Transcriptome analysis of MYB transcription factors family and PgMYB genes involved in salt stress resistance in Panax ginseng

Transcriptomic strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng

BACKGROUND

Panax ginseng C. A. Meyer, a well-known phytomedicine has been widely used in traditional medicine for centuries. However, its quality and yield are heavily influenced by environmental conditions and cultivation years. For example, ginsenosides as the primary active component of ginseng, the concentration increased with the age of the roots and unevenly distributed across different tissues. Recently, transcriptomic technologies have provided powerful tools for revealing the relationship between gene expression and ginsenoside accumulation during ginseng growth, and researches in this field is continuously expanding, influencing the quality and sustainability of ginseng cultivation.

PURPOSE

Investigating the relationship between ginseng growth and the accumulation of active components may provide new insights for improving ginseng performance and medicinal value. This requires a systematic review and in-depth discussion of relevant research.

STUDY DESIGN AND METHODS

This article reviews the application of transcriptomic strategies in studying the molecular mechanisms of ginseng growth and ginsenoside accumulation. A literature search and analysis were conducted using keywords such as "Panax ginseng" and "transcriptomics/transcriptome," along with terms including "ginsenoside biosynthesis," "microbe/microorganism," "RNA-seq," "cultivation years," "rhizosphere," and "stress."

RESULT

Our study focuses on the transcriptome strategy provides molecular insights into the growth and ginsenosides accumulation of Panax ginseng, we summarized and discussed the dynamic changes in gene expression across cultivation years, specific-tissue, environmental stress, and imbalance of rhizosphere microbes during the ginseng growth and ginsenosides accumulation process. In addition, we also highlight future directions.

CONCLUSION

The cultivation years, specific-tissue, environmental stress, and rhizosphere microbiome imbalance of Panax ginseng are indirectly or directly involved in plant health, biomass production, and the synthesis of ginsenosides. Harnessing these factors to improve the quality and yield of ginseng holds great promise.

Comparative Transcriptome Analysis of Two Types of Rye Under Low-Temperature Stress

Wheat is a crucial food crop, and low-temperature stress can severely disrupt its growth and development, ultimately leading to a substantial reduction in wheat yield. Understanding the cold-resistant genes of wheat and their action pathways is essential for revealing the cold-resistance mechanism of wheat, enhancing its yield and quality in low-temperature environments, and ensuring global food security. Rye (Secale cereale L.), on the other hand, has excellent cold resistance in comparison to some other crops. By studying the differential responses of different rye varieties to low-temperature stress at the transcriptome level, we aim to identify key genes and regulatory mechanisms related to cold tolerance. This knowledge can not only deepen our understanding of the molecular basis of rye's cold resistance but also provide valuable insights for improving the cold tolerance of other crops through genetic breeding strategies. In this study, young leaves of two rye varieties, namely "winter" rye and "victory" rye, were used as experimental materials. Leaf samples of both types were treated at 4 °C for 0, 6, 24, and 72 h and then underwent RNA-sequencing. A total of 144,371 Unigenes were reconstituted. The Unigenes annotated in the NR, GO, KEGG, and KOG databases accounted for 79.39%, 55.98%, 59.90%, and 56.28%, respectively. A total of 3013 Unigenes were annotated as transcription factors (TFs), mainly belonging to the MYB family and the bHLH family. A total of 122,065 differentially expressed genes (DEGs) were identified and annotated in the GO pathways and KEGG pathways. For DEG analysis, 0 h 4 °C treated samples were controls. With strict criteria (p < 0.05, fold-change > 2 or <0.5, |log2(fold-change)| > 1), 122,065 DEGs were identified and annotated in GO and KEGG pathways. Among them, the "Chloroplast thylakoid membrane" and "Chloroplast" pathways were enriched in both the "winter" rye and "victory" rye groups treated with low temperatures, but the degrees of significance were different. Compared with "victory" rye, "winter" rye has more annotated pathways such as the "hydrogen catabolic process". Although the presence of more pathways does not directly prove a more extensive cold-resistant mechanism, these pathways are likely associated with cold tolerance. Our subsequent analysis of gene expression patterns within these pathways, as well as their relationships with known cold-resistance-related genes, suggests that they play important roles in "winter" rye's response to low-temperature stress. For example, genes in the "hydrogen catabolic process" pathway may be involved in regulating cellular redox balance, which is crucial for maintaining cell function under cold stress.

Weighted gene co-expression network analysis and identification of ginsenoside biosynthesis candidate genes for ginseng adventitious roots under MeJA treatment

BACKGROUND

Ginseng (Panax ginseng) is an herb with a long history and a wide range of applications. Ginsenoside is one of the most representative and active ginseng compounds, with various pharmacological effects. Therefore, the development of bioreactors using methyl jasmonate (MeJA) as an inducer for targeted ginsenoside production is of great commercial value. Combined with transcriptomic research tools, screenings to obtain candidate genes involved in ginsenoside biosynthesis are crucial for future discoveries about the molecular mechanism of MeJA-regulated ginsenoside biosynthesis.

