A chromosome-scale genome of Peucedanum praeruptorum provide insights into Apioideae evolution and medicinal ingredient biosynthesis.

Peucedanum praeruptorum Dunn, a traditional Chinese medicine rich in coumarin, belongs to the Apiaceae family. A high-quality assembled genome of P. praeruptorum is lacking, which has posed obstacles to functional identification and molecular evolution studies of genes associated with coumarin production. Here, a chromosome-scale reference genome of P. praeruptorum, an important medicinal and aromatic plant, was first sequenced and assembled using Oxford Nanopore Technologies and Hi-C sequencing. The final assembled genome size was 1.83 Gb, with a contig N50 of 11.12 Mb. The entire BUSCO evaluation and second-generation read comparability rates were 96.0 % and 99.31 %, respectively. Furthermore, 99.91 % of the genome was anchored to 11 pseudochromosomes. The comparative genomic study revealed the presence of 18,593 orthogroups, which included 476 species-specific orthogroups and 1211 expanded gene families. Two whole-genome duplication (WGD) events and one whole-genome triplication (WGT) event occurred in P. praeruptorum. In addition to the γ-WGT shared by core eudicots or most eudicots, the first WGD was shared by Apiales, while the most recent WGD was unique to Apiaceae. Our study demonstrated that WGD events that occurred in Apioideae highlighted the important role of tandem duplication in the biosynthesis of coumarins and terpenes in P. praeruptorum. Additionally, the expansion of the cytochrome P450 monooxygenase, O-methyltransferase, ATP-binding cassette (ABC) transporter, and terpene synthase families may be associated with the abundance of coumarins and terpenoids. Moreover, we identified >170 UDP-glucosyltransferase members that may be involved in the glycosylation post-modification of coumarins. Significant gene expansion was observed in the ABCG, ABCB, and ABCC subgroups of the ABC transporter family, potentially facilitating the transmembrane transport of coumarins after bolting. The P. praeruptorum genome provides valuable insights into the machinery of coumarin biosynthesis and enhances our understanding of Apiaceae evolution.

WGCNA and transcriptome profiling reveal hub genes for key development stage seed size/oil content between wild and cultivated soybean.

BACKGROUND: Soybean is one of the most important oil crops in the world. The domestication of wild soybean has resulted in significant changes in the seed oil content and seed size of cultivated soybeans. To better understand the molecular mechanisms of seed formation and oil content accumulation, WDD01514 (E1), ZYD00463 (E2), and two extreme progenies (E23 and E171) derived from RILs were used for weighted gene coexpression network analysis (WGCNA) combined with transcriptome analysis. RESULTS: In this study, both seed weight and oil content in E1 and E171 were significantly higher than those in E2 and E23, and 20 DAF and 30 DAF may be key stages of soybean seed oil content accumulation and weight increase. Pathways such as "Photosynthesis", "Carbon metabolism", and "Fatty acid metabolism", were involved in oil content accumulation and grain formation between wild and cultivated soybeans at 20 and 30 DAF according to RNA-seq analysis. A total of 121 oil content accumulation and 189 seed formation candidate genes were screened from differentially expressed genes. WGCNA identified six modules related to seed oil content and seed weight, and 76 candidate genes were screened from modules and network. Among them, 16 genes were used for qRT-PCR and tissue specific expression pattern analysis, and their expression-levels in 33-wild and 23-cultivated soybean varieties were subjected to correlation analysis; some key genes were verified as likely to be involved in oil content accumulation and grain formation. CONCLUSIONS: Overall, these results contribute to an understanding of seed lipid metabolism and seed size during seed development, and identify potential functional genes for improving soybean yield and seed oil quantity.

Integrative analysis of chloroplast genome, chemicals, and illustrations in Bencao literature provides insights into the medicinal value of Peucedanum huangshanense.

