microbial interactions.

Identification and Genome Characterization of a Novel Virus within the Genus Totivirus from Chinese Bayberry (Myrica rubra)

Chinese bayberry (Myrica rubra) is an economically significant fruit tree native to eastern Asia and widely planted in south-central China. However, studies about the viruses infecting M. rubra remain largely lacking. In the present study, we employed the metatranscriptomic method to identify viruses in M. rubra leaves exhibiting yellowing and irregular margin symptoms collected in Fuzhou, a city located in China's Fujian province in the year 2022. As a consequence, a novel member of the genus Totivirus was identified and tentatively named "Myrica rubra associated totivirus 1" (MRaTV1). The genome sequencing of MRaTV1 was determined by overlapping reverse transcription polymerase chain reaction (RT-PCR) and rapid amplification of cDNA ends (RACE). The two deduced proteins encoded by MRaTV1 have the highest amino acid (aa) sequence identity to the coat protein (CP) and RNA-dependent RNA polymerase (RdRP) of Panax notoginseng virus A (PNVA), a member of the genus Totivirus within the family Totiviridae, at 49.7% and 61.7%, respectively. According to the results of the phylogenetic tree and the species demarcation criteria of the International Committee on Taxonomy of Viruses (ICTV) for the genus Totivirus, MRaTV1 is considered a new member of the genus Totivirus.

Al-Rejaie S, Li B, Liu E. The Effects of Accompanying Ryegrass on Bayberry Trees by Change of Soil Property, Rhizosphere Microbial Community Structure, and Metabolites

As a subtropical and tropical tree, bayberry (Myrica rubra) is an important fruit tree grown commercially in southern China. Interestingly, our studies found that the fruit quality of bayberry with accompanying ryegrass was significantly improved, but its mechanism remains unclear. The aim of this study was to explore the mechanism of accompanying ryegrass on the beneficial effect of the fruit quality of bayberry by measuring the vegetative growth parameters, fruit parameters with economic impact, physical and chemical properties of rhizosphere soil, microbial community structure, and metabolites of the bayberry with/without ryegrass. Notably, the results revealed a significant difference between bayberry trees with and without accompanying ryegrass in fruit quality parameters, soil physical and chemical properties, microbial community structure, and metabolites. Compared with the control without accompanying ryegrass, the planting of ryegrass increased the titratable sugar, vitamin C, and titratable flavonoid contents of bayberry fruits by 2.26%, 28.45%, and 25.00%, respectively, and decreased the titratable acid contents by 9.04%. Furthermore, based on 16S and ITS amplicon sequencing of soil microflora, the accompanying ryegrass caused a 12.47% increment in Acidobacteriota while a 30.04% reduction in Actinobacteria was recorded, respectively, when compared with the bayberry trees without ryegrass. Redundancy discriminant analysis of microbial communities and soil properties indicated that the main variables of the bacterial community included available nitrogen, available phosphorus, exchangeable aluminum, and available kalium, while the main variables of the fungal community included exchangeable aluminum, available phosphorus, available kalium, and pH. In addition, the change in microbial community structure was justified by the high correlation analysis between microorganisms and secondary metabolites. Indeed, GC-MS metabolomics analysis showed that planting ryegrass caused a 3.83%-144.36% increase in 19 metabolites such as 1,3-Dipentyl-heptabarbital and carbonic acid 1, respectively, and a 23.78%-51.79% reduction of 5 metabolites compared to the bayberry trees without the accompanying ryegrass. Overall, the results revealed the significant change caused by the planting of ryegrass in the physical and chemical properties, microbiota, and secondary metabolites of the bayberry rhizosphere soils, which provides a new insight for the ecological improvement of bayberry.