OBJECTIVE AND METHODS

In our study, the ginsenoside content of ginseng adventitious roots treated with MeJA at different times was analyzed. Transcriptome analysis was performed to investigate the effects of MeJA on changes in ginsenoside content in ginseng adventitious roots.

RESULTS

The MeJA could significantly increase changes in the content of pro-ginsenodiol ginsenosides as well as pro-triol ginsenosides Rg3, Re, and Rf in ginseng adventitious roots. Differential gene expression analysis showed that a total of 14,009 differentially expressed genes were obtained from the screening of the present study. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that differentially expressed genes were mainly enriched under GO terms in response to stimuli, metabolic processes, and the regulation of biological processes, with significant annotation to the metabolic terms of terpenoids and polyketides. Two expression modules of genes highly related to ginsenoside biosynthesis were obtained via WGCNA.

CONCLUSIONS

Our study provides a reference system for the targeted ginsenoside production using MeJA as an inducer, and also provides genetic and gene resources for subsequently validating genes related to the regulation of ginsenoside biosynthesis using weighted gene co-expression network analysis (WGCNA).

Regulatory Dynamics of Plant Hormones and Transcription Factors under Salt Stress

The negative impacts of soil salinization on ion homeostasis provide a significant global barrier to agricultural production and development. Plant physiology and biochemistry are severely affected by primary and secondary NaCl stress impacts, which damage cellular integrity, impair water uptake, and trigger physiological drought. Determining how transcriptional factors (TFs) and hormone networks are regulated in plants in response to salt stress is necessary for developing crops that tolerate salt. This study investigates the complex mechanisms of several significant TF families that influence plant responses to salt stress, involving AP2/ERF, bZIP, NAC, MYB, and WRKY. It demonstrates how these transcription factors (TFs) help plants respond to the detrimental effects of salinity by modulating gene expression through mechanisms including hormone signaling, osmotic stress pathway activation, and ion homeostasis. Additionally, it explores the hormonal imbalances triggered by salt stress, which entail complex interactions among phytohormones like jasmonic acid (JA), salicylic acid (SA), and abscisic acid (ABA) within the hormonal regulatory networks. This review highlights the regulatory role of key transcription factors in salt-stress response, and their interaction with plant hormones is crucial for developing genome-edited crops that can enhance agricultural sustainability and address global food security challenges.

A generalist regulator: MYB transcription factors regulate the biosynthesis of active compounds in medicinal plants

Medicinal plants are rich in a variety of secondary metabolites with therapeutic value. However, the yields of these metabolites are generally very low, making their extraction both time-consuming and labour-intensive. Transcription factor-targeted secondary metabolic engineering can efficiently regulate the biosynthesis and accumulation of secondary metabolites in medicinal plants. v-Myb avian myeloblastosis viral oncogene homolog (MYB) transcription factors are involved in regulating various morphological and developmental processes, responses to stress, and the biosynthesis of secondary metabolites in plants. This review discusses the biological functions and transcription regulation mechanisms of MYB transcription factors and summarizes research progress concerning MYB transcription factors involved in the biosynthesis of representative active components. In the transcriptional regulatory network, MYB transcription factors regulate multiple synthase genes to mediate the biosynthesis of active compounds. This work will serve as a reference for an in-depth analysis of the MYB transcription factor family in medicinal plants.

Transcriptome-Wide Identification and Integrated Analysis of a UGT Gene Involved in Ginsenoside Ro Biosynthesis in Panax ginseng

Panax ginseng as a traditional medicinal plant with a long history of medicinal use. Ginsenoside Ro is the only oleanane-type ginsenoside in ginseng, and has various pharmacological activities, including anti-inflammatory, detoxification, and antithrombotic activities. UDP-dependent glycosyltransferase (UGT) plays a key role in the synthesis of ginsenoside, and the excavation of UGT genes involved in the biosynthesis of ginsenoside Ro has great significance in enriching ginsenoside genetic resources and further revealing the synthesis mechanism of ginsenoside. In this work, ginsenoside-Ro-synthesis-related genes were mined using the P. ginseng reference-free transcriptome database. Fourteen hub transcripts were identified by differential expression analysis and weighted gene co-expression network analysis. Phylogenetic and synteny block analyses of PgUGAT252645, a UGT transcript among the hub transcripts, showed that PgUGAT252645 belonged to the UGT73 subfamily and was relatively conserved in ginseng plants. Functional analysis showed that PgUGAT252645 encodes a glucuronosyltransferase that catalyzes the glucuronide modification of the C3 position of oleanolic acid using uridine diphosphate glucuronide as the substrate. Furthermore, the mutation at 622 bp of its open reading frame resulted in amino acid substitutions that may significantly affect the catalytic activity of the enzyme, and, as a consequence, affect the biosynthesis of ginsenoside Ro. Results of the in vitro enzyme activity assay of the heterologous expression product in E. coli of PgUGAT252645 verified the above analyses. The function of PgUGAT252645 was further verified by the result that its overexpression in ginseng adventitious roots significantly increased the content of ginsenoside Ro. The present work identified a new UGT gene involved in the biosynthesis of ginsenoside Ro, which not only enriches the functional genes in the ginsenoside synthesis pathway, but also provides the technical basis and theoretical basis for the in-depth excavation of ginsenoside-synthesis-related genes.