The genus Peucedanum L. (Apiaceae) is a large group comprising more than 120 species distributed worldwide. Many plants of the genus Peucedanum have been studied and used in traditional Chinese medicine. In 2020, a new species, Peucedanum huangshanense Lu Q. Huang, H. S. Peng & S. S. Chu, was found in the Huangshan Mountains of Anhui Province, China. However, little is known about its medicinal properties. Thus, the objective of this study is to explore the potential medicinal value of P. huangshanense and its relationship with other Peucedanum species. Through textual research on illustrations of Qianhu in Bencao literature, it can be inferred that at least five species of genus Peucedanum have been used in Chinese medicine. Therefore, we chose these five species of Peucedanum and P. huangshanense together for subsequent research. We conducted morphological, chloroplast genome, and chemical analyses of six Peucedanum species, including the newly discovered P. huangshanense. The chloroplast genomes of Peucedanum showed a typical tetrad structure, and the gene structure and content were similar and conservative. There were significant differences in genome size and the expansion of the inverted repeat boundary. Through nucleotide polymorphism analysis, we screened 14 hotspot mutation regions that have the potential to be used as specific molecular markers for the taxonomy of Peucedanum. Our results showed an inversion of the trnD-trnY-trnE gene in the P. huangshanense chloroplast genome, which can be developed as a specific molecular marker for species identification. Phylogenetic analysis showed that the phylogenetic trees had high support and resolution, which strongly supports the view that Peucedanum is not a monophyletic group. P. huangshanense had the closest genetic relationship to P. ampliatum K. T. Fu, followed by P. harry-smithii Fedde ex Wolff. Furthermore, the main coumarins of P. huangshanense were most similar to those of P. japonicum Thunb. and P. harry-smithii. In summary, our research lays a foundation for the systematic classification of Peucedanum and sheds light on the medicinal value of P. huangshanense.

The first chromosome-level Fallopia multiflora genome assembly provides insights into stilbene biosynthesis.

Fallopia multiflora (Thunb.) Harald, a vine belonging to the Polygonaceae family, is used in traditional medicine. The stilbenes contained in it have significant pharmacological activities in anti-oxidation and anti-aging. This study describes the assembly of the F. multiflora genome and presents its chromosome-level genome sequence containing 1.46 gigabases of data (with a contig N50 of 1.97 megabases), 1.44 gigabases of which was assigned to 11 pseudochromosomes. Comparative genomics confirmed that F. multiflora shared a whole-genome duplication event with Tartary buckwheat and then underwent different transposon evolution after separation. Combining genomics, transcriptomics, and metabolomics data to map a network of associated genes and metabolites, we identified two FmRS genes responsible for the catalysis of one molecule of p-coumaroyl-CoA and three molecules of malonyl-CoA to resveratrol in F. multiflora. These findings not only serve as the basis for revealing the stilbene biosynthetic pathway but will also contribute to the development of tools for increasing the production of bioactive stilbenes through molecular breeding in plants or metabolic engineering in microbes. Moreover, the reference genome of F. multiflora is a useful addition to the genomes of the Polygonaceae family.

Integrated untargeted metabolome, full-length sequencing, and transcriptome analyses reveal insights into the fruit quality at different harvest times of Chaenomeles speciosa.

Chaenomeles speciosa fruit is a homologous medicine and food plant with a long history of multiple uses. It could be harvested near maturity and last for a long time. However, the optimal harvest strategy of Chaenomeles speciosa for various uses is currently unavailable. Here, untargeted metabolome at different harvest times during maturation was investigated for the first time, and 896 metabolites, including sugars, organic acids, amino acids, and phenylpropanoids, were identified. Optimal harvesting methods were proposed for different purposes. During the early maturation stages (before 105 days after full bloom), Ch. speciosa fruit could be harvested as Chinesemedicine. Whereas as snacks and food, Ch. speciosa fruit might be harvested at late maturity (after 120 days after full bloom). In addition, the overall network was revealed by integrating full-length Iso-seq and transcriptomics (RNA-seq) to investigate the association between quality-associated metabolites and Chaenomeles speciosa fruit gene expression during maturation. A few putative genes were captured via screening, dissecting and correlation analysis with the quality-associated metabolites (including d-glucose, catechin, gallocatechin, and succinic acid). Overall, in addition to providing a harvesting strategy for food and medicine, we also investigated the metabolism and gene expression pattern of Chaenomeles speciosa fruit during maturation. This comprehensive data and analyses laid the foundation for further investigating potential regulatory mechanisms during harvest and provided a new possibility for its development and utilization.