The MAP Kinase PvMK1 Regulates Hyphal Development, Autophagy, and Pathogenesis in the Bayberry Twig Blight Fungus Pestalotiopsis versicolor

Bayberry twig blight caused by the ascomycete fungus Pestalotiopsis versicolor is a devastating disease threatening worldwide bayberry production. However, the molecular basis underlying the pathogenesis of P. versicolor is largely unknown. Here, we identified and functionally characterized the MAP kinase PvMk1 in P. versicolor through genetic and cellular biochemical approaches. Our analysis reveals a central role of PvMk1 in regulating P. versicolor virulence on bayberry. We demonstrate that PvMk1 is involved in hyphal development, conidiation, melanin biosynthesis, and cell wall stress responses. Notably, PvMk1 regulates P. versicolor autophagy and is essential for hyphal growth under nitrogen-depleting conditions. These findings suggest the multifaceted role of PvMk1 in regulating P. versicolor development and virulence. More remarkably, this evidence of virulence-involved cellular processes regulated by PvMk1 has paved a fundamental way for further understanding the impact of P. versicolor pathogenesis on bayberry.

Improvement effect of biochar on soil microbial community structure and metabolites of decline disease bayberry

Decline disease is a new disease that has recently caused severe damage in bayberry industry. The effect of biochar on decline disease was determined by investigating the changes in the vegetative growth and fruit quality of bayberry trees as well as soil physical and chemical properties, microbial community structure, and metabolites. Results indicated that the application of biochar could improve the vigor and fruit quality of diseased trees, and rhizosphere soil microbial diversity at the levels of phyla, orders, and genera. The relative abundance of Mycobacterium, Crossiella, Geminibasidium, and Fusarium were significantly increased, while Acidothermus, Bryobacter, Acidibacter, Cladophialophora, Mycena, and Rickenella were significantly decreased by biochar in rhizosphere soil of decline diseased bayberry. Analysis of redundancies (RDA) of microbial communities and soil characteristics revealed that the composition of bacterial and fungal communities was significantly affected by the pH, organic matter, alkali hydrolyzable nitrogen, available phosphorus, available potassium, exchangeable calcium and exchangeable magnesium in bayberry rhizosphere soil, and the contribution rates to fungi were larger than those to bacteria at the genus level. Biochar greatly influenced the metabolomics distribution of rhizosphere soils of decline disease bayberry. One hundred and nine different metabolites from both the presence and absence of biochar, mainly include acid, alcohol, ester, amine, amino acid, sterol, sugar, and other secondary metabolites, of which the contents of 52 metabolites were increased significantly such as aconitic acid, threonic acid, pimelic acid, epicatechin, and lyxose. The contents of 57 metabolites decreased significantly, such as conduritol β-expoxide, zymosterol, palatinitol, quinic acid, and isohexoic acid. There was a great difference between the absence and presence of biochar in 10 metabolic pathways, including thiamine metabolism, arginine and proline metabolism, glutathione metabolism, ATP-binding cassette (ABC) transporters, butanoate metabolism, cyanoamino acid metabolism, tyrosine metabolism, phenylalanine metabolism, phosphotransferase system (pts), and lysine degradation. There was a significant correlation between the relative content of microbial species and the content of secondary metabolites in rhizosphere soil at the levels of bacterial and fungal phyla, order, and genus. Overall, this study highlighted the significant influence of biochar in decline disease by regulating soil microbial community, physical and chemical properties, and secondary metabolites in rhizosphere soil, which provided a novel strategy for managing bayberry decline disease.

