Integrated Metabolomics and Transcriptomics Analysis of Flavonoid Biosynthesis Pathway in Polygonatum cyrtonema Hua.

Flavonoids, a class of phenolic compounds, are one of the main functional components and have a wide range of molecular structures and biological activities in Polygonatum. A few of them, including homoisoflavonoids, chalcones, isoflavones, and flavones, were identified in Polygonatum and displayed a wide range of powerful biological activities, such as anti-cancer, anti-viral, and blood sugar regulation. However, few studies have systematically been published on the flavonoid biosynthesis pathway in Polygonatum cyrtonema Hua. Therefore, in the present study, a combined transcriptome and metabolome analysis was performed on the leaf, stem, rhizome, and root tissues of P. cyrtonema to uncover the synthesis pathway of flavonoids and to identify key regulatory genes. Flavonoid-targeted metabolomics detected a total of 65 active substances from four different tissues, among which 49 substances were first study to identify in Polygonatum, and 38 substances were flavonoids. A total of 19 differentially accumulated metabolites (DAMs) (five flavonols, three flavones, two dihydrochalcones, two flavanones, one flavanol, five phenylpropanoids, and one coumarin) were finally screened by KEGG enrichment analysis. Transcriptome analysis indicated that a total of 222 unigenes encoding 28 enzymes were annotated into three flavonoid biosynthesis pathways, which were "phenylpropanoid biosynthesis", "flavonoid biosynthesis", and "flavone and flavonol biosynthesis". The combined analysis of the metabolome and transcriptome revealed that 37 differentially expressed genes (DEGs) encoding 11 enzymes (C4H, PAL, 4CL, CHS, CHI, F3H, DFR, LAR, ANR, FNS, FLS) and 19 DAMs were more likely to be regulated in the flavonoid biosynthesis pathway. The expression of 11 DEGs was validated by qRT-PCR, resulting in good agreement with the RNA-Seq. Our studies provide a theoretical basis for further elucidating the flavonoid biosynthesis pathway in Polygonatum.

Genome-wide analysis of the HSP20 gene family and its response to heat and drought stress in Coix (Coix lacryma-jobi L.).

BACKGROUND: Heat shock protein 20 (HSP20) is a member of the heat stress-related protein family, which plays critical roles in plant growth, development, and response to abiotic stresses. Although many HSP20 genes have been associated with heat stress in numerous types of plants, little is known about the details of the HSP20 gene family in Coix. To investigate the mechanisms of the ClHSP20 response to heat and drought stresses, the ClHSP20 gene family in Coix was identified and characterized based on genome-wide analysis. RESULTS: A total of 32 putative ClHSP20 genes were identified and characterized in Coix. Phylogenetic analysis indicated that ClHSP20s were grouped into 11 subfamilies. The duplicated event analysis demonstrated that tandem duplication and segment duplication events played crucial roles in promoting the expansion of the ClHSP20 gene family. Synteny analysis showed that Coix shared the highest homology in 36 HSP20 gene pairs with wheat, followed by 22, 19, 15, and 15 homologous gene pairs with maize, sorghum, barley, and rice, respectively. The expression profile analysis showed that almost all ClHSP20 genes had different expression levels in at least one tissue. Furthermore, 22 of the 32 ClHSP20 genes responded to heat stress, with 11 ClHSP20 genes being significantly upregulated and 11 ClHSP20 genes being significantly downregulated. Furthermore, 13 of the 32 ClHSP20 genes responded to drought stress, with 6 ClHSP20 genes being significantly upregulated and 5 ClHSP20 genes being significantly downregulated. CONCLUSIONS: Thirty-two ClHSP20 genes were identified and characterized in the genome of Coix. Tandem and segmental duplication were identified as having caused the expansion of the ClHSP20 gene family. The expression patterns of the ClHSP20 genes suggested that they play a critical role in growth, development, and response to heat and drought stress. The current study provides a theoretical basis for further research on ClHSP20s and will facilitate the functional characterization of ClHSP20 genes.

Assembly and phylogenetic analysis of the mitochondrial genome of endangered medicinal plant Huperzia crispata.

