Identification of the lateral organ boundary domain gene family and its preservation by exogenous salicylic acid in Cerasus humilis.

The gene family known as the Lateral Organ Boundary Domain (LBD) is responsible for producing transcription factors unique to plants, which play a crucial role in controlling diverse biological activities, including their growth and development. This research focused on examining Cerasus humilis'ChLBD gene, owing to its significant ecological, economic, and nutritional benefits. Examining the ChLBD gene family's member count, physicochemical characteristics, phylogenetic evolution, gene configuration, and motif revealed 41 ChLBD gene family members spread across 8 chromosomes, with ChLBD gene's full-length coding sequences (CDSs) ranging from 327 to 1737 base pairs, and the protein sequence's length spanning 109 (ChLBD30)-579 (ChLBD35) amino acids. The molecular weights vary from 12.068 (ChLBD30) to 62.748 (ChLBD35) kDa, and the isoelectric points span from 4.74 (ChLBD20) to 9.19 (ChLBD3). Categorizing them into two evolutionary subfamilies: class I with 5 branches, class II with 2, the majority of genes with a single intron, and most members of the same subclade sharing comparable motif structures. The results of collinearity analysis showed that there were 3 pairs of tandem repeat genes and 12 pairs of fragment repeat genes in the Cerasus humilis genome, and in the interspecific collinearity analysis, the number of collinear gene pairs with apples belonging to the same family of Rosaceae was the highest. Examination of cis-acting elements revealed that methyl jasmonate response elements stood out as the most abundant, extensively dispersed in the promoter areas of class 1 and class 2 ChLBD. Genetic transcript analysis revealed that during Cerasus humilis' growth and maturation, ChLBD developed varied control mechanisms, with ChLBD27 and ChLBD40 potentially playing a role in managing color alterations in fruit ripening. In addition, the quality of calcium fruit will be affected by the environment during transportation and storage, and it is particularly important to use appropriate means to preserve the fruit. The research used salicylic acid-treated Cerasus humilis as the research object and employed qRT-PCR to examine the expression of six ChLBD genes throughout storage. Variations in the expression of the ChLBD gene were observed when exposed to salicylic acid, indicating that salicylic acid could influence ChLBD gene expression during the storage of fruits. This study's findings lay the groundwork for additional research into the biological role of the LBD gene in Cerasus humilis. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-024-01438-5.

Genome-Wide Analysis of the HSF Gene Family Reveals Its Role in Astragalus mongholicus under Different Light Conditions.

Astragalus mongholicus is a traditional Chinese medicine (TCM) with important medicinal value and is widely used worldwide. Heat shock (HSF) transcription factors are among the most important transcription factors in plants and are involved in the transcriptional regulation of various stress responses, including drought, salinity, oxidation, osmotic stress, and high light, thereby regulating growth and developmental processes. However, the HFS gene family has not yet been identified in A. mongholicus, and little is known regarding the role of HSF genes in A. mongholicus. This study is based on whole genome analysis of A. mongholicus, identifying a total of 22 AmHSF genes and analyzing their physicochemical properties. Divided into three subgroups based on phylogenetic and gene structural characteristics, including subgroup A (12), subgroup B (9), and subgroup C (1), they are randomly distributed in 8 out of 9 chromosomes of A. mongholicus. In addition, transcriptome data and quantitative real time polymerase chain reaction (qRT-PCR) analyses revealed that AmHSF was differentially transcribed in different tissues, suggesting that AmHSF gene functions may differ. Red and blue light treatment significantly affected the expression of 20 HSF genes in soilless cultivation of A. mongholicus seedlings. AmHSF3, AmHSF3, AmHSF11, AmHSF12, and AmHSF14 were upregulated after red light and blue light treatment, and these genes all had light-corresponding cis-elements, suggesting that AmHSF genes play an important role in the light response of A. mongholicus. Although the responses of soilless-cultivated A. mongholicus seedlings to red and blue light may not represent the mature stage, our results provide fundamental research for future elucidation of the regulatory mechanisms of HSF in the growth and development of A. mongholicus and its response to different light conditions.

Genus Paeonia monoterpene glycosides: A systematic review on their pharmacological activities and molecular mechanisms.