Comparing the Volatile and Soluble Profiles of Fermented and Integrated Chinese Bayberry Wine with HS-SPME GC-MS and UHPLC Q-TOF

To evaluate the flavor characteristics of Chinese bayberry alcoholic beverages, fermented bayberry wine (FBW) and integrated bayberry wine (IBW) were investigated for their volatile and soluble profiles using HS-SPME GC-MS and UHPLC Q-TOF and were analyzed with multidimensional statistical analysis, including PCA and OPLS-DA. The volatile compounds 1-pentanol, β-caryophyllene and isopentanol were only detected in IBW. β-caryophyllene, the key flavor component of bayberry, was found to be the most abundant volatile compound in IBW (25.89%) and was 3.73 times more abundant in IBW than in FBW. The levels of ethyl octanoate, ethyl nonanoate, and ethyl decanoate were also several times higher in IBW than in FBW. These compounds contributed to the strong bayberry aroma and better fruity flavor of IBW. On the other hand, high levels of ethyl acetate and octanoic acid in FBW, representing pineapple/overripe or sweat odor, were key contributors to the fermented flavor of FBW. Soluble sugars, such as sucrose, D-glucose, and D-tagatose, as well as amino acids, such as L-glutamate and L-aspartate, had much higher levels in IBW. The anthocyanin pigment cyanidin 3-glucoside, which generates red color, was also higher in IBW. On the other hand, most of the differentially expressed alcohols, acids, amino acids, purines/pyrimidines and esters were present in higher concentrations in FBW compared to IBW. This demonstrated that IBW has a much sweeter and more savory taste as well as a better color generated by more anthocyanins, while FBW presents a more acidic and drier taste as well as a complex formation of alcohols and esters. The study also prompts the need for further research on the flavor profiles of IBW and its potential application and market value.

Molecular cloning and functional analysis of Chinese bayberry MrSPL4 that enhances growth and flowering in transgenic tobacco

Chinese bayberry (Myrica rubra) is an important tree in South China, with its fruit being of nutritional and high economic value. In this study, early ripening (ZJ), medium ripening (BQ) and late ripening (DK) varieties were used as test materials. Young leaves of ZJ, BQ and DK in the floral bud morphological differentiation periods were selected for transcriptome sequencing to excavate earliness related genes. A total of 4,538 differentially expressed genes were detected. Based on clustering analysis and comparisons with genes reportedly related to flowering in Arabidopsis thaliana, 25 homologous genes were identified. Of these, one gene named MrSPL4 was determined, with its expression down-regulated in DK but up-regulated in ZJ and BQ. MrSPL4 contained SBP domain and the target site of miR156, and its total and CDS length were 1,664 bp and 555 bp respectively. The overexpression vector of MrSPL4 (35S::35S::MrSPL4-pCambia2301-KY) was further constructed and successfully transfected into tobacco to obtain MrSPL4-positive plants. Based on the results of qRT-PCR, the relative expression of MrSPL4 was up regulated by 3,862.0-5,938.4 times. Additionally, the height of MrSPL4-positive plants was also significantly higher than that of wild-type (WT), with the bud stage occurring 12 days earlier. Altogether, this study identified an important gene -MrSPL4 in Chinese bayberry, which enhanced growth and flowering, which provided important theoretical basis for early-mature breeding of Chinese bayberry.

Mechanism of Tao Hong Decoction in the treatment of atherosclerosis based on network pharmacology and experimental validation

Background

Atherosclerosis (AS) has long been recognized as a cardiovascular disease and stroke risk factor. A well-known traditional Chinese medicine prescription, Tao Hong decoction (THD), has been proven effective in treating AS, but its mechanism of action is still unclear.

Objective

To assess the effects, explore THD's primary mechanism for treating AS, and provide a basis for rational interpretation of its prescription compatibility.

Methods

Based on network pharmacology, we evaluated the mechanism of THD on AS by data analysis, target prediction, the construction of PPI networks, and GO and KEGG analysis. AutoDockTools software to conduct Molecular docking. Then UPLC-Q-TOF-MS was used to identify significant constituents of THD. Furthermore, an AS mice model was constructed and intervened with THD. Immunofluorescence, RT-qPCR, and Western blot were used to verify the critical targets in animal experiments.