Huperzia crispata is a traditional Chinese herb plant and has attracted special attention in recent years for its products Hup A can serve as an acetylcholinesterase inhibitor (AChEI). Although the chloroplast (cp) genome of H. crispata has been studied, there are no reports regarding the Huperzia mitochondrial (mt) genome since the previously reported H. squarrosa has been revised as Phlegmariurus squarrosus. The mt genome of H. crispata was sequenced using a combination of long-read nanopore and Illumina sequencing platforms. The entire H. crispata mt genome was assembled in a circular with a length of 412,594 bp and a total of 91 genes, including 45 tRNAs, 6 rRNAs, 37 protein-coding genes (PCGs), and 3 pseudogenes. Notably, the rps8 gene was present in P. squarrosus and a pseudogene rps8 was presented in H. crispata, which was lacking in most of Pteridophyta and Gymnospermae. Intron-encoded maturase (mat-atp9i85 and mat-cobi787) genes were present in H. crispata and P. squarrosus, but lost in other examined lycophytes, ferns, and Gymnospermae plants. Collinearity analysis showed that the mt genome of H. crispata and P. squarrossus is highly conservative compared to other ferns. Relative synonymous codon usage (RSCU) analysis showed that the amino acids most frequently found were phenylalanine (Phe) (4.77%), isoleucine (Ile) (4.71%), lysine (Lys) (4.26%), while arginine (Arg) (0.32%), and histidine (His) (0.42%) were rarely found. Simple sequence repeats (SSR) analysis revealed that a total of 114 SSRs were identified in the mt genome of H. crispata and account for 0.35% of the whole mt genome. Monomer repeats were the majority types of SSRs and represent 91.89% of the total SSRs. In addition, a total of 1948 interspersed repeats (158 forward, 147 palindromic, and 5 reverse repeats) with a length ranging from 30 bp to 14,945 bp were identified in the H. crispata mt genome and the 30-39-bp repeats were the most abundant type. Gene transfer analysis indicated that a total of 12 homologous fragments were discovered between the cp and mt genomes of H. crispata, accounting for 0.93% and 2.48% of the total cp and mt genomes, respectively. The phylogenetic trees revealed that H. crispata was the sister of P. squarrosus. The Ka/Ks analysis results suggested that most PCGs, except atp6 gene, were subject to purification selection during evolution. Our study provides extensive information on the features of the H. crispata mt genome and will help unravel evolutionary relationships, and molecular identification within lycophytes.

Diversity of endophytic fungal community in Huperzia serrata from different ecological areas and their correlation with Hup A content.

BACKGROUND: Huperzine A (Hup A) has attracted considerable attention as an effective therapeutic candidate drug used to treat Alzheimer's disease. Whereas, the production of Hup A from wild plants faced a major challenge, which is the wild Huperzia Serrata harbor a low Hup A content, has a long-life cycle, and has a small yield. At present, several reports showed that Hup A is produced by various endophytic fungal strains isolated from H. serrata, thereby providing an alternative method to produce the compound and reduce the consumption of this rare and endangered plant. However, till now, very few comprehensive studies are available on the biological diversity and structural composition of endophytic fungi and the effects of endophytic fungi on the Hup A accumulation in H. serrata. RESULTS: In this research, the composition and diversity of fungal communities in H. serrata were deciphered based on high-throughput sequencing technology of fungal internal transcribed spacer regions2 (ITS2). The correlation between endophytic fungal community and Hup A content was also investigated. Results revealed that the richness and the diversity of endophytic fungi in H. serrata was various according to different tissues and different ecological areas. The endophytic fungal communities of H. serrata exhibit species-specific, ecological-specific, and tissue-specific characteristics. There are 6 genera (Ascomycota_unclassified, Cyphellophora, Fungi_unclassified, Sporobolomyces, and Trichomeriaceae_unclassified) were significantly positively correlated with Hup A content in all two areas, whereas, there are 6 genera (Auricularia, Cladophialophora, Cryptococcus, Mortierella, and Mycena) were significantly negatively correlated with Hup A content of in all two areas. CONCLUSIONS: This study indicated a different composition and diverse endophytic fungal communities in H. serrata from different organs and ecological areas. The current study will provide the realistic basis and theoretical significance for understanding the biological diversity and structural composition of endophytic fungal communities in H. serrata, as well as providing novel insights into the interaction between endophytic fungi and Hup A content.

Structure characterization and bioactivity of neutral polysaccharides from different sources of Polygonatum Mill.

