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Tartary buckwheat (Fagopyrum tataricum) is a significant medicinal crop, with flavonoids serving as a crucial measure of its quality. Presently, the artificial cultivation of Tartary buckwheat yields low results, and the quality varies across different origins. Therefore, it is imperative to identify an effective method to enhance the yield and quality of buckwheat. Endophytic fungi reside within plants and form a mutually beneficial symbiotic relationship, aiding plants in nutrient absorption, promoting host growth, and improving secondary metabolites akin to the host. In this study, high-throughput sequencing technology was employed to assess the diversity of endophytic fungi in Tartary buckwheat. Subsequently, a correlation analysis was performed between fungi and metabolites, revealing potential increases in flavonoid content due to endophytic fungi such as Bipolaris, Hymenula, and Colletotrichum. Additionally, a correlation analysis between fungi and phenotypic traits unveiled the potential influence of endophytic fungi such as Bipolaris, Buckleyzyma, and Trichosporon on the phenotypic traits of Tartary buckwheat. Notably, the endophytic fungi of the Bipolaris genus exhibited the potential to elevate the content of Tartary buckwheat metabolites and enhance crop growth. Consequently, this study successfully identified the resources of endophytic fungi in Tartary buckwheat, explored potential functional endophytic fungi, and laid a scientific foundation for future implementation of biological fertilizers in improving the quality and growth of Tartary buckwheat.

Abstract Rhodophyta are among the closest known relatives of green plants. Studying the codons of their genomes can help us understand the codon usage pattern and characteristics of the ancestor of green plants. By studying the codon usage pattern of all available red algae, it was found that although there are some differences among species, high-bias genes in most red algae prefer codons ending with GC. Correlation analysis, Nc-GC3s plots, parity rule 2 plots, neutrality plot analysis, differential protein region analysis and comparison of the nucleotide content of introns and flanking sequences showed that the bias phenomenon is likely to be influenced by local mutation pressure and natural selection, the latter of which is the dominant factor in terms of translation accuracy and efficiency. It is worth noting that selection on translation accuracy could even be detected in the low-bias genes of individual species. In addition, we identified 15 common optimal codons in seven red algae except for G. sulphuraria for the first time, most of which were found to be complementary and bound to the tRNA genes with the highest copy number. Interestingly, tRNA modification was found for the highly degenerate amino acids of all multicellular red algae and individual unicellular red algae, which indicates that highly biased genes tend to use modified tRNA in translation. Our research not only lays a foundation for exploring the characteristics of codon usage of the red algae as green plant ancestors, but will also facilitate the design and performance of transgenic work in some economic red algae in the future.

As an essential trace element, iron is a necessary micronutrient for most organisms. Conyza blinii (C. blinii) is a traditional Chinese medicine grown in Sichuan, China. We chose C. blinii as material to explore the way plants respond to iron. Our results showed that iron increased the content of endogenous auxin, glandular trichomes (GTs) density and the content of blinin, the characteristic diterpene in C. blinii. Most of the key enzymes in the blinin synthesis pathway (MEP) were upregulated under iron by RNA sequencing. CbHO-1 (Heme oxygenase gene) was upregulated under exogenous IAA treatment. Taken together, these results suggest that C. blinii respond to iron through auxin- terpenoids metabolism, and this process may be related to CbHO-1.

The dried tuber of Alisma orientale (Sam.) Juzep. (AOJ) is a traditional Chinese medicine with high medicinal value. The endophytic fungi of medicinal plants are a treasure house of natural compounds. However, there is a lack of research on the diversity and biological activity of endophytic fungi of AOJ. In this study, high-throughput sequencing technology was used to study the diversity of endophytic fungi in the roots and stems of AOJ, and endophytic fungi with a high output of phenols and flavonoids were screened by chromogenic reaction, and the antioxidant and antibacterial activities and chemical constituents of crude extracts of their fermentation broth were studied. A total of 3,426 amplicon sequence variants (ASVs) belonging to 9 phyla, 27 classes, 64 orders, 152 families, and 277 genera were identified from AOJ. There were significant differences in the endophytic fungal communities of AOJ roots and stems, as well as in the endophytic fungal communities of triangular AOJ and circular AOJ. In addition, 31 strains of endophytic fungi were isolated from AOJ, of which 6 strains had good antioxidant and antibacterial activities. The crude extract of YG-2 had the strongest free radical scavenging ability and bacteriostatic ability, and its IC50DPPH, IC50ABTS, and IC50⋅OH values were 0.009 ± 0.000 mg/mL, 0.023 ± 0.002 mg/mL, and 0.081 ± 0.006 mg/mL, respectively. The results of LC-MS showed that the main component of the crude extract of YG-2 was caffeic acid (10.12 μmol/g). Overall, the results of this study preliminarily elucidated the diversity and community composition of endophytic fungi of AOJ, indicating that AOJ endophytic fungi have abundant secondary metabolites and good antioxidant and antibacterial activities. This study provides an important reference for further research, development and utilization of AOJ endophytic fungi and a theoretical basis for the further development of the endophytic fungus YG-2 (Chaetomium globosum) as a source of antioxidants.

The main objective of this study was to investigate the influence of Serendipita indica on the growth of Tartary buckwheat plants. This study highlighted that the roots of Tartary buckwheat can be colonized by S. indica and that this fungal endophyte improved plants height, fresh weight, dry weight, and grain yield. In the meantime, the colonization of S. indica in Tartary buckwheat leaves resulted in elevated levels of photosynthesis, plant hormone content, antioxidant enzyme activity, proline content, chlorophyll content, soluble sugars, and protein content. Additionally, the introduction of S. indica to Tartary buckwheat roots led to a substantial rise in the levels of flavonoids and phenols found in the leaves and seeds of Tartary buckwheat. In addition, S. indica colonization reduced the content of malondialdehyde and hydrogen peroxide when compared to non-colonized plants. Importantly, the drought tolerance of Tartary buckwheat plants is increased, which benefits from physiology and bio-chemical changes in plants after S. indica colonized. In conclusion, we have shown that S. indica can improve systematic resistance and promote the growth of Tartary buckwheat by enhancing the photosynthetic capacity of Tartary buckwheat, inducing the production of IAA, increasing the content of secondary metabolites such as total phenols and total flavonoids, and improving the antioxidant enzyme activity of the plant.