Results

The network pharmacology results indicate that eight core targets and seven core active ingredients play an essential role in this process. The GO and KEGG analysis results suggested that the mechanism is mainly involved in Fluid shear stress and atherosclerosis and Lipid and atherosclerosis. The molecular docking results indicate a generally strong affinity. The animal experiment showed that THD reduced plaque area, increased plaque stability, and decreased the levels of inflammatory cytokines (NF-κB, IL-1α, TNF-α, IL-6, IL-18, IL-1β) in high-fat diet -induced ApoE-/-mice. Decreased levels of PTGS2, HIF-1α, VEGFA, VEGFC, FLT-4, and the phosphorylation of PI3K, AKT, and p38 were detected in the THD-treated group.

Conclusion

THD plays a vital role in treating AS with multiple targets and pathways. Angiogenesis regulation, oxidative stress regulation, and immunity regulation consist of the crucial regulation cores in the mechanism. This study identified essential genes and pathways associated with the prognosis and pathogenesis of AS from new insights, demonstrating a feasible method for researching THD's chemical basis and pharmacology.

Flavan-3-ol Galloylation-Related Functional Gene Cluster and the Functional Diversification of SCPL Paralogs in Camellia sp

The high accumulation of galloylated flavan-3-ols in Camellia sp. is a noteworthy phenomenon. We identified a flavan-3-ol galloylation-related functional gene cluster in tannin-rich plant Camellia sp., which included UGT84A22 and SCPL-AT gene clusters. We investigated the possible correlation between the accumulation of metabolites and the expression of SCPL-ATs and UGT84A22. The results revealed that C. sinensis, C. ptilophylla, and C. oleifera accumulated galloylated cis-flavan-3-ols (EGCG), galloylated trans-flavan-3-ols (GCG), and hydrolyzed tannins, respectively; however, C. nitidissima did not accumulate any galloylated compounds. C. nitidissima exhibited no expression of SCPL-AT or UGT84A22, whereas the other three species of Camellia exhibited various expression patterns. This indicated that the functions of the paralogs of SCPL-AT vary. Enzymatic analysis revealed that SCPL5 was neofunctionalized as a noncatalytic chaperone paralog, a type of chaerone-like protein, associating with flavan-3-ol galloylation; moreover, CsSCPL4 was subfunctionalized in association with the galloylation of cis- and trans-flavan-3-ols. In C. nitidissima, an SCPL4 homolog was noted with mutations in two cysteine residues forming a disulfide bond, which suggested that this homolog was defunctionalized. The findings of this study improve our understanding of the functional diversification of SCPL paralogs in Camellia sp.

Conserved hierarchical gene regulatory networks for drought and cold stress response in Myrica rubra

Stress response in plant is regulated by a large number of genes co-operating in diverse networks that serve multiple adaptive process. To understand how gene regulatory networks (GRNs) modulating abiotic stress responses, we compare the GRNs underlying drought and cold stresses using samples collected at 4 or 6 h intervals within 48 h in Chinese bayberry (Myrica rubra). We detected 7,583 and 8,840 differentially expressed genes (DEGs) under drought and cold stress respectively, which might be responsive to environmental stresses. Drought- and cold-responsive GRNs, which have been built according to the timing of transcription under both abiotic stresses, have a conserved trans-regulator and a common regulatory network. In both GRNs, basic helix-loop-helix family transcription factor (bHLH) serve as central nodes. MrbHLHp10 transcripts exhibited continuous increase in the two abiotic stresses and acts upstream regulator of ASCORBATE PEROXIDASE (APX) gene. To examine the potential biological functions of MrbHLH10, we generated a transgenic Arabidopsis plant that constitutively overexpresses the MrbHLH10 gene. Compared to wild-type (WT) plants, overexpressing transgenic Arabidopsis plants maintained higher APX activity and biomass accumulation under drought and cold stress. Consistently, RNAi plants had elevated susceptibility to both stresses. Taken together, these results suggested that MrbHLH10 mitigates abiotic stresses through the modulation of ROS scavenging.