Polygonati rhizoma (PR), a traditional medical and edible product, is rich in polysaccharides and exhibits physiological activity, including antioxidant, hypoglycemic and hypolipidemic properties. Neutral polysaccharides have been reported to be one of the main active ingredients of Polygonatum, with many of these fractions being responsible for the biological activity. This behavior was shown to be closely connected to the chemical structure, monosaccharide composition, and glycosidic bond type. There are few reports on the chemical constituents of the neutral polysaccharides from different sources of PR. In this study, neutral polysaccharides of PR from four different regions of China (Chun'an (Zhejiang), Xixia (Henan), Danfeng (Shanxi), and Pan'an (Zhejiang)), named CAZJ, XXHN, DFSX, and PAZJ, respectively, were isolated by anion-exchange and gel-permeation chromatography. Structures of the four polysaccharides were investigated. The results showed that all of them were mainly glucose and mannose, while the monosaccharide composition and content of polysaccharides from different sources varied. The molecular weights of CAZJ, XXHN, DFSX, and PAZJ were 14.119, 22.352, 18.127, and 15.699 kDa, respectively. Infrared spectra illustrated the existence of α-glycosidic bond and ß-glycosidic bond in the polysaccharides. CAZJ, XXHN, and DFSX possessed a pyranose ring structure, whereas PAZJ had a furanose ring structure. Congo red test indicated that XXHN, DFSX, and PAZJ had a triple-helix structure. X-ray diffraction showed that the polysaccharides consisted of crystalline and amorphous regions. All four polysaccharides exhibited different degrees of antioxidant and hypoglycemic activities with a dose-dependent manner in the 1.0-10.0 mg/mL concentration range. Correlation analysis revealed that the bioactivities of polysaccharides was significantly related to monosaccharide composition, uronic acid, and protein content. The results suggested that neutral polysaccharides could be used as potential natural antioxidants and hypoglycemic agents for functional and nutraceutical applications.

The complete chloroplast genome of the medical plant Huperzia crispata from the Huperziaceae family: structure, comparative analysis, and phylogenetic relationships.

BACKGROUND: Huperzia crispata, belonging to the Huperziaceae family, is one of the most essential resources of huperzine A for candidate drugs to treat Alzheimer's diseases. However, there is very limited information about H. crispat, and its taxonomic status and interspecific relationships between Huperzia species are still unclear. To investigate the taxonomic classification of Huperzia species and identify species discrimination markers, the complete chloroplast (cp) genome of H. crispata was sequenced and characterized for the first time. METHODS AND RESULTS: Total genomic DNA was isolated and sequenced using the next-generation Illumina NovaSeq 6000 platform. The data were filtered, assembled and annotated by a series software and web service. The results were as follows: the cp genome of H. crispata was 154,320 bp long with a large single-copy (LSC) region of 104,023 bp, a small single-copy (SSC) region of 19,671 bp, and a pair of inverted repeat (IRa and IRb) regions of 15,313 bp. A total of 131 genes, including 87 protein-coding genes, 36 transfer RNA genes (tRNAs), and eight ribosome RNA genes (rRNAs), were annotated in the cp genome. The contraction and expansion of the inverted repeat (IR) regions were relatively conserved in the Huperzia genus. Codon usage bias analysis showed that the encoding rate at the 3-end of codon A/T (74.34%) was significantly higher than that of C/G (25.66%). A total of 8 hotspot loci with high Pi values (> 0.06) were identified in the four Huperzia species based on nucleic acid diversity analysis. Ka/Ks selective pressure analysis demonstrated that the cemA gene is the most common gene undergoing positive selection among Huperzia. In addition, a total of 261 simple sequence repeats and 179 interspersed repeats were identified in the cp genome. Phylogenetic tree analysis based on the complete protein sequences of 23 related species of H. crispata indicated that H. serrata f. longipetiolata is a sister of H. crispata, suggesting that H. serrata f. longipetiolata and H. crispata are more closely related than H. serrata and H. lucidula. CONCLUSIONS: The results strongly supported that H. crispata was more closely related to H. serrata f. longipetiolata than to H. serrata and H. lucidula within the Huperzia genus. The outcome provided important information for the phylogenetic analysis of the subsequent specific molecular species identification in Huperzia. The present results will provide valuable information for further research into the classification, phylogeny and species identification of Huperzia plants.