GmEIL4 enhances soybean (Glycine max) phosphorus efficiency by improving root system development.

Phosphorus (P) deficiency seriously affects plant growth and development and ultimately limits the quality and yield of crops. Here, a new P efficiency-related major quantitative trait locus gene, GmEIL4 (encoding an ethylene-insensitive 3-like 1 protein), was cloned at qP2, which was identified by linkage analysis and genome-wide association study across four environments. Overexpressing GmEIL4 significantly improved the P uptake efficiency by increasing the number, length and surface area of lateral roots of hairy roots in transgenic soybeans, while interfering with GmEIL4 resulted in poor root phenotypic characteristics compared with the control plants under low P conditions. Interestingly, we found that GmEIL4 interacted with EIN3-binding F box protein 1 (GmEBF1), which may regulate the root response to low P stress. We conclude that the expression of GmEIL4 was induced by low-P stress and that overexpressing GmEIL4 improved P accumulation by regulating root elongation and architecture. Analysis of allele variation of GmEIL4 in 894 soybean accessions suggested that GmEIL4 is undergoing artificial selection during soybean evolution, which will benefit soybean production. Together, this study further elucidates how plants respond to low P stress by modifying root structure and provides insight into the great potential of GmEIL4 in crop P-efficient breeding.

Full-length transcriptome analysis of two chemotype and functional characterization of genes related to sesquiterpene biosynthesis in Atractylodes lancea.

Atractylodes lancea (Thunb.) DC. is an important medicinal plant mainly distributed in China. A. lancea is rich in volatile oils and has a significant effect on various diseases, including coronavirus disease 2019 (COVID-19). Based on the signature constituents of volatile oils, A. lancea is divided into two chemotypes: the Dabieshan and Maoshan chemotype. Gas chromatography-mass spectrometry (GC-MS) results revealed that the hinesol and ß-eudesmol contents in the Dabieshan chemotype were higher than those in the Maoshan chemotype. Next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technologies were combined to investigate the molecular mechanisms of sesquiterpenoid biosynthesis in A. lancea. A total of 42 differentially expressed genes (DEGs) for terpenoid biosynthesis were identified in the two chemotype groups, and nine full-length terpene synthase (TPS) genes were identified. Subcellular localization revealed that AlTPS1 and AlTPS2 proteins were localized in the nucleus and endoplasmic reticulum. They use FPP as a substrate to generate sesquiterpenoids. AlTPS1 catalyzes biosynthesis of elemol while AlTPS2 is observed to perform ß-farnesene synthase activity. This study provides information for understanding the differences in the accumulation of terpenoids in two chemotypes of A. lancea and lays a foundation for further elucidation of the molecular mechanism of sesquiterpenoid biosynthesis.

The purple acid phosphatase GmPAP17 predominantly enhances phosphorus use efficiency in soybean.

Purple acid phosphatase (PAP) is an important plant acid phosphatase, which can secrete to the rhizosphere to decompose organophosphorus, promote phosphorus use efficiency, plant growth and development. However, little is known about the functions of intracellular PAP in plants, especially for soybean. Our previous study integrating QTL mapping and transcriptome analysis identified an promising low phosphorus (LP)-induced gene GmPAP17. Here, we determined that GmPAP17 was mainly expressed in roots and had a strong response to LP stress. Furthermore, and the relative expression in the root of LP tolerant genotypes NN94-156 was significantly greater than that of LP sensitive genotype Bogao after LP stress treatment. The overexpression of GmPAP17 significantly enhanced both acid phosphatase activity and growth performance of hairy roots under LP stress condition, it was vice versa for RNAi interference of GmPAP17, indicating that GmPAP17 plays an important role in P use efficiency. Moreover, yeast two-hybrid and bimolecular fluorescence complementation analysis showed that GmRAP2.2 was involved in the regulation network of GmPAP17. Taken together, our results suggest that GmPAP17 is a novel plant PAP that functions in the adaptation of soybean to LP stress, possibly through its involvement in P recycling in plants.