The water-soluble polysaccharides from plants have attracted ever-increasing attention in the field of food and drug due to their various activities and low toxicity. CBP50-1, as a purified fraction of polysaccharide from the rhizome of Cibotium barometz (CBP), mainly consisted of glucose (55.45%) and xylose (25.27%). CBP50-1 showed excellent antioxidant activity for scavenging 2,2‑Diphenyl‑1‑picryl‑hydrazy (DPPH) radical and hydroxyl radical, further inhibiting lipid peroxidation. CBP50-1 significantly improved the survival rate of Caenorhabditis elegans under thermal and oxidative stress. Furthermore, CBP50-1 reduced the paralysis and oxidative damage induced by amyloid-beta (Aβ) and increased the antioxidant enzyme activity in Alzheimer’s disease (AD) model C. elegans CL4176 through c-Jun N-terminal kinase (JNK) mitogen-activated protein kinase (MAPK) signal pathway. Thus, CBP50-1 had a potential application in health industries.

Bacterial growth, under laboratory conditions or in a natural environment, goes through different growth phases. Some gene expressions are regulated with respect to the growth phase, which allows bacteria to adapt to changing conditions. Among them, many gene transcriptions are controlled by RpoHI or RpoHII in Rhodobacter sphaeroides. In a previous study, it was proven that the alternative sigma factors, RpoE, RpoHI, and RpoHII, are the major regulators of oxidative stress. Moreover, the growth of bacteria reached a stationary phase, and following the outgrowth, rpoE, rpoHI, and rpoHII mRNAs increased with respect to the growth phase. In this study, we demonstrated the regulatory function of alternative sigma factors in the rsp_0557 gene. The gene rsp_0557 is expressed with respect to the growth phase and belongs to the RpoHI/RpoHII regulons. Reporter assays showed that the antisigma factor ChrR turns on or over the RpoE activity to regulate rsp_0557 expression across the growth phase. In the exponential phase, RpoHII and sRNA Pos19 regulate the expression of rsp_0557 to an appropriate level under RpoE control. In the stationary phase, RpoHI and Pos19 stabilize the transcription of rsp_0557 at a high level. During outgrowth, RpoHI negatively regulates the transcription of rsp_0557. Taken together, our data indicate that these regulators are recruited by cells to adapt to or survive under different conditions throughout the growth phase. However, they still did not display all of the regulators involved in growth phase-dependent regulation. More research is still needed to learn more about the interaction between the regulators and the process of adapting to changed growth conditions and environments.

The research on the development of dragon fruit and kiwi fruit through LAB-yeast compound fermentation is very limited, and there are few related fermentation products on the market. The purpose of this study was to evaluate the stability of the antioxidant capacity of fermented beverages (FB) through in vitro simulated digestion, to evaluate the changes in metabolites of juice after fermentation through untargeted metabolomics, and used Caenorhabditis elegans as a model to evaluate its anti-aging activity. The results showed that FB not only has good in vitro antioxidant activity, but also the total phenol content (TPC), total flavonoid content (TFC), ABTS scavenging ability, and hydroxyl radical scavenging ability of FB were significantly increased during gastric digestion and intestinal digestion. Metabolomics showed that the contents of phenols and flavonoids related to antioxidant increased after fermentation, and fermentation had a significant effect on organic acids and amino acids in FB. Finally, compared with the control group, although the original concentration of FB has a side-toxic effect on nematodes, the mean lifespan of C. elegans fed with 1.56% FB increased by 18.01%, SOD activity significantly increased by 96.16% and MDA content significantly decreased by 40.62%. FB has good antioxidant activity in vitro and in vivo, and the antioxidant activity is stable during the simulated digestion process.

Ligusticum chuanxiong Hort. (CX) is a medicinal and edible plant including a variety of active substances, which may be an available resource for the treatment of related diseases. To expand the medicinal uses of CX, this study aims to explore the antioxidant, anti-aging and neuroprotective effects of the Ligusticum chuanxiong leaves (CXL) and rhizome (CXR) extracts. We first characterize CX phytochemical spectrum by LC-MS as well as antioxidant capacity. Acute toxicity, anti-oxidative stress capacity, lifespan and healthspan was evaluated in C elegans N2. Neuroprotective effect was evaluated in vitro and in vivo (C elegans CL4176 and CL2355). In this study, we detected 74 and 78 compounds from CXR and CXL, respectively, including phthalides, alkaloids, organic acids, terpenes, polyphenols and others. Furthermore, we found that CXs not only protect against oxidative stress, but also prolong the lifespan, alleviate lipofuscin, malondialdehyde (MDA) and reactive oxygen species (ROS) accumulation, and improve movement level, antioxidant enzyme activity in C elegans N2. However, only CXR reduced the β-amyloid peptide (Aβ)-induced paralysis phenotype in CL4176s and alleviated chemosensory behavior dysfunction in CL2355s. In addition, CXR treatment reduced the production of Aβ and ROS, enhanced SOD activity in CL4176s. The possible mechanism of anti-aging of CXL and CXR is to promote the expression of related antioxidant pathway genes, increase the activity of antioxidant enzymes, and reduce the accumulation of ROS, which is dependent on DAF-16 and HSF-1 (only in CXR). CXR was able to activate antioxidase-related (sod-3 and sod-5) and heat shock protein genes (hsp-16.1 and hsp-70) expression, consequently ameliorating proteotoxicity related to Aβ aggregation. In summary, these findings demonstrate the antioxidant, anti-aging and neuroprotective (only in CXR) activities of the CX, which provide an important pharmacological basis for developing functional foods and drugs to relieve the symptoms of aging and AD. However, the material basis of neuroprotective activity and antiaging effects need to be elucidated, and the relationship between these activities should also be clarified in future studies.