BACKGROUND: Genus Paeonia, which is the main source of Traditional Chinese Medicine (TCM) Paeoniae Radix Rubra (Chishao in Chinese), Paeoniae Radix Alba (Baishao in Chinese) and Moutan Cortex (Mudanpi in Chinese), is rich in active pharmaceutical ingredient such as monoterpenoid glycosides (MPGs). MPGs from Paeonia have extensive pharmacological effects, but the pharmacological effects and molecular mechanisms of MPGs has not been comprehensively reviewed. PURPOSE: MPGs compounds are one of the main chemical components of the genus Paeonia, with a wide variety of compounds and strong pharmacological activities, and the structure of the mother nucleus-pinane skeleton is similar to that of a cage. The purpose of this review is to summarize the pharmacological activity and mechanism of action of MPGs from 2012 to 2023, providing reference direction for the development and utilization of Paeonia resources and preclinical research. METHODS: Keywords and phrases are widely used in database searches, such as PubMed, Web of Science, Google Scholar and X-Mol to search for citations related to the new compounds, extensive pharmacological research and molecular mechanisms of MPGs compounds of genus Paeonia. RESULTS: Modern research confirms that MPGs are the main compounds in Paeonia that exert pharmacological effects. MPGs with extensive pharmacological characteristics are mainly concentrated in two categories: paeoniflorin derivatives and albiflflorin derivatives among MPGs, which contains 32 compounds. Among them, 5 components including paeoniflorin, albiflorin, oxypaeoniflorin, 6'-O-galloylpaeoniflorin and paeoniflorigenone have been extensively studied, while the other 28 components have only been confirmed to have a certain degree of anti-inflammatory and anticomplementary effects. Studies of pharmacological effects are widely involved in nervous system, endocrine system, digestive system, immune system, etc., and some studies have identified clear mechanisms. MPGs exert pharmacological activity through multilateral mechanisms, including anti-inflammatory, antioxidant, inhibition of cell apoptosis, regulation of brain gut axis, regulation of gut microbiota and downregulation of mitochondrial apoptosis, etc. CONCLUSION: This systematic review delved into the pharmacological effects and related molecular mechanisms of MPGs. However, there are still some compounds in MPGs whose pharmacological effects and pharmacological mechanisms have not been clarified. In addition, extensive clinical randomized trials are needed to verify the efficacy and dosage of MPGs.

Trollius chinensis Bunge: A Comprehensive Review of Research on Botany, Materia Medica, Ethnopharmacological Use, Phytochemistry, Pharmacology, and Quality Control.

Trollius chinensis Bunge, a perennial herb belonging to the Ranunculaceae family, has been extensively used in traditional Chinese medicine. Documented in the Supplements to the Compendium of Materia Medica, its medicinal properties encompass a spectrum of applications, including heat clearance, detoxification, alleviation of oral/throat sores, earaches, eye pain, cold-induced fever, and vision improvement. Furthermore, T. chinensis is used in clinical settings to treat upper respiratory infections, pharyngitis, tonsillitis, esoenteritis, canker, bronchitis, etc. It is mainly used to treat inflammation, such as inflammation of the upper respiratory tract and nasal mucosa. This comprehensive review explores the evolving scientific understanding of T. chinensis, covering facets of botany, materia medica, ethnopharmacological use, phytochemistry, pharmacology, and quality control. In particular, the chemical constituents and pharmacological research are reviewed. Polyphenols, mainly flavonoids and phenolic acids, are highly abundant among T. chinensis and are responsible for antiviral, antimicrobial, and antioxidant activities. The flower additionally harbors trace amounts of volatile oil, polysaccharides, and other bioactive compounds. The active ingredients of the flower have fewer side effects, and it is used in children because of its minimal side effects, which has great research potential. These findings validate the traditional uses of T. chinensis and lay the groundwork for further scientific exploration. The sources utilized in this study encompass Web of Science, Pubmed, CNKI site, classic monographs, Chinese Pharmacopoeia, Chinese Medicine Dictionary, and doctoral and master's theses.

The complete chloroplast genome of Aegle marmelos and its phylogenetic analysis.

Aegle marmelos (L.) Correa 1800, a plant belonging to the Rutaceae family, is extensively used in Tibetan medicine. We employed Illumina HiSeq reads to assemble the complete chloroplast (cp) genome of A. marmelos, which spans 144,538 bp. The genome comprises 114 genes, including 75 protein-coding genes, 31 tRNA genes, and 8 rRNA genes. It is characterized by four regions: The large single-copy (LSC) region (74,253 bp), the inverted repeat A (IRa) region (26,015 bp), the small single-copy (SSC) region (18,255 bp), and the inverted repeat B (IRb) region (26,015 bp). Phylogenomic analysis demonstrated a close relationship between A. marmelos and Citrus. The assembly of The cp genome in this study serves as a foundation for conservation efforts and phylogenetic investigations of A. marmelos, paving the way for future experimentation.

Genome-wide identification of the NAC transcription factors family and regulation of metabolites under salt stress in Isatis indigotica.