Transcriptome Analysis of Different Sections of Rhizome in Polygonatum sibiricum Red. and Mining Putative Genes Participate in Polysaccharide Biosynthesis.

As a traditional Chinese herb, the rhizomes of Polygonatum sibiricum Red. are rich in various compounds which have plenty of pharmacological applications and biological activities. Among them, Polygonatum sibiricum polysaccharides (PSP) are the main active ingredients and exhibit a broad range of pharmacological. Based on previous researches, identifying genes involved in PSP biosynthesis will help delineate such pathway at the molecular level. In that case, we performed RNA sequencing analysis for two sections of P. sibiricum Red.'s rhizomes significantly different in PSP content. A total of 435,858 unigenes were obtained by assembling transcripts from both sections and 29,548 (6.77%) ones were annotated in all seven public databases. Analyzing count data of RNA-seq, 13,460 differential expression genes (DEGs) between two sections of rhizomes were acquired. After DEGs were mapped to KEGG databases, twelve represented KEGG pathways related to PSP biosynthesis were summed up. And most DEGs were assigned to the pathway of "Starch and sucrose metabolism". Finally, seventeen candidate genes whose expression levels were related to the polysaccharide content, were considered involving PSP biosynthesis in P. sibiricum Red. The present study lays a foundation of researching the molecular mechanisms of PSP biosynthesis.

Characterization of the sdw1 semi-dwarf gene in barley.

BACKGROUND: The dwarfing gene sdw1 has been widely used throughout the world to develop commercial barley varieties. There are at least four different alleles at the sdw1 locus. RESULTS: Mutations in the gibberellin 20-oxidase gene (HvGA20ox2) resulted in multiple alleles at the sdw1 locus. The sdw1.d allele from Diamant is due to a 7-bp deletion in exon 1, while the sdw1.c allele from Abed Denso has 1-bp deletion and a 4-bp insertion in the 5' untranslated region. The sdw1.a allele from Jotun resulted from a total deletion of the HvGA20ox2 gene. The structural changes result in lower gene expression in sdw1.d and lack of expression in sdw1.a. There are three HvGA20ox genes in the barley genome. The partial or total loss of function of the HvGA20ox2 gene could be compensated by enhanced expression of its homolog HvGA20ox1and HvGA20ox3. A diagnostic molecular marker was developed to differentiate between the wild-type, sdw1.d and sdw1.a alleles and another molecular marker for differentiation of sdw1.c and sdw1.a. The markers were further tested in 197 barley varieties, out of which 28 had the sdw1.d allele and two varieties the sdw1.a allele. To date, the sdw1.d and sdw1.a alleles have only been detected in the modern barley varieties and lines. CONCLUSIONS: The results provided further proof that the gibberellin 20-oxidase gene (HvGA20ox2) is the functional gene of the barley sdw1 mutants. Different deletions resulted in different functional alleles for different breeding purposes. Truncated protein could maintain partial function. Partial or total loss of function of the HvGA20ox2 gene could be compensated by enhanced expression of its homolog HvGA20ox1 and HvGA20ox3.

Marker development using SLAF-seq and whole-genome shotgun strategy to fine-map the semi-dwarf gene ari-e in barley.

BACKGROUND: Barley semi-dwarf genes have been extensively explored and widely used in barley breeding programs. The semi-dwarf gene ari-e from Golden Promise is an important gene associated with some agronomic traits and salt tolerance. While ari-e has been mapped on barley chromosome 5H using traditional markers and next-generation sequencing technologies, it has not yet been finely located on this chromosome. RESULTS: We integrated two methods to develop molecular markers for fine-mapping the semi-dwarf gene ari-e: (1) specific-length amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) to develop SNP markers, and (2) the whole-genome shotgun sequence to develop InDels. Both SNP and InDel markers were developed in the target region and used for fine-mapping the ari-e gene. Linkage analysis showed that ari-e co-segregated with marker InDel-17 and was delimited by two markers (InDel-16 and DGSNP21) spanning 6.8 cM in the doubled haploid (DH) Dash × VB9104 population. The genetic position of ari-e was further confirmed in the Hindmarsh × W1 DH population which was located between InDel-7 and InDel-17. As a result, the overlapping region of the two mapping populations flanked by InDel-16 and InDel-17 was defined as the candidate region spanning 0.58 Mb on the POPSEQ physical map. CONCLUSIONS: The current study demonstrated the SLAF-seq for SNP discovery and whole-genome shotgun sequencing for InDel development as an efficient approach to map complex genomic region for isolation of functional gene. The ari-e gene was fine mapped from 10 Mb to 0.58 Mb interval.