The chemical composition and antioxidant activity of extracts (POE) of Penicillium oxalate isolated from Ligusticum chuanxiong Hort have been investigated. However, the biological activity of POE is limited, and its antioxidant, stress resistance and DNA protection effects in vivo are unclear. The current study aims to explore the beneficial effects of POE on DNA damage protection in pBR322 plasmid and lymphocytes and stress resistance in Caenorhabditis elegans. The results showed that POE increased the survival rate of C. elegans under 35°C, UV and H2O2 stress, attenuated ROS and MDA accumulation, and enhanced the activity of some important enzymes (SOD, CTA, and GSH-PX). In addition, the POE-mediated stress resistance involved the upregulation of the expression of the sod-3, sod-5, gst-4, ctl-1, ctl-2, daf-16, hsp-16.1, hsp-16.2, and hsf-1 genes and acted dependently on daf-16 and hsf-1 rather than skn-1. Moreover, POE also reduced lipofuscin levels, but did not prolong the lifespan or damage the growth, reproduction and locomotion of C. elegans. Furthermore, POE showed a protective effect against DNA scission in the pBR322 plasmid and lymphocytes. These results suggested that P. oxalate extracts have significant anti-stress and DNA protection potential and could be potential drug candidates in the pharmaceutical field, thus greatly broadening the understanding of the biological effects of the endophytic fungus P. oxalate.

In this study, ultrasound-assisted extraction of polyphenols from C. cicadae was optimized by response surface methodology (RSM). The optimized conditions were determined as extraction time of 39 min, liquid-to-solid ratio of 1:29 g/mL, extraction temperature of 69 °C and ethanol concentration of 55% with a yield of 21.9 mg gallic acid equivalent/g dry weight. Four resins were used for polyphenol purification. D101 resin had the highest ratio of adsorption and was further applied in polyphenol purification test. A total of 19 different phenolic compounds were identified by LC-MS, including 12 phenolic acids and 7 organic acids. In addition, C. cicadae polyphenols displayed higher antioxidant activity in vitro and anti-aging activity of C. elegans in vivo. Lastly, C. cicadae polyphenols showed the potential to protect DNA from oxidative damage. Overall, our results suggest that polyphenols from C. cicadae may be considered as novel sources of anti-oxidation, anti-aging and recommended as reagents to protect DNA from oxidative damage in food and pharmaceutical industries.

The polysaccharides from C. cicadae were extracted by ultrasonically-assisted enzymatic extraction (UAEE). Response surface analysis was used to determine the optimum parameters as follows: addition of enzymes, 0.71%; extraction temperature, 60°C; extraction time, 18 min; liquid-solid ratio, 46:1 (mL/g). The extraction yield of polysaccharide was 3.66 ± 0.87%. A novel polysaccharide fraction (JCH-a1) from C. cicadae was extracted and then purified by cellulose DEAE-32 and Sephadex G-100 anion exchange chromatography. The analysis results showed that the molar ratio of galactose, glucose, and mannose in JCH-a1 cells (60.7 kDa) was 0.89:1:0.39. JCH-a1 with a triple helix contains more α-glycosides and has strong thermal stability. Moreover, JCH-a1 showed strong antioxidant activity and acted as a strong inhibitor of α-glucosidase in vitro. In addition, JCH-a1 can prolong the lifespan of C. elegans. The present study might provide a basis for further study of JCH-a1 as an antioxidant and hypoglycemic food or drug.

Under dry-hot valley climates, Conyza blinii (also known as Jin Long Dan Cao), suffers from nocturnal low-temperature stress (LTS) during winter. Here, to investigate the biological significance of terpenoid metabolism during LTS adaptation, the growth state and terpenoid content of C. blinii under different LTS were detected, and analyzed with the changes in phytohormone. When subjected to LTS, the results demonstrated that the growth activity of C. blinii was severely suppressed, while the metabolism activity was smoothly stimulated. Meanwhile, the fluctuation in phytohormone content exhibited three different physiological stages, which are considered the stress response, signal amplification, and stress adaptation. Furthermore, drastic changes occurred in the distribution and accumulation of terpenoids, such as blinin (diterpenoids from MEP) accumulating specifically in leaves and oleanolic acid (triterpenoids from MVA) accumulating evenly and globally. The gene expression of MEP and MVA signal transduction pathways also changes under LTS. In addition, a pharmacological study showed that it may be the ABA-SA crosstalk driven by the LTS signal, that balances the metabolic flux in the MVA and MEP pathways in an individual manner. In summary, this study reveals the different standpoints of ABA and SA, and provides a research foundation for the optimization of the regulation of terpenoid metabolic flux within C. blinii.

Abstract Background Heat shock transcription factor (Hsfs) is widely found in eukaryotes and prokaryotes. Hsfs can not only help organisms resist high temperature, but also participate in the regulation of plant growth and development (such as involved in the regulation of seed maturity and affects the root length of plants). The Hsf gene was first isolated from yeast and then gradually found in plants and sequenced, such as Arabidopsis thaliana, rice, maize. Tartary buckwheat is a rutin-rich crop, and its nutritional value and medicinal value are receiving more and more attention. However, there are few studies on the Hsf genes in Tartary buckwheat. With the whole genome sequence of Tartary buckwheat, we can effectively study the Hsf gene family in Tartary buckwheat. Results According to the study, 29 Hsf genes of Tartary buckwheat (FtHsf) were identified and renamed according to location of FtHsf genes on chromosome after removing a redundant gene. Therefore, only 29 FtHsf genes truly had the functional characteristics of the FtHsf family. The 29 FtHsf genes were located on 8 chromosomes of Tartary buckwheat, and we found gene duplication events in the FtHsf gene family, which may promote the expansion of the FtHsf gene family. Then, the motif compositions and the evolutionary relationship of FtHsf proteins and the gene structures, cis-acting elements in the promoter, synteny analysis of FtHsf genes were discussed in detail. What’s more, we found that the transcription levels of FtHsf in different tissues and fruit development stages were significantly different by quantitative real-time PCR (qRT-PCR), implied that FtHsf may differ in function. Conclusions In this study, only 29 Hsf genes were identified in Tartary buckwheat. Meanwhile, we also classified the FtHsf genes, and studied their structure, evolutionary relationship and the expression pattern. This series of studies has certain reference value for the study of the specific functional characteristics of Tartary buckwheat Hsf genes and to improve the yield and quality of Tartary buckwheat in the future.