Behavioral, histopathological, genetic, and organism-wide responses to phenanthrene-induced oxidative stress in Eisenia fetida earthworms in natural soil microcosms.

Phenanthrene (PHE) contamination not only changes the quality of soil environment but also threatens to the soil organisms. There is lack of focus on the eco-toxicity potential of this contaminant in real soil in the current investigation. Here, we assessed the toxic effects of PHE on earthworms (Eisenia fetida) in natural soil matrix. PHE exhibited a relatively high toxicity to E. fetida in natural soil, with the LC50 determined to be 56.68 mg kg-1 after a 14-day exposure. Excessive ROS induced by PHE, leading to oxidative damage to biomacromolecules in E. fetida, including lipid peroxidation, protein carbonylation, and DNA damage. The antioxidant defense system (total antioxidant capacity, glutathione S-transferase, peroxidase, catalase, carboxylesterase, and superoxide dismutase) in E. fetida responded quickly to scavenge excess ROS and free radicals. Exposure to PHE resulted in earthworm avoidance responses (2.5 mg kg-1) and habitat function loss (10 mg kg-1). Histological observations indicated that the intestine, body wall, and seminal vesicle in E. fetida were severely damaged after exposure to high-dose PHE. Moreover, earthworm growth (weight change) and reproduction (cocoon production and the number of juvenile) were also inhibited after exposure to this pollutant. Furthermore, the integrated toxicity of PHE toward E. fetida at different doses and exposure times was assessed by the integrated biomarker response (IBR), which confirmed that PHE is more toxic to earthworms in the high-dose and long-term exposure groups. Our results showed that PHE exposure induced oxidative stress, disturbed antioxidant defense system, and caused oxidative damage in E. fetida. These effects can trigger behavior changes and damage histological structure, finally cause growth inhibition, genotoxicity, and reproductive toxicity in earthworms. The strength of this study is the comprehensive toxicity evaluation of PHE to earthworms and highlights the need to investigate the eco-toxicity potential of exogenous environmental pollutants in a real soil environment.

Colour, chemical compounds, and antioxidant capacity of Astragali Radix based on untargeted metabolomics and targeted quantification.

INTRODUCTION: Astragali Radix has been used for over 2000 years in traditional Chinese medicine. Its secondary xylem "Jinjing" and secondary phloem "Yulan" are important for evaluating the quality of the Daodi medicinal material in China. However, its systematic characterisation has not been conducted. OBJECTIVE: This study aims to investigate the colour, chemical compounds, and antioxidant capacity of the secondary xylem and phloem of Astragali Radix on the basis of untargeted metabolomics, broadening the application scope of Astragali Radix in food and pharmaceutical industries. METHODS: The L*, a*, and b* of the secondary xylem and phloem were measured by colorimetry, and the chemical compounds were identified and quantified by ultra-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and high-performance liquid chromatography-diode array detector-evaporative light scattering detection. 2,2-Diphenyl-1-picrylhydrazyl (DPPH) and 2-azino-bis-(3-ethylbenzothiazoline-6-sulphonic acid) (ABTS) assays were conducted to evaluate their antioxidant capacity. RESULTS: Thirty-one compounds were identified by UPLC-Q-TOF-MS. The secondary xylem exhibited high parameter b*, flavonoid content, and antioxidant capacity, while the secondary phloem was rich in astragalosides. The colour parameters of well-defined type A significantly varied from those of the other types. Well-defined type A also exhibited the highest antioxidant activity and flavonoid content, followed by middle type A-like, middle type B-like, and yellow shading type B. CONCLUSION: The colour parameters, chemical compounds, and antioxidant capacity among the different transverse sections of secondary xylem and phloem varied. The yellow colour of secondary xylem was correlated to high flavonoid content and antioxidant activity, and well-defined type A of Astragali Radix had better quality than other types.