NAC (NAM, ATAF1/2 and CUC2) transcription factors (TFs) are a class of TFs families unique to plants, which not only play an important role in the growth and developmental stages of plants but also function in response to stress and regulation of secondary metabolite biosynthesis. However, there are few studies on NAC genes in the medicinal plant Isatis indigotica. In this study, 96 IiNAC genes were identified based on the whole-genome data of I. indigotica, distributed in seven chromosomes and three contigs. IiNAC genes were structurally conserved and divided into 15 subgroups. Cis-elements were identified in the promoter region of the IiNAC gene in response to plant growth and development, abiotic stresses and hormones. In addition, transcriptome and metabolome data of I. indigotica leaves under salt stress were analyzed to construct a network of IiNAC gene co-expression and metabolite association. Ten differentially expressed IiNAC genes were co-expressed with 109 TFs, and Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed that most of these genes were associated with plant growth and development and abiotic stress responses. Eleven IiNAC genes were positively associated with 72 metabolites. Eleven IiNAC genes were positively or negatively associated with 47 metabolites through 37 TFs. Commonly associated secondary metabolites include two terpenoids, abscisic acid and bilobalide, two flavonoids, dihydrokaempferol and syringaldehyde, a coumarin, 7-methoxycoumarin, an alkaloid, lupinine, and quinone dihydrotanshinone I. This study provides important data to support the identification of the NAC gene family in I. indigotica and the regulatory functions of IiNAC genes in metabolites under salt stress.

Identification and expression analysis of YABBY family genes in Platycodon grandiflorus.

Platycodon grandiflorus set ornamental, edible, and medicinal plant with broad prospects for further application development. However, there are no reports on the YABBY transcription factor in P. grandiflorus. Identification and analysis of the YABBY gene family of P. grandiflorus using bioinformatics means. Six YABBY genes were identified and divided into five subgroups. Transcriptome data and qRT-PCR were used to analyze the expression patterns of YABBY. YABBY genes exhibited organ-specific patterns in expression in P grandiflorus. Upon salt stress and drought induction, P. grandiflorus presented different morphological and physiological changes with some dynamic changes. Under salt treatment, the YABBY gene family was down-regulated; PgYABBY5 was up-regulated in leaves at 24 h. In drought treatment, PgYABBY1, PgYABBY2, and PgYABBY3 were down-regulated to varying degrees, but PgYABBY3 was significantly up-regulated in the roots. PgYABBY5 was up-regulated gradually after being down-regulated. PgYABBY5 was significantly up-regulated in stem and leaf at 48 h. PgYABBY6 was down-regulated at first and then significantly up-regulated. The dynamic changes of salt stress and drought stress can be regarded as the responses of plants to resist damage. During the whole process of salt and drought stress treatment, the protein content of each tissue part of P grandiflorus changed continuously. At the same time, we found that the promoter region of the PgYABBY gene contains stress-resistant elements, and the regulatory role of YABBY transcription factor in the anti-stress mechanism of P grandiflorus remains to be studied. PgYABBY1, PgYABBY2, and PgYABBY5 may be involved in the regulation of saponins in P. grandiflorus. PgYABBY5 may be involved in the drought resistance mechanism in P. grandiflorus stems and leaves. This study may provide a theoretical basis for studying the regulation of terpenoids by the YABBY transcription factor and its resistance to abiotic stress.

Identification of Apiaceae using ITS, ITS2 and psba-trnH barcodes.

Apiaceae plants are used as medicinal herbs, pesticides, spices, and vegetables; thus, accurately identifying Apiaceae species is important. The grassland ecosystem of Heilongjiang Province in northern China has huge reserves of wild Apiaceae plants, but few reports have systematically documented their diversity. In this study, 275 Apiaceae plants of 23 species in 18 genera were collected from this area. We identified Apiaceae species by using nuclear internal transcribed spacer (ITS/ITS2) and psbA-trnH (chloroplast non-coding region) sequences based on experimental data. The identification efficiency of ITS, ITS2 and psbA-trnH sequences was determined and evaluated by sequence alignment and analysis, intraspecific and interspecific genetic distance analyses, and phylogenetic tree construction. ITS, ITS2 could distinguish 21 species from 17 genera of Apiaceae with good identification effect. When identifying species in the Apiaceae family, ITS2 can be used as the core barcode and psbA-trnH can be used as the supplementary barcode. These results can enrich the reference Apiaceae DNA barcode database.

Bioactive extracts and association with C and N in Eleutherococcus senticosus subjected to chitosan nanoparticles in contrasting light spectra.