The objective of this study was to evaluate the diversity of endophytic fungi of different parts of Ligusticum chuanxiong Hort (CX) and further characterize their biological activities and identify chemical compounds produced by these endophytic fungi. A total of 21 endophytic fungi were isolated and identified from CX. Penicillium oxalicum, Simplicillium sp., and Colletotrichum sp. were identified as promising strains by the color reaction. Comparing different organic extracts of the three strains, it was observed that the ethyl acetate extract of Penicillium oxalicum and Simplicillium sp. and the n-butanol extract of Colletotrichum sp. showed significant antioxidant and antibacterial activities. The ethyl acetate extracts of Penicillium oxalicum had outstanding antioxidant and antibacterial effects, and its radical scavenging rates for ABTS and DPPH were 98.43 ± 0.006% and 90.11 ± 0.032%, respectively. At the same time, their IC50 values were only 0.18 ± 0.02 mg/mL and 0.04 ± 0.003 mg/mL. The ethyl acetate extract of Penicillium oxalicum showed MIC value of only 0.5 mg/mL against Escherichia coli and Staphylococcus aureus. By liquid chromatography-mass spectrometry (LC-MS), we found that Penicillium oxalicum could produce many high-value polyphenols, such as hesperidin (36.06 μmol/g), ferulic acid (1.17 μmol/g), and alternariol (12.64 μmol/g), which can be a potential resource for the pharmaceutical industry. In conclusion, these results increase the diversity of CX endophytic fungi and the antioxidant and antibacterial activities of their secondary metabolites.

Background Functional fermented beverages are popular worldwide due to their potential to promote health. Starter culture is the main determinant of the final quality and flavor of fermented beverages. The co-cultivation of lactic acid bacteria (LAB) and yeast makes a significant contribution to the safe flavor of fermented beverages. However, the research on the potential of antioxidant, antimicrobial, and anti-biofilm formation of strawberry fermented beverage obtained by combining the LAB and yeast as starter cultures has not been well explored. Methods In this study, LAB and yeast were combined as starter culture to obtain strawberry fermented beverage. Fourier transform infrared (FTIR ) spectroscopy was used for the qualitative analysis of the fresh strawberry juice and fermented beverage. From the changes in antioxidant content, free radical scavenging ability, total superoxide dismutase (T-SOD) activity and total antioxidant capacity (T-AOC) to evaluate the antioxidant capacity of fermented beverage in vitro. The antibacterial ability was tested by the Oxford cup method. The biofilms of Escherichia coli ATCC 25922, Staphylococcus aureus ATCC 6538 under fermented beverages treatment was observed by Fluorescence microscope. In addition, sensory analysis was conducted in this study. Results In this study, the absorption peaks of Fourier transform infrared between 1,542 cm−1 and 976 cm−1, suggest the existence of organic acids, sugars and ethanol. The total phenols and total flavonoids content decreased by 91.1% and 97.5%, respectively. T-SOD activity increased by 33.33%.The scavenging ability of fermented beverage on superoxide anion free radicals was enhanced, and the scavenging ability on DPPH free radicals, hydroxyl free radicals, and ABTS free radicals was weakened. However, the T-AOC increased from 4.15 ± 0.81 to 8.43 ± 0.27 U/mL. Fermented beverage shows antibacterial activity against four pathogens. The minimum inhibitory concentration (MIC) values of Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC 6538 were 0.05 mL/mL and 0.025 mL/mL, respectively, and the minimum bactericidal concentration (MBC) were both 0.2 mL/mL. It was observed by fluorescence microscope that the green fluorescence area of the two biofilms is greatly reduced after being treated with fermented beverage. Sensory analysis results show that the average scores of fermented beverage in color, appearance and taste were increased. The overall impression and flavor were decreased. Conclusion These results demonstrated that strawberry fermented beverage has potential benefits such as an antioxidant, antibacterial, and anti-biofilm formation, providing the potential for the fermented beverage to become promising candidates for natural antioxidants, antibacterial agents and anti-biofilm agents.

Abstract Background GRAS are plant-specific transcription factors that play important roles in plant growth and development. Although the GRAS gene family has been studied in many plants, there has been little research on the GRAS genes of Tartary buckwheat (Fagopyrum tataricum), which is an important crop rich in rutin. The recently published whole genome sequence of Tartary buckwheat allows us to study the characteristics and expression patterns of the GRAS gene family in Tartary buckwheat at the genome-wide level. Results In this study, 47 GRAS genes of Tartary buckwheat were identified and divided into 10 subfamilies: LISCL, HAM, DELLA, SCR, PAT1, SCL4/7, LAS, SHR, SCL3, and DLT. FtGRAS genes were unevenly distributed on 8 chromosomes, and members of the same subfamily contained similar gene structures and motif compositions. Some FtGRAS genes may have been produced by gene duplications; tandem duplication contributed more to the expansion of the GRAS gene family in Tartary buckwheat. Real-time PCR showed that the transcription levels of FtGRAS were significantly different in different tissues and fruit development stages, implying that FtGRAS might have different functions. Furthermore, an increase in fruit weight was induced by exogenous paclobutrazol, and the transcription level of the DELLA subfamily member FtGRAS22 was significantly upregulated during the whole fruit development stage. Therefore, FtGRAS22 may be a potential target for molecular breeding or genetic editing. Conclusions Collectively, this systematic analysis lays a foundation for further study of the functional characteristics of GRAS genes and for the improvement of Tartary buckwheat crops.