Comparative analysis in different organs and tissue-specific metabolite profiling of Atractylodes lancea from four regions by GC-MS and laser microdissection.

Traditional Chinese medicine is made from the rhizome of Atractylodes lancea (Thunb.) DC. (Compositae), known as Cangzhu. In this study, gas chromatography-mass spectrometry was used to identify and quantify the volatile oils of different organs of A. lancea from four regions of China: Jiangsu, Anhui, Henan, and Hubei provinces. The volatile oils of A. lancea were qualitatively and quantitatively characterized using gas chromatography-mass spectrometry combined with laser microdissection. The results identified 21 components in A. lancea, the majority of the components were found in the rhizomes, followed by the fibrous roots, flowers, leaves, and stems. According to the contents of volatile oils in A. lancea, it was divided into Dabieshan (mainly includes hinesol and ß-eudesmol) and Maoshan types (mainly includes atractylon and atractylodin), and the ratios of hinesol:ß-eudesmol:atractylon:atractylodin were 17.06:4.55:0:1, 12.66:11.71:0.99:1, 7.43:6.23:0:1, and 0.13:0.16:1.52:1 in A. lancea from AH, HN, HB, and JS, respectively. Tissue-specific study indicated that Dabieshan type mainly includes elemol, hinesol, and ß-eudesmol in the periderm and secretory cavities of A. lancea, whereas Maoshan type mainly includes atractylon, atractylodin, little hinesol, and ß-eudesmol in the secretory cavities. Conversely, no volatile oils were detected in the cortex, phloem, xylem, vascular ray, or pith. This study provides a foundation for further evaluation and utilization of A. lancea.

The differential diagnosis of pneumonia in two patients infected by atypical pathogens.

The current study presents two patients who lived in a rural family with close contact and suffered from rapidly progressive pneumonia. Chest computed tomography images and lymphocytopenia indicated the possibility of COVID-19 infection, but antibody and nucleic acid tests excluded this possibility. Negative results were obtained from corresponding tests for pneumococcal, adenovirus, fungal and legionella infection. Metagenomics analysis and subsequent antibody tests confirmed mycoplasma pneumonia. After treating with moxifloxacin, both patients recovered well and left the hospital. In terms of complicated infectious disease, consideration of atypical pathogens and medical and epidemiological history were important for differential diagnosis of COVID-19; metagenomics analysis was useful to provide direct references for diagnosis.

Full-length transcriptome sequences by a combination of sequencing platforms applied to isoflavonoid and triterpenoid saponin biosynthesis of Astragalus mongholicus Bunge.

BACKGROUND: Astragalus mongholicus Bunge is an important medicinal plant used in traditional Chinese medicine. It is rich in isoflavonoids and triterpenoid saponins. Although these active constituents of A. mongholicus have been discovered for a long time, the genetic basis of isoflavonoid and triterpenoid saponin biosynthesis in this plant is virtually unknown because of the lack of a reference genome. Here, we used a combination of next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing to identify genes involved in the biosynthetic pathway of secondary metabolites in A. mongholicus. RESULTS: In this study, NGS, SMRT sequencing, and targeted compound analysis were combined to investigate the association between isoflavonoid and triterpenoid saponin content, and specific gene expression in the root, stem, and leaves of A. mongholicus. Overall, 643,812 CCS reads were generated, yielding 121,107 non-redundant transcript isoforms with an N50 value of 2124 bp. Based on these highly accurate transcripts, 104,756 (86.50%) transcripts were successfully annotated by any of the seven databases (NR, NT, Swissprot, KEGG, KOG, Pfam and GO). Levels of four isoflavonoids and four astragalosides (triterpenoid saponins) were determined. Forty-four differentially expressed genes (DEGs) involved in isoflavonoid biosynthesis and 44 DEGs from 16 gene families that encode enzymes involved in triterpenoid saponin biosynthesis were identified. Transcription factors (TFs) associated with isoflavonoid and triterpenoid saponin biosynthesis, including 72 MYBs, 53 bHLHs, 64 AP2-EREBPs, and 11 bZIPs, were also identified. The above transcripts showed different expression trends in different plant organs. CONCLUSIONS: This study provides important genetic information on the A. mongholicus genes that are essential for isoflavonoid and triterpenoid saponin biosynthesis, and provides a basis for developing the medicinal value of this plant.