Molecular characterization and functional analysis of barley semi-dwarf mutant Riso no. 9265.

BACKGROUND: sdw1/denso is one of the most important and useful semi-dwarf genes in barley breeding. At least four sdw1/denso alleles have been reported and HvGA20ox 2 is considered as the candidate gene. Up to date, results of studies have not univocally proven the genetic relationship between sdw1/denso and HvGA20ox 2 . RESULTS: In the present study, a complete deletion of Morex_contig_40861 including both HvGA20ox 2 and Mloc_56463 genes was identified at the sdw1 locus from a semi-dwarf mutant Riso no. 9265. Expression of the genes encoding gibberellin biosynthesis (HvGA20ox 1 and HvGA3ox 2 ) were increased in the mutant compared to the wild type Bomi, while the expression of GA catabolic gene HvGA2ox 3 was decreased. Over-expression of HvGA20ox 2 could rescue the semi-dwarf phenotype and increase GAs concentration. CONCLUSIONS: We confirmed that a GA biosynthetic enzyme HvGA20ox2, acted as GA 20-oxidase, is the functional gene for the sdw1/denso semi-dwarfism. Lose of HvGA20ox 2 is partially compensated by HvGA20ox 1 and further feedback is regulated by gibberellin. We also deduced that the sdw1/denso allele itself affects later heading owing to its reduced endogenous GAs concentration.

Mapping a major QTL for malt extract of barley from a cross between TX9425 × Naso Nijo.

KEY MESSAGE: One major QTL-controlling malt extract was identified on 2H, based on the data from four different environments and a large number of DH lines, determining 48% of phenotypic variation. This QTL is of a high value for marker-assisted selection. Improving malting quality traits is one of the major breeding objectives for barley breeding programmes. Among different quality traits, malt extract is one of the most important, determining the yield of beer production. The use of molecular markers linked to loci affecting the quality traits can greatly improve selection efficiency. However, the discovery of closely linked markers relies on not only the availability of the loci, but the accuracy of phenotyping. In this experiment, 188 doubled-haploid lines derived from the cross between a Japanese malting barley and a Chinese feed barley were grown in four different environments (two sites × 2 years). Different quality traits were determined and used to map QTL for these traits. Several QTLs were identified for different quality traits. One major QTL-controlling malt extract was identified on 2H and determined 48% of phenotypic variation with the closest marker of GBM1121. This QTL was consistently expressed in all four environments and is of a high value for marker-assisted selection in malting barley breeding.

The accumulation of active ingredients of Polygonatum cyrtonema Hua is associated with soil characteristics and bacterial community.

Introduction: With the increasing demand for health products derived from Polygonati rhizoma (PR), people begin to artificially plant Polygonatum cyrtonema Hua (P. cyrtonema) in the middle and lower reaches of the Yangtze River. To promote P. cyrtonema cultivation and increase farmers' income, efforts are needed to understand the ways to obtain high-quality PR under artificial cultivation conditions. Methods: Rhizomes of artificial planting P. cyrtonema and rhizosphere soils were collected across five regions in Zhejiang Province, China. Subsequently, the contents of the main active ingredients of P. cyrtonema and soil properties were analyzed, and both rhizosphere and endophytic bacteria of P. cyrtonema were detected by 16S rDNA sequencing. The relationship between the active ingredients and soil properties, and the dominant bacteria were investigated by correlation analysis. Results: The content of active ingredients of P. cyrtonema from the five regions varied significantly, especially polysaccharides and saponins. High-throughput sequencing demonstrated that Proteobacteria was the dominant bacterial phylum in all samples, and Burkholderia-Caballeronia-Paraburkholderia was the main endophytic bacterial genus in rhizome. In addition, the bacterial diversity and richness of rhizosphere soil samples were higher than those of rhizome samples. Soil physicochemical properties and enzyme activities were significantly different across regions, leading to notable variations in the community structures of rhizosphere and endophytic bacteria. Redundancy analysis (RDA) displayed that pH and urease (UE) were the major factors altering shifting rhizosphere bacteria community structure. Moreover, the composition and diversity of rhizome endophytic bacteria were principally affected by both soil physicochemical properties and soil enzyme activities. Soil properties and bacteria from rhizosphere soil and rhizome had a considerable impact on certain active ingredients in P. cyrtonema under artificial cultivation conditions after Pearson correlation analysis. Polysaccharides were significantly correlated with nutrient-rich soil and endophytic bacteria, such as Burkholderia-Caballeronia-Paraburkholderia, Pseudomonas, Ralstonia, and Bacillus. However, flavonoids were associated with nutrient-poor soil. Saponins were positively correlated with OM and available phosphorous (AP) and were significantly negatively affected by rhizosphere bacterial communities. Conclusion: The study demonstrated that bacterial microorganisms were involved in the accumulation of active ingredients of P. cyrtonema together with soil physicochemical properties and enzyme activities, which provided a theoretical basis for the scientific and effective artificial cultivation of high-quality P. cyrtonema.