Effect of Humic Acid on Soil Physical and Chemical Properties, Microbial Community Structure, and Metabolites of Decline Diseased Bayberry

In recent years, bayberry decline disease has caused significant damage to the bayberry industry. In order to evaluate whether humic acid can be used to effectively control the disease, this research examined the nutritional growth and fruit quality of bayberry, soil physical and chemical properties, soil microbial community structure, and metabolites. Results indicated that the application of humic acid not only improved the vigor and fruit quality of diseased trees, but also increased the diversity of microbial communities in the rhizosphere soil. A great increase was observed in the relative abundance of bacterial genus Mycobacterium and Crossiella; fungal genus Fusarium and Coniosporium. In contrast, a significant decrease was observed in the relative abundance of bacterial genus Acidothermus, Bryobacter, Acidibacter, fungal genus of Geminibasidium and Mycena. Analysis of redundancies (RDA) for microbial communities and soil characteristics showed that the main four variables, including available nitrogen, phosphorus, potassium, and calcium, had a great effect on the composition of bacterial and fungal communities in bayberry rhizosphere soil at the genus level. The main four variables had a greater effect on bacterial communities than on fungal communities. In addition, ABC transporter, arginine and proline metabolism, galactose metabolism, and glutathione metabolism were significantly affected by humic acid, which changed the content of 81 metabolites including 58 significantly down-regulated metabolites such as isohexonic acid and carinitine, and 23 significantly up-regulated metabolites such as acidic acid, guaninosuccinate, lyxose, 2-monoolein, epicatechin, and pentonolactone. These metabolites also significantly correlated with rhizosphere soil microbiota at the phylum, order, and genus levels. In conclusion, the results demonstrated the role of humic acid on plant growth and fruit quality, as well as rhizosphere soil characteristics, microbiota, and secondary metabolites, which provides novel insights into the control of bayberry decline disease.

An overview of the nutritional value, health properties, and future challenges of Chinese bayberry

Chinese bayberry (CB) is among the most popular and valuable fruits in China owing to its attractive color and unique sweet/sour taste. Recent studies have highlighted the nutritional value and health-related benefits of CB. CB has special biological characteristics of evergreen, special aroma, dioecious, nodulation, nitrogen fixation. Moreover, the fruits, leaves, and bark of CB plants harbor a number of bioactive compounds including proanthocyanidins, flavonoids, vitamin C, phenolic acids, and anthocyanins that have been linked to the anti-cancer, anti-oxidant, anti-inflammatory, anti-obesity, anti-diabetic, and neuroprotective properties and to the treatment of cardiovascular and cerebrovascular diseases. The CB fruits have been used to produce a range of products: beverages, foods, and washing supplies. Future CB-related product development is thus expected to further leverage the health-promoting potential of this valuable ecological resource. The present review provides an overview of the botanical characteristics, processing, nutritional value, health-related properties, and applications of CB in order to provide a foundation for further research and development.

Minor tropical fruits as a potential source of bioactive and functional foods

Tropical fruits are defined as fruits that are grown in hot and humid regions within the Tropic of Cancer and Tropic of Capricorn, covering most of the tropical and subtropical areas of Asia, Africa, Central America, South America, the Caribbean and Oceania. Depending on the cultivation area covered, economic value and popularity these tropical fruits are divided into major and minor tropical fruits. There is an annual increment of 3.8% in terms of commercialization of the tropical fruits. In total 26 minor tropical fruits (Kiwifruit, Lutqua, Carambola, Tree Tomato, Elephant apple, Rambutan, Bay berry, Mangosteen, Bhawa, Loquat, Silver berry, Durian, Persimon, Longan, Passion fruit, Water apple, Pulasan, Indian gooseberry, Guava, Lychee, Annona, Pitaya, Sapodilla, Pepino, Jaboticaba, Jackfruit) have been covered in this work. The nutritional composition, phytochemical composition, health benefits, traditional use of these minor tropical fruits and their role in food fortification have been portrayed.