Abstract Background SPL (SQUAMOSA promoter binding protein-like) is a class of plant-specific transcription factors that play important roles in many growth and developmental processes, including shoot and inflorescence branching, embryonic development, signal transduction, leaf initiation, phase transition, and flower and fruit development. The SPL gene family has been identified and characterized in many species but has not been well studied in tartary buckwheat, which is an important edible and medicinal crop. Results In this study, 24 Fagopyrum tataricum SPL (FtSPL) genes were identified and renamed according to the chromosomal distribution of the FtSPL genes. According to the amino acid sequence of the SBP domain and gene structure, the SPL genes were divided into eight groups (group I to group VII) by phylogenetic tree analysis. A total of 10 motifs were detected in the tartary buckwheat SPL genes. The expression patterns of 23 SPL genes in different tissues and fruits at different developmental stages (green fruit stage, discoloration stage and initial maturity stage) were determined by quantitative real-time polymerase chain reaction (qRT-PCR). Conclusions The tartary buckwheat genome contained 24 SPL genes, and most of the genes were expressed in different tissues. qRT-PCR showed that FtSPLs played important roles in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This work provides a comprehensive understanding of the SBP-box gene family in tartary buckwheat and lays a significant foundation for further studies on the functional characteristics of FtSPL genes and improvement of tartary buckwheat crops.

Abstract Background ZF-HD is a family of genes that play an important role in plant growth, development, some studies have found that after overexpression AtZHD1 in Arabidopsis thaliana, florescence advance, the seeds get bigger and the life span of seeds is prolonged, moreover, ZF-HD genes are also participate in responding to adversity stress. The whole genome of the ZF-HD gene family has been studied in several model plants, such as Arabidopsis thaliana and rice. However, there has been little research on the ZF-HD genes in Tartary buckwheat (Fagopyrum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of Tartary buckwheat allows us to study the tissue and expression profiles of the ZF-HD gene family in Tartary buckwheat on a genome-wide basis. Results In this study, the whole genome and expression profile of the ZF-HD gene family were analyzed for the first time in Tartary buckwheat. We identified 20 FtZF-HD genes and divided them into MIF and ZHD subfamilies according to phylogeny. The ZHD genes were divided into 5 subfamilies. Twenty FtZF-HD genes were distributed on 7 chromosomes, and almost all the genes had no introns. We detected seven pairs of chromosomes with fragment repeats, but no tandem repeats were detected. In different tissues and at different fruit development stages, the FtZF-HD genes obtained by a real-time quantitative PCR analysis showed obvious expression patterns. Conclusions In this study, 20 FtZF-HD genes were identified in Tartary buckwheat, and the structures, evolution and expression patterns of the proteins were studied. Our findings provide a valuable basis for further analysis of the biological function of the ZF-HD gene family. Our study also laid a foundation for the improvement of Tartary buckwheat crops.

Abstract Background In reported plants, the bZIP family is one of the largest transcription factor families. bZIP genes play roles in the light signal, seed maturation, flower development, cell elongation, seed accumulation protein, abiotic and biological stress and other biological processes. While, no detailed identification and genome-wide analysis of bZIP family genes in Fagopyum talaricum (tartary buckwheat) has previously been published. The recently reported genome sequence of tartary buckwheat provides theoretical basis for us to study and discuss the characteristics and expression of bZIP genes in tartary buckwheat based on the whole genome. Results In this study, 96 FtbZIP genes named from FtbZIP1 to FtbZIP96 were identified and divided into 11 subfamilies according to their genetic relationship with 70 bZIPs of A. thaliana. FtbZIP genes are not evenly distributed on the chromosomes, and we found tandem and segmental duplication events of FtbZIP genes on 8 tartary buckwheat chromosomes. According to the results of gene and motif composition, FtbZIP located in the same group contained analogous intron/exon organizations and motif composition. By qRT-PCR, we quantified the expression of FtbZIP members in stem, root, leaf, fruit, and flower and during fruit development. Exogenous ABA treatment increased the weight of tartary buckwheat fruit and changed the expressions of FtbZIP genes in group A. Conclusions Through our study, we identified 96 FtbZIP genes in tartary buckwheat and synthetically further analyzed the structure composition, evolution analysis and expression pattern of FtbZIP proteins. The expression pattern indicates that FtbZIP is important in the course of plant growth and development of tartary buckwheat. Through comprehensively analyzing fruit weight and FtbZIP genes expression after ABA treatment and endogenous ABA content of tartary buckwheat fruit, ABA may regulate downstream gene expression by regulating the expression of FtPinG0003523300.01 and FtPinG0003196200.01, thus indirectly affecting the fruit development of tartary buckwheat. This will help us to further study the function of FtbZIP genes in the tartary buckwheat growth and improve the fruit of tartary buckwheat.

Abstract Background AP2/ERF transcription factors perform indispensable functions in various biological processes, such as plant growth, development, biotic and abiotic stresses responses. The AP2/ERF transcription factor family has been identified in many plants, and several AP2/ERF transcription factors from Arabidopsis thaliana (A. thaliana) have been functionally characterized. However, little research has been conducted on the AP2/ERF genes of tartary buckwheat (Fagopyum tataricum), which is an important edible and medicinal crop. The recently published whole genome sequence of tartary buckwheat allowed us to study the tissue and expression profiles of AP2/ERF genes in tartary buckwheat on a genome-wide basis. Results In this study, 134 AP2/ERF genes of tartary buckwheat (FtAP2/ERF) were identified and renamed according to the chromosomal distribution of the FtAP2/ERF genes. According to the number conserved domains and gene structure, the AP2/ERF genes were divided into three subfamilies by phylogenetic tree analysis, namely, AP2 (15 members), ERF (116 members) and RAV (3 members). A total of 10 motifs were detected in tartary buckwheat AP2/ERF genes, and some of the unique motifs were found to be important for the function of AP2/ERF genes. Conclusion A comprehensive analysis of AP2/ERF gene expression patterns in different tissues and fruit development stages by quantitative real-time PCR (qRT-PCR) showed that they played an important role in the growth and development of tartary buckwheat, and genes that might regulate flower and fruit development were preliminarily identified. This systematic analysis establishes a foundation for further studies of the functional characteristics of FtAP2/ERF genes and improvement of tartary buckwheat crops.