Tissue-specific metabolite profiling of Fallopia multiflora (Heshouwu) and Fallopia multiflora var. angulata by mass spectrometry imaging and laser microdissection combined with UPLC-Q/TOF-MS.

Heshouwu, derived from root tubers of Fallopia multiflora (Thunb.) Harald., is a well-known herb used for millennia in traditional Chinese medicine. However, different forms of root tubers of Heshouwu have occurred in current Chinese herbal market and used in clinic, although it is still unknown whether their quality is consistent. In the present study, a mass spectrometry imaging and laser microdissection combined with UPLC-Q/TOF-MS were therefore used for the metabolite profiling on the whole and different parts of root tubers of F. multiflora and F. multiflora var. angulata. Our results suggested that the character of "woody heart" root tubers of F. multiflora was similar to that of F. multiflora var. angulata, but the latter had more phloem fibers and larger diameter vessel in the normal vascular bundle. Moreover, 140 compounds including stilbenes, anthraquinones, phenolic acids, naphthalenes, and other compounds were identified or putatively characterized from F. multiflora and F. multiflora var. angulata. Both unsupervised principal component analysis (PCA) and supervised Orthogonal Partial Least Squares Discrimination Analysis (OPLS-DA) multivariate statistics allowed discriminating F. multiflora and F. multiflora var. angulata. And a total of 32 potential markers were identified. The tissue-specific study indicated that the compounds in the phelloderm of F. multiflora and F. multiflora var. angulata were the most abundant. This is the first study on metabolite profiling and comparison of root tubers between F. multiflora and F. multiflora var. angulata, which would provide reasonable basis for further quality evaluation and safe medication of F. multiflora.

[Formation history of Dao-di herbs in Dabie Mountains].

Dabie Mountains, a unique transition area of subtropical and warm temperate zone, span Anhui, Hubei and Henan pro-vinces with a humid and suitable climate. It is rich in traditional Chinese medicine resources including many Dao-di herbs, and has a profound culture of traditional Chinese medicine with many herbalists in the past. This paper combed the historical geography of Dabie Mountains and development vein of medicinal materials recorded in history, and a textual research on the historical evolution of Dao-di herbs and special herbs in Dabie Mountains was carried out. The administrative region of Dabie Mountains has been changing constantly in history, which includes 25 counties and districts of six cities in Anhui, Henan and Hubei provinces at present. Dabie Mountains abound in a variety of Chinese herbal medicines, which have been recorded in herbal works in the past dynasties and local chronicles in detail. The recorded Dao-di herbs Dendrobium huoshanense, Artemisia argyi, and Poria cocos are well-known in China, and the output of Gastrodia elata, Ganoderma lucidum, and P. cocos is in the forefront of the country. Additionally, there are still many local special herbs emerging in modern times. In a word, this paper reviewed development of historical geography and ancient records of medicinal materials in Dabie Mountains, and made a textual research on the Dao-di herbs and special herbs, will provide a reference for the mo-dern research and intellectual property protection of Dao-di herbs in Dabie Mountains.