Effect of Two Kinds of Fertilizers on Growth and Rhizosphere Soil Properties of Bayberry with Decline Disease

Decline disease causes severe damage to bayberry. However, the cause of this disease remains unclear. Interestingly, our previous studies found that the disease severity is related with the level of soil fertilizer. This study aims to explore the effect and mechanism of compound fertilizer (CF) and bio-organic fertilizer (OF) in this disease by investigating the vegetative growth, fruit characters, soil property, rhizosphere microflora and metabolites. Results indicated that compared with the disease control, CF and OF exhibited differential effect in plant healthy and soil quality, together with the increase in relative abundance of Burkholderia and Mortierella, and the reduction in that of Rhizomicrobium and Acidibacter, Trichoderma, and Cladophialophora reduced. The relative abundance of Geminibasidium were increased by CF (251.79%) but reduced by OF (13.99%). In general, the composition of bacterial and fungal communities in rhizosphere soil was affected significantly at genus level by exchangeable calcium, available phosphorus, and exchangeable magnesium, while the former two variables had a greater influence in bacterial communities than fungal communities. Analysis of GC-MS metabonomics indicated that compared to the disease control, CF and OF significantly changed the contents of 31 and 45 metabolites, respectively, while both fertilizers changed C5-branched dibasic acid, galactose, and pyrimidine metabolic pathway. Furthermore, a significant correlation was observed at the phylum, order and genus levels between microbial groups and secondary metabolites of bayberry rhizosphere soil. In summary, the results provide a new way for rejuvenation of this diseased bayberry trees.

The bayberry database: a multiomic database for Myrica rubra, an important fruit tree with medicinal value

BACKGROUND

Chinese bayberry (Myrica rubra Sieb. & Zucc.) is an important fruit tree in China, and has high medicinal value. At present, the genome, transcriptome and germplasm resources of bayberry have been reported. In order to make more convenient use of these data, the Bayberry Database was established.

RESULTS

The Bayberry Database is a comprehensive and intuitive data platform for examining the diverse annotated genome and germplasm resources of this species. This database contains nine central functional domains to interact with multiomic data: home, genome, germplasm, markers, tools, map, expression, reference, and contact. All domains provide pathways to a variety of data types composed of a reference genome sequence, transcriptomic data, gene patterns, phenotypic data, fruit images of Myrica rubra varieties, gSSR data, gene maps with annotation and evolutionary analyses. The tools module includes BLAST search, keyword search, sequence fetch and enrichment analysis functions.

CONCLUSIONS

The web address of the database is as follows http://www.bayberrybase.cn/ . The Myrica rubra database is an intelligent, interactive, and user-friendly system that enables researchers, breeders and horticultural personnel to browse, search and retrieve relevant and useful information and thus facilitate genomic research and breeding efforts concerning Myrica rubra. This database will be of great help to bayberry research and breeding in the future.

The Damage Caused by Decline Disease in Bayberry Plants through Changes in Soil Properties, Rhizosphere Microbial Community Structure and Metabolites

Decline disease causes serious damage and rapid death in bayberry, an important fruit tree in south China, but the cause of this disease remains unclear. The aim of this study was to investigate soil quality, microbial community structure and metabolites of rhizosphere soil samples from healthy and diseased trees. The results revealed a significant difference between healthy and diseased bayberry in soil properties, microbial community structure and metabolites. Indeed, the decline disease caused a 78.24% and 78.98% increase in Rhizomicrobium and Cladophialophora, but a 28.60%, 57.18%, 38.84% and 68.25% reduction in Acidothermus, Mortierella, Trichoderma and Geminibasidium, respectively, compared with healthy trees, based on 16S and ITS amplicon sequencing of soil microflora. Furthermore, redundancy discriminant analysis of microbial communities and soil properties indicated that the main variables of bacterial and fungal communities included pH, organic matter, magnesium, available phosphorus, nitrogen and calcium, which exhibited a greater influence in bacterial communities than in fungal communities. In addition, there was a high correlation between the changes in microbial community structure and secondary metabolites. Indeed, GC-MS metabolomics analysis showed that the healthy and diseased samples differed over six metabolic pathways, including thiamine metabolism, phenylalanine-tyrosine-tryptophan biosynthesis, valine-leucine-isoleucine biosynthesis, phenylalanine metabolism, fatty acid biosynthesis and fatty acid metabolism, where the diseased samples showed a 234.67% and 1007.80% increase in palatinitol and cytidine, respectively, and a 17.37-8.74% reduction in the other 40 metabolites compared to the healthy samples. Overall, these results revealed significant changes caused by decline disease in the chemical properties, microbiota and secondary metabolites of the rhizosphere soils, which provide new insights for understanding the cause of this bayberry disease.