Abstract Background The NAC (NAM, ATAF1/2, and CUC2) transcription factor family represents a group of large plant-specific transcriptional regulators, participating in plant development and response to external stress. However, there is no comprehensive study on the NAC genes of Tartary buckwheat (Fagopyrum tataricum), a large group of extensively cultivated medicinal and edible plants. The recently published Tartary buckwheat genome permits us to explore all the FtNAC genes on a genome-wide basis. Results In the present study, 80 NAC (FtNAC) genes of Tartary buckwheat were obtained and named uniformly according to their distribution on chromosomes. Phylogenetic analysis of NAC proteins in both Tartary buckwheat and Arabidopsis showed that the FtNAC proteins are widely distributed in 15 subgroups with one subgroup unclassified. Gene structure analysis found that multitudinous FtNAC genes contained three exons, indicating that the structural diversity in Tartary buckwheat NAC genes is relatively low. Some duplication genes of FtNAC have a conserved structure that was different from others, indicating that these genes may have a variety of functions. By observing gene expression, we found that FtNAC genes showed abundant differences in expression levels in various tissues and at different stages of fruit development. Conclusions In this research, 80 NAC genes were identified in Tartary buckwheat, and their phylogenetic relationships, gene structures, duplication, global expression and potential roles in Tartary buckwheat development were studied. Comprehensive analysis will be useful for a follow-up study of functional characteristics of FtNAC genes and for the development of high-quality Tartary buckwheat varieties.

Background Flavonoids are widely used in the market because of their antibacterial, antiviral, and antioxidant activities. But the production speed of flavonoids is limited by the growth of plants. CBL9 (Chaetomium cruentum) is a flavonoid-producing endophytic fungi from Conyza blinii H. Lév, which has potential to produce flavonoids. Methods In this study, we isolated total flavonoids from endophytic fungus CBL9 of Conyza blinii H. Lév using macroporous resin D101. The process was optimized by response surface and the best extraction process was obtained. The antioxidant activities of total flavonoids were analyzed in vitro. Results It was found that the best parameters were 25 °C pH 2.80, 1.85 h, and the adsorption ratio reached (64.14 ± 0.04)%. A total of 60% ethanol was the best elution solvent. The elution ratio of total flavonoid reached to (81.54 ± 0.03)%, and the purity was 7.13%, which was increased by 14.55 times compared with the original fermentation broth. Moreover its purity could rise to 13.69% after precipitated by ethanol, which is very close to 14.10% prepared by ethyl acetate extraction. In the antioxidant research, the clearance ratio of L9F-M on DPPH, ABTS, •OH, •O2−, (96.44 ± 0.04)% and (75.33 ± 0.03)%, (73.79 ± 0.02)%, (31.14 ± 0.01)% at maximum mass concentration, was higher than L9F. Conclusion The result indicated using macroporous resin in the extraction of total flavonoid from endophytic fungus is better than organic solvents with higher extraction ratio, safety and lower cost. In vitro testing indicated that the flavonoid extracted by macroporous resin have good antioxidant activity, providing more evidence for the production of flavonoid by biological fermentation method.

Background Dye wastewater increases cancer risk in humans. For the treatment of dyestuffs, biodegradation has the advantages of economy, high efficiency, and environmental protection compared with traditional physical and chemical methods. Laccase is the best candidate for dye degradation because of its multiple substrates and pollution-free products. Methods Here, we modified the laccase gene of Bacillus licheniformis by error-prone PCR and site-directed mutagenesis and expressed in E. coli. The protein was purified by His-tagged protein purification kit. We tested the enzymatic properties of wild type and mutant laccase by single factor test, and further evaluated the decolorization ability of laccase to acid violet, alphazurine A, and methyl orange by spectrophotometry. Results Mutant laccase Lacep69and D500G were superior to wild type laccase in enzyme activity, stability, and decolorization ability. Moreover, the laccase D500G obtained by site-directed mutagenesis had higher enzyme activity in both, and the specific activity of the purified enzyme was as high as 426.13 U/mg. Also, D500G has a higher optimum temperature of 70 °C and temperature stability, while it has a more neutral pH 4.5 and pH stability. D500G had the maximum enzyme activity at a copper ion concentration of 12 mM. The results of decolorization experiments showed that D500G had a strong overall decolorization ability, with a lower decolorization rate of 18% for methyl orange and a higher decolorization rate of 78% for acid violet. Conclusion Compared with the wild type laccase, the enzyme activity of D500G was significantly increased. At the same time, it has obvious advantages in the decolorization effect of different dyes. Also, the advantages of temperature and pH stability increase its tolerance to the environment of dye wastewater.

Phyllanthus emblica L. (PE) is commonly known as a medicine and food homologous plant, which is abundant in natural products polyphenols. In the present study, polyphenols were extracted from PE fruit by response surface method, and the anti-aging ability was determined. PE fruit polyphenols exhibited strong antioxidant capacities in scavenging free radicals, and anti-cholinesterase ability by inhibition of AChE (IC50 0.2186 ± 0.0416 mg/mL) and BuChE (IC50 0.0542 ± 0.0054 mg/mL) in vitro. Moreover, PE fruit polyphenols showed strong protective effect against the aging process in Caenorhabditis elegans model, including increased thermal resistance, extended lifespan by 18.53% (p < 0.05), reduced activity of AChE by 34.71% and BuChE by 45.38% (p < 0.01). This was accompanied by the enhancement in antioxidant enzymes activity of SOD by 30.74% (p < 0.05) and CAT by 8.42% (p > 0.05), while decrease in MDA level by 36.25% (p < 0.05). These properties might be interrelated with the presence of abundant flavonols and phenolic acids identified by UPLC-ESI-QTOF-MS, such as quercetin, myricetin, ellagic, gallic, and chlorogenic acids, together with their glycosides. The remarkable antioxidant and anti-aging potential of PE fruit polyphenols could be implemented in the food and pharmaceutical industry.