Comparative Elucidation of Age, Diameter, and "Pockmarks" in Roots of Paeonia lactiflora Pall. (Shaoyao) by Qualitative and Quantitative Methods.

Paeonia lactiflora Pall. is a world-famous ornamental plant, whose roots have been used as an important traditional Chinese medicine, Shaoyao, to treat diseases for more than 1,000 years. Because of the excellent curative effect of Shaoyao, its quality has attracted wide attention, however, there is a lack of comprehensive research on the different influencing factors of quality of Shaoyao. In this study, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF-MS) and high-performance liquid chromatography with diode-array detection (HPLC-DAD) were utilized to systematically analyze the Shaoyao of different ages, diameters and roots with "pockmarks." 60 metabolites were detected and identified from Shaoyao using the UPLC-Q/TOF-MS, of which 20 potential quality markers of dissected roots with and without "pockmarks" were selected for the first time using the orthogonal partial least squares discriminant analysis (OPLS-DA) and the variable importance for projection (VIP) plot. Then, a selective and accurate HPLC-DAD quantitative assay has been developed for the simultaneous determination of 11 bioactive components in Shaoyao. The results showed that the total content of five monoterpene glycosides including oxypaeoniflorin, albiflorin, paeoniflorin, lactiflorin, and benzoylpaeoniflorin and six phenols including gallic acid, catechin, methyl gallate, ethyl gallate, apiopaeonoside and benzoic acid in the 3-year-old Shaoyao was higher than that of 4-year-old and 5-year-old Shaoyao. In Shaoyao of the same age, the total content of five monoterpene glycosides and six phenols decreased with an increase in diameter. In addition, regardless of whether it is a whole or a divided root, the contents of five monoterpene glycosides and six phenols in Shaoyao with "pockmarks" were higher than those of Shaoyao without "pockmarks." In summary, this work has explored several factors that might affect the quality of Shaoyao, and provide a guide for more comprehensive quality evaluation in its further production, processing, and rational utilization.

Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing.

MicroRNAs (miRNAs) have been reported to be correlated with various stress responses in soybean, but only a few miRNAs have been demonstrated to respond to low phosphorus (LP) stress. To unravel the response mechanisms of miRNAs to low-P stress, the roots of two representative soybean genotypes with different P efficiency, Nannong94-156 (a LP-tolerant genotype) and Bogao (a LP-sensitive genotype), were used for the construction of RNA sequencing (RNA-seq) libraries under low/normal-P treatment by high-throughput sequencing. In total, 603 existing miRNAs and 1699 novel miRNAs belonging to 248 and 1582 families in all samples were identified, respectively. Among these miRNAs, 777 miRNAs were differentially expressed (DE) across different P levels and genotypes. Furthermore, putative targets of DE miRNAs were predicted, and these miRNAs mainly targeted ERF (ethylene responsive factor), auxin response factors (ARF), zinc finger protein, MYB, and NAC domain transcription factors. Gene ontology (GO) analysis showed that targets of DE miRNAs were significantly enriched in binding, metabolic processes, biological regulation, response to stress, and phosphorus metabolic processes. In addition, the expression profiles of chosen P-responsive miRNAs and target genes were validated by quantitative real-time PCR (qRT-PCR). Our study focused on genome-wide miRNA identification in two representative soybean genotypes under low-P stress. Overall, the DE miRNAs across different P levels and genotypes and their putative target genes will provide useful information for further study of miRNAs mediating low-P response and facilitate improvements in soybean breeding.

Genome-Wide Analysis Reveals Dynamic Epigenomic Differences in Soybean Response to Low-Phosphorus Stress.