Chinese bayberry Jiaosu fermentation – changes of mycobiota composition and antioxidant properties

The aim of the study was to investigate the dynamic changes of mycobiota community, and the resultant effects on the antioxidant properties during the Chinese bayberry Jiaosu fermentation. The structure and composition of mycobiota during the Chinese bayberry Jiaosu fermentation were significantly changed (p < 0.001) and clearly clustered into two distinct phases (Phase 1: Day 5–20; Phase 2: Day 30–60, p < 0.001). From Phase 1 to Phase 2, the dominant fungi gradually changed from Saccharomycetales fam Incertae sedis to Saccharomyces cerevisiae. The antioxidative properties (total polyphenols, 1,1-diphenyl-2-picrylhydrazyl [DPPH], superoxide and 2,2′-azino-bis-(3-ethylbenzthiazoline-6-sulphonate) [ABTS] radical scavenging) of Chinese bayberry Jiaosu were significantly increased by 250.4, 73.9, 25.3 and 40.0% respectively (p < 0.001). Co-occurrence network analysis revealed that Saccharomyces cerevisiae contributed to the increase of antioxidative properties in the Chinese bayberry Jiaosu fermentation. Our research indicates that fermentation into Chinese bayberry Jiaosu is an effective and new method for high-valued utilization of Chinese bayberry.

Construction of a High-Density Genetic Map and Identification of Leaf Trait-Related QTLs in Chinese Bayberry (Myrica rubra)

Chinese bayberry (Myrica rubra) is an economically important fruit tree that is grown in southern China. Owing to its over 10-year seedling period, the crossbreeding of bayberry is challenging. The characteristics of plant leaves are among the primary factors that control plant architecture and potential yields, making the analysis of leaf trait-related genetic factors crucial to the hybrid breeding of any plant. In the present study, molecular markers associated with leaf traits were identified via a whole-genome re-sequencing approach, and a genetic map was thereby constructed. In total, this effort yielded 902.11 Gb of raw data that led to the identification of 2,242,353 single nucleotide polymorphisms (SNPs) in 140 F1 individuals and parents (Myrica rubra cv. Biqizhong × Myrica rubra cv. 2012LXRM). The final genetic map ultimately incorporated 31,431 SNPs in eight linkage groups, spanning 1,351.85 cM. This map was then used to assemble and update previous scaffold genomic data at the chromosomal level. The genome size of M. rubra was thereby established to be 275.37 Mb, with 94.98% of sequences being assembled into eight pseudo-chromosomes. Additionally, 18 quantitative trait loci (QTLs) associated with nine leaf and growth-related traits were identified. Two QTL clusters were detected (the LG3 and LG5 clusters). Functional annotations further suggested two chlorophyll content-related candidate genes being identified in the LG5 cluster. Overall, this is the first study on the QTL mapping and identification of loci responsible for the regulation of leaf traits in M. rubra, offering an invaluable scientific for future marker-assisted selection breeding and candidate gene analyses.