Background Amaranthus hybridus L. is an annual, erect or less commonly ascending herb that is a member of the Amaranthaceae family. Polysaccharides extracted from traditional Chinese medicines may be effective substances with antioxidant activity. Methods In this study, we isolated crude polysaccharides from A. hybridus (AHP-M) using microwave-assisted extraction. Then, the AHP-M was purified by chromatography with DEAE-32 cellulose, and two fractions, AHP-M-1 and AHP-M-2, were obtained. The structural characteristics of AHP-M-1 and AHP-M-2 were investigated, and their antioxidant activities were analyzed in vitro. Results We found that the monosaccharide composition of AHP-M-1 was different from that of AHP-M-2. The molecular weights of AHP-M-1 and AHP-M-2 were 77.625 kDa and 93.325 kDa, respectively. The results showed that the antioxidant activity of AHP-M-2 was better than that of AHP-M-1. For AHP-M-2, the DPPH radical scavenging rate at a concentration of 2 mg/mL was 78.87%, the hydroxyl radical scavenging rate was 39.34%, the superoxide anion radical scavenging rate was 80.2%, and the reduction ability of Fe3+ was approximately 0.90. The total antioxidant capacity per milligram of AHP-M-2 was 6.42, which was higher than that of Vitamin C (Vc). Conclusion The in vitro test indicated that AHP-M-1 and AHP-M-2 have good antioxidant activity, demonstrating that A. hybridus L. polysaccharide has immense potential as a natural antioxidants.

Background Conyza blinii H. Lév is a medicinal plant that has a variety of pharmacological activities, but its study is at a standstill due to the shortage of resources. Method This study utilized the surface sterilization method to isolate endophytic fungi, and they were preliminarily identified by morphology. Flavonoid-producing strains were screened by NaNO2-Al(NO)3 colorimetry and further identified by the ITS sequence. Additionally, we used five antioxidant assays (DPPH, Hydroxyl radical, ABTS, FRAP and T-AOC assays) to systematically evaluate the antioxidant capacity of total flavonoids , and we also determined their antibacterial activity. Results In this study, 21 endophytic fungi were isolated from wild Conyza blinii H. Lév for the first time. There were six flavonoid-producing strains, especially CBL11, whose total flavonoid content reached 50.78 ± 2.4 mg/L. CBL12, CBL12-2 and CBL1-1 all exhibited excellent antioxidant activity. The effect of CBL12 was similar to that of ascorbic acid at low concentrations, and its radical scavenging rates for DPPH and ABTS were 94.56 ± 0.29 % and 99.88 ± 0.27%, respectively, while its IC50 values were only 0.11 ± 0.01 mg/mL and 0.2 ± 0.01 mg/mL. Through LC-MS, we found that CBL12 could produce many high-value flavonoids, such as 3-methoxyflavone, nobiletin, formononetin, scopoletin, and daidzein. Additionally, CBL9 had good antibacterial activity against both gram-positive and gram-negative bacteria. Notably, we obtained the high-yield strains CBL12 and CBL9, which not only had high yields (10.64 ± 1.01 mg/L and 10.17 ± 0.11 mg/L, respectively) but also had excellent biological activity. Hence, the results of this study provide new ideas for endophytic fungi that can be exploited as a source of flavonoids and other medicinal components from Conyza blinii H. Lév. Moreover, this study can serve as a reference for the development of rare medicinal materials.

Abstract Background Tartary buckwheat (Fagopyrum tataricum Gaertn.) is a widely cultivated medicinal and edible crop with excellent economic and nutritional value. The development of tartary buckwheat seeds is a very complex process involving many expression-dependent physiological changes and regulation of a large number of genes and phytohormones. In recent years, the gene regulatory network governing the physiological changes occurring during seed development have received little attention. Results Here, we characterized the seed development of tartary buckwheat using light and electron microscopy and measured phytohormone and nutrient accumulation by using high performance liquid chromatography (HPLC) and by profiling the expression of key genes using RNA sequencing with the support of the tartary buckwheat genome. We first divided the development of tartary buckwheat seed into five stages that include complex changes in development, morphology, physiology and phytohormone levels. At the same time, the contents of phytohormones (gibberellin, indole-3-acetic acid, abscisic acid, and zeatin) and nutrients (rutin, starch, total proteins and soluble sugars) at five stages were determined, and their accumulation patterns in the development of tartary buckwheat seeds were analyzed. Second, gene expression patterns of tartary buckwheat samples were compared during three seed developmental stages (13, 19, and 25 days postanthesis, DPA), and 9 765 differentially expressed genes (DEGs) were identified. We analyzed the overlapping DEGs in different sample combinations and measured 665 DEGs in the three samples. Furthermore, expression patterns of DEGs related to phytohormones, flavonoids, starch, and storage proteins were analyzed. Third, we noted the correlation between the trait (physiological changes, nutrient changes) and metabolites during seed development, and discussed the key genes that might be involved in the synthesis and degradation of each of them. Conclusion We provided abundant genomic resources for tartary buckwheat and Polygonaceae communities and revealed novel molecular insights into the correlations between the physiological changes and seed development of tartary buckwheat.

Background Amaranthus hybridus L. is an annual herb that belongs to the Amaranthceae family, a type of multi-purpose grain, vegetable and feed crop that has received considerable attention due to its great economic value. However, the composition of polysaccharides from A. hybridus has rarely been previously reported. Methods In this study, the aboveground part of A. hybridus was used as material and polysaccharides were isolated by the hot water extraction method. Two acidic polysaccharides were isolated and purified by the Sevage method and diethylaminoethyl cellulose-32 column chromatography. Results Two acidic polysaccharides were obtained from A. hybridus: AHP-H-1 and AHP-H-2. There were significant differences between the monosaccharide content from each sample according to gas chromatography-mass spectrometer. AHP-H-2 had higher antioxidant activity in vitro than AHP-H-1. The 2,2-diphenyl-1-picrylhydrazyl radical scavenging rate of two mg/mL AHP-H-2 was 80%, its hydroxyl radical scavenging rate was approximately 48.5%, its superoxide anion radical scavenging rate was 85.3% and its reduction ability of Fe3+ was approximately 0.92. The total antioxidant capacity of each milligram of AHP-H-2 was 6.5, which was higher than ascorbic acid. Conclusion The results of the study promote the effective use of A. hybridus and provide a theoretical basis for its development.