Bioactive compounds are major reasons for the value of Eleutherococcus senticosus, which can be modified by different lighting spectra. Light-emitting diode (LED) provides lights with specific spectra which can interact with other treatments to impact plant bioactive production. Chitosan nanoparticle (CN) is a biopolymer derived from marine creatures. It's usage may be a practical approach to cope with uncertainties in secondary metabolites induced by illumination. Carbon (C) and nitrogen (N) cyclings link plant eco-physiological performance and bioactive substance; hence their associations may reveal the mechanism of joint light-CN interaction. In this study, E. senticosus seedlings were raised under artificial lighting spectra from high-pressure sodium (HPS) lamps (44% red, 55% green, 1% blue) and white (44% red, 47% green, 8% blue) and red colored (73% red, 13% green, 14% blue) LED panels. Half of the seedlings received CN and the other half received distilled water as the control. Compared to the HPS spectrum, the red-light induced stronger shoot growth with greater biomass accumulation and higher water uptake but resulted in lower N concentration and biomass ratio in the root. The white light caused more biomass allocated to the root and strengthened stem C concentration. Stem eleutheroside B increased with shoot growth, while root eleutheroside B had a positive association with leaf C and stem protocatechuic acid had a negative association with leaf N. Having the CN treatment in white and red LED lights is recommended for increasing accumulation of bioactive compounds in the shoots and roots of E. senticosus seedlings, respectively.

[Transcriptomics of therapeutic effect of Huangqi Liuyi decoction in treating type 2 diabetes].

In this study, Illumina sequencing platform was applied in sequencing rat pancreas, counting expression of target points, analyzing expression differences among blank group, model group and Huangqi Liuyi decoction group and exploring the therapeutic effect and mechanism of Huangqi Liuyi decoction on type 2 diabetes mellitus. According to the result, 24.25% of these genes belonged to the unknown functional class, which was the largest classification unit according to the classification analysis of genes by eggNOG. The rest were classified as energy conversion, amino acid transport and metabolism, nucleotide transport and metabolism, carbohydrate transport and metabolism, coenzyme transport and metabolism, and lipid transport and metabolism, etc.Huangqi Liuyi decoction may play a therapeutic role in the treatment of type 2 diabetes mellitus through four metabolic pathways, namely environmental information processing, cellular process, organismal system and human diseases according to KEGG enrichment analysis. This study shows that, Huangqi Liuyi decoction can significantly improve the fasting blood glucose and glycosylated hemoglobin in type 2 diabetic rats.

[Model Predicts of Astragalus membranceus Transcriptional Gene].

Objective: Astragali Radix, one of the most widely used traditional Chinese medicines, has been extracted a variety of efficiently ingredients. However, the formation mechanism of the secondary metabolites is still unclear and the genome of Astragali Radix has not been sequenced yet. This study aimed at predicting gene model according to transcriptome data, which can be helpful to the use of Astragalus membranceus in the medicine field. Methods: Based on the transcriptome data of Astragalus membranceus and the existing whole genome sequence of its closely related species, the unigene of transcriptome of Astragalus membranceus was predicted and analyzed. Results: Astragalus membranceus had close genetic relationship with Glycine max,Medicago truncatula and Lotus japonicus. Astragalus membranceus shared 2 039 sequences with Medicago truncatula, and their base similarity was 90. 14%. There were 1 948 sequences matched up with Glycine max, and their base similarity was 90. 40%. In the aligement of Astragalus membranceus and Lotus corniculatus, the matched sequences dropped to 1 003,and the base similarity dropped to 89. 77%. Conclusion: The matched gene with three species discributed in chromosome genomes and extrachromosomal genome.

High-throughput analysis and characterization of Astragalus membranaceus transcriptome using 454 GS FLX.

Astragalus membranaceus (Fisch.) Bge (AR), one of the most important medicinal plants in Asia, was found to exhibit various bioactivities. Due to limited genomic and transcriptomic data, the biosynthetic pathway of the major bioactive compound in AR, is currently unclear. In this study, 454 GS FLX technology was employed to produce a substantial expressed sequence tag (EST) dataset from the AR. In all, 742721 high-quality reads from the AR were produced using Roche GS FLX Titanium. A total of 9893 unique sequences were obtained and annotated by a similarity search against the public databases, and involved in the secondary metabolic pathway, which would facilitate deciphering the molecular mechanism of secondary metabolism in AR. The assembled sequences were annotated with gene names and Gene Ontology (GO) terms. GO revealed the unique sequences that could be assigned to 34 vocabularies. In the KEGG mapping, unique sequences were established as associated with 46 biochemical pathways. These results provided the largest EST collections in AR and will contribute to biosynthetic and biochemical studies that lead to drug improvement. With respect to the genes related to metabolism and biosynthesis pathway were also found. Our work demonstrated the utility of 454 GS FLX as a method for the rapid and cost-effective identification of AR transcriptome, and this EST dataset will be a powerful resource for further studies such as taxonomy, molecular breeding, and secondary metabolism in AR.