Comprehensive Evaluation of the Nutritional Properties of Different Germplasms of Polygonatum cyrtonema Hua.

Polygonatum cyrtonema Hua, an edible resource and medical material, is mainly consumed as a food in China. However, few published studies have comprehensively assessed its nutritional components. In this study, the proximate, carbohydrate, and dietary fiber contents as well as the mineral, vitamin, and amino acid compositions of five sources of P. cyrtomena grown in Yuhang district, Hangzhou city, Zhejiang province, were investigated. The nutritional profile of the five germplasms was investigated using analytical chemistry methods. All germplasms had a low starch content and contained greater amounts of carbohydrates (23.25-34.29%), protein (2.96-5.40%), Ca (195.08-282.08 mg/100 g), Fe (29.68-59.37 mg/100 g), and vitamin C (60.49-149.86 mg/100 g) in comparison to ginger, yam, and potatoes. The polysaccharide content ranged from 16.92% to 28.48%, representing the main source of carbohydrates. Fructose, a desirable sweetener, was the most abundant monosaccharide, representing 1.06% to 4.88% of the content. P. cyrtonema was found to be high in dietary fiber, with pectin and resistant starch being the major soluble components and hemicellulose being the dominant insoluble dietary fiber. A correlation analysis (CA) revealed significant correlations for the carbohydrate components and dietary fiber fractions with other nutrients. A principal component analysis (PCA) identified significant differences between the nutritional characteristics of the five germplasms, with Huanggang having the highest comprehensive quality scores. Moreover, ten nutrient components were selected as potential indicators that could be used to further evaluate the nutritional quality of P. cyrtomena. Our results demonstrate the rich nutrient composition and characteristics of P. cyrtonema and provide a valuable reference for the future development and utilization of Polygonatum.

Succession of endophytic fungi and rhizosphere soil fungi and their correlation with secondary metabolites in Fagopyrum dibotrys.

Golden buckwheat (Fagopyrum dibotrys, also known as F. acutatum) is a traditional edible herbal medicinal plant with a large number of secondary metabolites and is considered to be a source of therapeutic compounds. Different ecological environments have a significant impact on their compound content and medicinal effects. However, little is known about the interactions between soil physicochemical properties, the rhizosphere, endophytic fungal communities, and secondary metabolites in F. dibotrys. In this study, the rhizosphere soil and endophytic fungal communities of F. dibotrys in five different ecological regions in China were identified based on high-throughput sequencing methods. The correlations between soil physicochemical properties, active components (total saponins, total flavonoids, proanthocyanidin, and epicatechin), and endophytic and rhizosphere soil fungi of F. dibotrys were analyzed. The results showed that soil pH, soil N, OM, and P were significantly correlated with the active components of F. dibotrys. Among them, epicatechin, proanthocyanidin, and total saponins were significantly positively correlated with soil pH, while proanthocyanidin content was significantly positively correlated with STN, SAN, and OM in soil, and total flavone content was significantly positively correlated with P in soil. In soil microbes, Mortierella, Trechispora, Exophiala, Ascomycota_unclassified, Auricularia, Plectosphaerella, Mycena, Fungi_unclassified, Agaricomycetes_unclassified, Coprinellus, and Pseudaleuria were significantly related to key secondary metabolites of F. dibotrys. Diaporthe and Meripilaceae_unclassified were significantly related to key secondary metabolites in the rhizome. This study presents a new opportunity to deeply understand soil-plant-fungal symbioses and secondary metabolites in F. dibotrys, as well as provides a scientific basis for using biological fertilization strategies to improve the quality of F. dibotrys.