Quantitative real-time reverse transcriptase polymerase chain reaction is a sensitive technique for quantifying gene expression levels. By implementing three distinct algorithms (geNorm, normFinder and BestKeeper), we have validated the stability of the expression of seven candidate reference genes in tartary buckwheat, including FtSAND, FtCACS, FtExpressed1, FtGAPDH, FtActin, FtEF-1a and FtH3. In this study, the results indicated that FtCACS and FtSAND were the best reference genes for ‘abiotic cotyledons’, FtExpressed1 and FtEF-1α were the best reference genes for aluminium treatment, FtCACS and FtExpressed1 performed the best for the immature seed stage, FtCACS was best for the abiotic treatment, and FtH3 appeared to be the most suitable reference gene for the abiotic treatment in hypocotyls and all samples in this study. In contrast, FtActin and FtGAPDH are unsuitable genes. Our findings offer additional stable reference genes for gene expression research on tartary buckwheat at the immature seed stage and under abiotic treatment.

The thick and hard fruit shell of Fagopyrum tataricum (F. tataricum) represents a processing bottleneck. At the same time, soil salinization is one of the main problems faced by modern agricultural production. Bioinformatic analysis indicated that the F. tataricum transcription factor FtNAC16 could regulate the hull cracking of F. tataricum, and the function of this transcription factor was verified by genetic transformation of Arabidopsis thaliana (A. thaliana). Phenotypic observations of the wild-type (WT), OE-FtNAC16, nst1/3 and nst1/3-FtNAC16 plant lines confirmed that FtNAC16 negatively regulated pod cracking by downregulating lignin synthesis. Under salt stress, several physiological indicators (POD, GSH, Pro and MDA) were measured, A. thaliana leaves were stained with NBT (Nitroblue Tetrazolium) and DAB (3,3’-diaminobenzidine), and all genes encoding enzymes in the lignin synthesis pathway were analyzed. These experiments confirmed that FtNAC16 increased plant sensitivity by reducing the lignin content or changing the proportions of the lignin monomer. The results of this study may help to elucidate the possible association between changes in lignin monomer synthesis and salt stress and may also contribute to fully understanding the effects of FtNAC16 on plant growth and development, particularly regarding fruit pod cracking and environmental adaptability. In future studies, it may be useful to obtain suitable cracking varieties and salt-tolerant crops through molecular breeding.

Wild emmer wheat (Triticum dicoccoides), the tetraploid progenitor of cultivated wheats, is indigenous to the Near East Fertile Crescent. An important center of distribution is found today in and around the catchment area of the upper Jordan Valley in Israel and surrounding regions. In the current study, the field stripe rust resistance and morphological traits were analyzed using 98 sample accessions that represented the geographical distribution of wild emmer populations in Israel and its vicinity. The resistance tests at two field locations revealed that the majority of the wild emmer accessions possess quantitative resistance against stripe rust. This could be due to the high frequency of Yr36 in the wild emmer populations. The identification of potentially novel stripe rust resistance in this set of germplasm is highly significant. In total, 11 morphological traits were examined in this study. Wide range of natural variation was revealed in the tested morphological traits. Most of the morphological traits had significant correlations with climate variables, indicating that the local environmental conditions have a profound effect on shaping the genetic structure of wild emmer wheat. Our results suggest that wild emmer wheat has the enormous potential to improve stripe rust resistance and various important agronomical traits in wheat.

Auxin signaling plays an important role in plant growth and development. It responds to various developmental and environmental events, such as embryogenesis, organogenesis, shoot elongation, tropical growth, lateral root formation, flower and fruit development, tissue and organ architecture, and vascular differentiation. However, there has been little research on the Auxin Response Factor (ARF) genes of tartary buckwheat (Fagopyrum tataricum), an important edible and medicinal crop. The recent publication of the whole-genome sequence of tartary buckwheat enables us to study the tissue and expression profile of the FtARF gene on a genome-wide basis. In this study, 20 ARF (FtARF) genes were identified and renamed according to the chromosomal distribution of the FtARF genes. The results showed that the FtARF genes belonged to the related sister pair, and the chromosomal map showed that the duplication of FtARFs was related to the duplication of the chromosome blocks. The duplication of some FtARF genes shows conserved intron/exon structure, which is different from other genes, suggesting that the function of these genes may be diverse. Real-time quantitative PCR analysis exhibited distinct expression patterns of FtARF genes in various tissues and in response to exogenous auxin during fruit development. In this study, 20 FtARF genes were identified, and the structure, evolution, and expression patterns of the proteins were studied. This systematic analysis laid a foundation for the further study of the functional characteristics of the ARF genes and for the improvement of tartary buckwheat crops.

Tartary buckwheat is a type of cultivated medicinal and edible crop with good economic and nutritional value. Knowledge of the final fruit size of buckwheat is critical to its yield increase. In this study, the fruit development of two species of Tartary buckwheat in the Polygonaceae was analyzed. During fruit development, the size/weight, the contents of auxin (AUX)/abscisic acid (ABA), the number of cells, and the changes of embryo were measured and observed; and the two fruit materials were compared to determine the related mechanisms that affected fruit size and the potential factors that regulated the final fruit size. The early events during embryogenesis greatly influenced the final fruit size, and the difference in fruit growth was primarily due to the difference in the number of cells, implicating the effect of cell division rate. Based on our observations and recent reports, the balance of AUX and ABA might be the key factor that regulated the cell division rate. They induced the response of auxin response factor 2 (FtARF2) and downstream small auxin upstream RNA (FtSAURs) through hormone signaling pathway to regulate the fruit size of Tartary buckwheat. Further, through the induction of fruit expansion by exogenous auxin, FtARF2b was significantly downregulated. The FtARF2b is a potential target for molecular breeding or gene editing.