Low-phosphorus (low-P) stress has a significant limiting effect on crop yield and quality. Although the molecular mechanisms of the transcriptional level responsible for the low-P stress response have been studied in detail, the underlying epigenetic mechanisms in gene regulation remain largely unknown. In this study, we evaluated the changes in DNA methylation, gene expression and small interfering RNAs (siRNAs) abundance genome-wide in response to low-P stress in two representative soybean genotypes with different P-efficiencies. The DNA methylation levels were slightly higher under low-P stress in both genotypes. Integrative methylation and transcription analysis suggested a complex regulatory relationship between DNA methylation and gene expression that may be associated with the type, region, and extent of methylation. Association analysis of low-P-induced differential methylation and gene expression showed that transcriptional alterations of a small part of genes were associated with methylation changes. Dynamic methylation alterations in transposable element (TE) regions in the CHH methylation context correspond with changes in the amount of siRNA under low-P conditions, indicating an important role of siRNAs in modulating TE activity by guiding CHH methylation in TE regions. Together, these results could help to elucidate the epigenetic regulation mechanisms governing the responses of plants to abiotic stresses.

Comparative analysis and chemical profiling of different forms of Peucedani Radix.

Peucedani Radix, derived from roots of Peucedanum praeruptorum Dunn, is a well-known herb used for centuries in traditional Chinese medicine, which is rich in various coumarins. Four different forms including "earthworm head", "bamboo-like", taproots and multi-branched roots have occurred in current producing areas, but the differences in their external features and chemistry have not been concerned till now. In this study, the morphological and microscopic characters of "earthworm head" and "bamboo-like" roots were compared in detail, and qualitative and quantitative characterization of main active coumarins in different forms of Peucedani Radix have been developed by UPCL-Q/TOF-MS and HPLC-DAD, respectively. The results showed that both "earthworm head" and "bamboo-like" consisted of rhizome and root, exhibiting distinct features from normal taproots. Moreover, 53 coumarins including simple coumarins, furanocoumarins and pyranocoumarins were identified or putatively characterized from the four forms samples under the established UPLC-Q/TOF-MS conditions. In addition, the developed quantitative method was successfully applied to simultaneously determine eight main coumarins in 24 batches of four forms Peucedani Radix and 12 batches of dissected "earthworm head" and "bamboo-like" samples. The quantitative results proved that wild "earthworm head" showed higher content of active coumarins and the "bamboo-like" was a rich source of coumarins in cultivated samples, especially for furanocoumarins. These findings would provide reasonable basis for further quality evaluation, grades classification and comprehensive utilization of P. praeruptorum resources.

Quantitative trait loci analysis of seed oil content and composition of wild and cultivated soybean.

BACKGROUND: Soybean oil is a major source of edible oil, and the domestication of wild soybean has resulted in significant changes in oil content and composition. Extensive efforts have been made to identify genetic loci that are related to soybean oil traits. The objective of this study was to identify quantitative trait loci (QTLs) related to soybean seed oil and compare the fatty acid composition between wild and cultivated soybean. RESULTS: Using the specific-locus amplified fragment sequencing (SLAF-seq) method, a total of 181 recombinant inbred lines (RILs) derived from a cross between wild soybean ZYD00463 (Glycine soja) and cultivated soybean WDD01514 (Glycine max) were genotyped. Finally, a high-density genetic linkage map comprising 11,398 single-nucleotide polymorphism (SNP) markers on 20 linkage groups (LGs) was constructed. Twenty-four stable QTLs for seed oil content and composition were identified by model-based composite interval mapping (CIM) across multiple environments. Among these QTLs, 23 overlapped with or were adjacent to previously reported QTLs. One QTL, qPA10_1 (5.94-9.98 Mb) on Chr. Ten is a novel locus for palmitic acid. In the intervals of stable QTLs, some interesting genes involved in lipid metabolism were detected. CONCLUSIONS: We developed 181 RILs from a cross between wild soybean ZYD00463 and cultivated soybean WDD01514 and constructed a high-density genetic map using the SLAF-seq method. We identified 24 stable QTLs for seed oil content and compositions, which includes qPA10_1 on Chr. 10, a novel locus for palmitic acid. Some interesting genes in the QTL regions were also detected. Our study will provide useful information for scientists to learn about genetic variations in lipid metabolism between wild and cultivated soybean.