Genome-wide investigation of ARF transcription factor gene family and its responses to abiotic stress in Coix (Coix lacryma-jobi L.).

Auxin response factor (ARF) is an important transcription factor that regulates the expression of auxin-responsive genes by direct binding to their promoters, which play a central role in plant growth, development, and response to abiotic stresses. The availability of the entire Coix (Coix lacryma-jobi L.) genome sequence provides an opportunity to investigate the characteristics and evolutionary history of the ARF gene family in this medicine and food homology plant for the first time. In this study, a total of 27 ClARF genes were identified based on the genome-wide sequence of Coix. Twenty-four of the 27 ClARF genes were unevenly distributed on 8 chromosomes except Chr 4 and 10, and the remaining three genes (ClARF25-27) were not assigned to any chromosome. Most of the ClARF proteins were predicted to be localized to the nucleus, except ClARF24, which was localized to both the plasma membrane and nucleus. Twenty-seven ClARFs were clustered into six subgroups based on the phylogenetic analysis. Duplication analysis showed that segmental duplication, rather than tandem duplications promoting the expansion of the ClARF gene family. Synteny analysis showed that purifying selection might have been a primary driving force in the development of the ARF gene family in Coix and other investigated cereal plants. The prediction of the cis element of the promoter showed that 27 ClARF genes contain several stress response elements, suggesting that ClARFs might be involved in the abiotic stress response. Expression profile analysis shows that 27 ClARF genes were all expressed in the root, shoot, leaf, kernel, glume, and male flower of Coix with varying expression levels. Furthermore, qRT-PCR analyses revealed that the majority of ClARFs members were upregulated or downregulated in response to hormone treatment and abiotic stress. The current study expands our understanding of the functional roles of ClARFs in stress responses and provides basic information for the ClARF genes.

SSR Loci Analysis in Transcriptome and Molecular Marker Development in Polygonatum sibiricum.

To study the SSR loci information and develop molecular markers, a total of 435,858 unigenes in transcriptome of Polygonatum sibiricum were used to explore SSR. The distribution frequency of SSR and the basic characteristics of repeat motifs were analyzed using MISA software, and SSR primers were designed by Primer 3.0 software and then validated by PCR. Moreover, the gene function analysis of SSR Unigene was obtained by Blast. The results showed that 112,728 SSR loci were found in the transcriptome of Polygonatum sibiricum, which distributed in 435,858 unigenes with a distribution frequency of 25.86%. Mo-nucleotide and Di-nucleotide repeat were the main types, accounted for 83.83% of all SSRs. The repeat motifs of A/T and AC/GT were the predominant repeat types of Mo-nucleotide and Di-nucleotide, respectively. A total of 113,305 pairs of SSR primers with the potential to produce polymorphism were designed for maker development. One hundred and fifty-four of the 500 randomly selected primers not only produced fragments with expected molecular size but also had high polymorphism, which could accurately separate the tested varieties. The gene function of unigenes containing SSR was mostly related to the molecular function of Polygonatum sibiricum. The SSR markers in transcriptome of Polygonatum sibiricum show rich type, strong specificity, and high potential of polymorphism, which will benefit the candidate gene mining and marker-assisted breeding. The developed markers can also provide technical methods for molecular identification of intraspecific species of Polygonatum Mill. and maker-assisted breeding of superior varieties of Polygonatum Mill.

Cloning and Characterization of the Gene Encoding HMGS Synthase in Polygonatum sibiricum.