Response of Resistant and Susceptible Bayberry Cultivars to Infection of Twig Blight Pathogen by Histological Observation and Gibberellin Related Genes Expression

Bayberry is an important fruit tree native to the subtropical regions of China. However, a systematic twig blight disease caused by Pestalotiopsis versicolor and P. microspora, resulted in the death of the whole tree of bayberry. The main variety Dongkui is highly sensitive to the twig blight disease, but the variety Zaojia is very highly resistant to the disease. Therefore, it is very necessary to clear the difference between resistant and susceptible varieties in response to the fungal infection. In this paper, we investigated the response of resistant and susceptible bayberry cultivars to infection of twig blight pathogen by histological observation and gibberellin signaling pathway-related genes expression. Microscopic observation revealed the difference in the infection process between resistant and susceptible varieties. The results of frozen scanning electron microscopy showed that the Pestalotiopsis conidia were shrunk, the mycelium was shriveled and did not extend into the cells of resistant cultivars, while the conidia were full and the top was extended, the mycelia was normal and continued to extend to the cells of a susceptible cultivar. Indeed, the medulla cells were almost intact in resistant cultivar, but obviously damaged in susceptible cultivar after inoculation of the main fungal pathogen P. versicolor conidia, which is earlier germinated on sterile glass slide than that of a hard plastic slide. The quantitative real-time PCR results showed a significant difference between resistant and susceptible cultivars in the expression of gibberellin signaling pathway-related genes in leaves and stems of bayberry, which is closely related to infection time, the type of genes and varieties. Overall, this study provides a clue for our understanding of the resistance mechanism of bayberry against the twig blight disease.

Review on the Development and Applications of Medicinal Plant Genomes

With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.

Genome-wide analysis of tandem duplicated genes and their contribution to stress resistance in pigeonpea (Cajanus cajan)

Pigeonpea is the main protein source for more than one billion people, and it shows a strong adaptation to biotic stress and abiotic stress. Gene duplication is a fundamental process in genome evolution. Although the draft sequence of the pigeonpea genome has been available since 2011, further analysis of tandem duplicated genes (TDGs) and their contribution to the evolution of pigeonpea has not been reported. In this study, we identify 3211 TDGs in the pigeonpea genome and KEGG enrichment analysis of these genes shows that the TDGs are significantly enriched in resistance-related pathways. In addition, we find that TDGs are more abundant in retrotransposon-related genes in pigeonpea than in the other species included in our study. These results indicate that stress resistance in pigeonpea may be ascribed to resistance-related pathways and retrotransposons originating from tandem duplications. Our study will provide an important basis for further research in pigeonpea breeding.

Genetic Diversity, Pedigree Relationships, and A Haplotype-Based DNA Fingerprinting System of Red Bayberry Cultivars

High throughput sequencing was used to reveal the distribution of whole-genome variations in cultivated Morella rubra (Sieb. et Zucc.). A total of 3,151,123 SNPs, 371,757 small indels, and 15,904 SVs were detected in 52 accessions. Verification by Sanger sequencing demonstrated that the positive rate of the SNPs was approximately 97.3%. Search for more genetic variations was expanded to 141 red bayberry accessions, most of which were cultivars, by sequencing 19 selected genomic segments (SEG1-19). The results showed that each segment harbored, on average, 7.8 alleles (haplotypes), a haplotype diversity of 0.42, and a polymorphic information content (PIC) of 0.40. Seventy-two different genotypes were identified from the 141 accessions, and statistical analysis showed that the accessions with duplicated genotypes were either somatic mutants or simply synonyms. Core set selection results showed that a minimum of 34 genotypes could already have covered all the alleles on the segments. A DNA fingerprinting system was developed for red bayberry, which used the diversity information of only 8 DNA segments yet still achieved a very high efficiency without losing robustness. No large clade was robustly supported by hierarchical clustering, and well-supported small clusters mainly included close relatives. These results should lead to an improved understanding of the genetic diversity of red bayberry and be valuable for future molecular breeding and variety protection.