The saponins of Polygonatum sibiricum had many pharmacological activities such as antitumor, antioxidation, and blood sugar lowering, which were synthesized by two pathways: mevalonate (MVA) and methylerythritol phosphate (MEP). 3-Hydroxy-3-methylglutaryl coenzyme A synthase (HMGS) was the key enzyme in the MVA synthesis pathway, and its expression level may affect the accumulation of saponins which were the main active ingredients of P. sibiricum. In this study, we successfully cloned HMGS1 and HMGS2 from P. sibiricum and their sequence similarity was 93.71% with 89 different sites. The multiple sequence alignment results indicated that the N-terminal sequences of HMGS were conserved. Phylogenetic analysis showed that P. sibiricum, A. officinalis, N. tazetta, D. nobile, and other relatives had a common evolutionary ancestor. The expression levels of both HMGSs and the total saponin content in different tissues revealed that HMGS expression in rhizomes was positively correlated with total saponin content. Further study of the abiotic stress effect of Methyl Jasmonate (MeJA) demonstrated that the expression of HMGS1 and HMGS2 genes was induced by MeJA, peaked at 24 h, and fell by 48 h. Our present findings would provide a blueprint for future studies of HMGS and its role in triterpenoid biosynthesis in P. sibiricum.

Advances in Mechanism Research on Polygonatum in Prevention and Treatment of Diabetes.

Diabetes mellitus is a fast-growing disease with a major influence on people's quality of life. Oral hypoglycemic drugs and insulin are currently the main effective drugs in the treatment of diabetes, but chronic consumption of these drugs has certain side effects. Polysaccharides, saponins, flavonoids, and phenolics are the primary secondary metabolites isolated from the rhizomes of Polygonatum sibiricum Redouté [Asparagaceae], Polygonatum kingianum Collett & Hemsl [Asparagaceae], or Polygonatum cyrtonema Hua [Asparagaceae], which have attracted much more attention owing to their unique therapeutic role in the treatment and prevention of diabetes. However, the research on the mechanism of these three Polygonatum spp. in diabetes has not been reviewed. This review provides a summary of the research progress of three Polygonatum spp. on diabetes and its complications, reveals the potential antidiabetic mechanism of three Polygonatum spp., and discusses the effect of different processed products of three Polygonatum spp. in treating diabetes, for the sake of a thorough understanding of its effects on the prevention and treatment of diabetes and diabetes complications.

Expression level of a gibberellin 20-oxidase gene is associated with multiple agronomic and quality traits in barley.

The use of dwarfing genes has resulted in the most significant improvements in yield and adaptation in cereal crops. The allelic dwarfing gene sdw1/denso has been used throughout the world to develop commercial barley varieties. The sdw1 gene has never been used successfully for malting barley, but only for a large number of feed varieties. One of the gibberellin 20-oxidase genes (Hv20ox2) was identified as the candidate gene for sdw1/denso. Semi-quantitative real-time RT-PCR revealed that Hv20ox2 was expressed at different levels in various organs of barley. Transcriptional levels were reduced in leaf blade, sheath, stem and rachis tissue in the barley variety Baudin with the denso gene. Subsequently, the relative expression levels of Hv20ox2 were determined by quantitative real-time RT-PCR in a doubled haploid population and mapped as a quantitative trait. A single expression quantitative trait locus (eQTL) was identified and mapped to its structural gene region on chromosome 3H. The eQTL was co-located with QTLs for yield, height, development score, hectolitre weight and grain plumpness. The expression level of Hv20ox2 was reduced fourfold in the denso mutant, but around 60-fold in the sdw1 mutant, compared to the control variety. The reduced expression level of Hv20ox2 enhanced grain yield by increasing the number of effective tillers, but had negative effects on grain and malting quality. The sdw1 gene can be used only in feed barley due to its severe reduction of Hv20ox2 expression. The gene expression marker for Hv20ox2 can be used to distinguish different alleles of sdw1/denso.

Advances in Pathophysiology of Triple-Negative Breast Cancer: The Potential of lncRNAs for Clinical Diagnosis, Treatment, and Prognostic Monitoring.

Recent studies have shown that long non-coding RNAs (lncRNAs) are involved in several gene expression regulation processes, including epigenetic regulation, transcriptional regulation, post-transcriptional regulation, and translation regulation. It also plays a crucial role in the regulation of several characteristics of cancer biology, and the dysregulation of lncRNA expression in cancer may be part of the cause of cancer progression. Meanwhile, more and more studies are trying to determine the association between lncRNA expression and TNBC, as well as the functional role and molecular mechanism of the abnormally expressed lncRNA. Therefore, this review lists some abnormal lncRNAs in TNBC, further analyzes their molecular mechanisms and biological roles in the development of TNBC, and summarizes the potential of lncRNAs as biomarkers and therapeutic targets of TNBC, so as to provide ideas for clinical diagnosis, targeted therapy, and prognosis monitoring of TNBC.