Transcriptional Landscape of Cotton Roots in Response to Salt Stress at Single-cell Resolution

Increasing soil salinization has led to severe losses of plant yield and quality. Thus, it is urgent to investigate the molecular mechanism of the salt stress response. In this study, we took systematically analyzed cotton root response to salt stress by single-cell transcriptomics technology; 56,281 high-quality cells were totally obtained from 5-days-old lateral root tips of Gossypium arboreum under natural growth and different salt-treatment conditions. Ten cell types with an array of novel marker genes were synthetically identified and confirmed with in situ RNA hybridization, and some specific-type cells of pesudotime analysis also pointed out their potential differentiation trajectory. The prominent changes of cell numbers responding to salt stress were observed on outer epidermal and inner endodermic cells, which were significantly enriched in response to stress, amide biosynthetic process, glutathione metabolism, and glycolysis/gluconeogenesis. Other functional aggregations were concentrated on plant-type primary cell wall biogenesis, defense response, phenylpropanoid biosynthesis and metabolic pathways by analyzing the abundant differentially expressed genes (DEGs) identified from multiple comparisons. Some candidate DEGs related with transcription factors and plant hormones responding to salt stress were also identified, of which the function of Ga03G2153, an annotated auxin-responsive GH3.6, was confirmed by using virus-induced gene silencing (VIGS). The GaGH3.6-silenced plants presented severe stress-susceptive phenotype, and suffered more serious oxidative damages by detecting some physiological and biochemical indexes, indicating that GaGH3.6 might participate in salt tolerance in cotton through regulating oxidation-reduction process. For the first time, a transcriptional atlas of cotton roots under salt stress were characterized at a single-cell resolution, which explored the cellular heterogeneityand differentiation trajectory, providing valuable insights into the molecular mechanism underlying stress tolerance in plants.

Genome-Wide Identification and Analysis of MYB Transcription Factors in Pyropia yezoensis

MYB transcription factors are one of the largest transcription factor families in plants, and they regulate numerous biological processes. Red algae are an important taxonomic group and have important roles in economics and research. However, no comprehensive analysis of the MYB gene family in any red algae, including Pyropia yezoensis, has been conducted. To identify the MYB gene members of Py. yezoensis, and to investigate their family structural features and expression profile characteristics, a study was conducted. In this study, 3 R2R3-MYBs and 13 MYB-related members were identified in Py. yezoensis. Phylogenetic analysis indicated that most red algae MYB genes could be clustered with green plants or Glaucophyta MYB genes, inferring their ancient origins. Synteny analysis indicated that 13 and 5 PyMYB genes were orthologous to Pyropia haitanensis and Porphyra umbilicalis, respectively. Most Bangiaceae MYB genes contain several Gly-rich motifs, which may be the result of an adaptation to carbon limitations and maintenance of important regulatory functions. An expression profile analysis showed that PyMYB genes exhibited diverse expression profiles. However, the expression patterns of different members appeared to be diverse, and PyMYB5 was upregulated in response to dehydration, low temperature, and Pythium porphyrae infection. This is the first comprehensive study of the MYB gene family in Py. Yezoensis and it provides vital insights into the functional divergence of MYB genes.

Genome-wide characterization, evolutionary analysis, and expression pattern analysis of the trihelix transcription factor family and gene expression analysis under MeJA treatment in Panax ginseng

Panax ginseng is a well-known medicinal plant with several pharmacological uses in China. The trihelix family transcription factors, also known as GT factors, can be involved in the regulation of growth and developmental processes in plants. There have been no in-depth reports or systematic studies about the trihelix transcription factor in ginseng. In this study, the structure, chromosomal localization, gene duplication, phylogeny, functional differentiation, expression patterns and coexpression interactions of trihelix transcripts were analysed using bioinformatics methods based on the ginseng transcriptome database. Thirty-two trihelix transcription factor genes were identified in ginseng, and these genes were alternatively spliced to obtain 218 transcripts. These transcripts were unevenly distributed on different chromosomes of ginseng, and phylogenetic analysis classified the PgGT transcripts into five subgroups. Gene Ontology (GO) analysis classified PgGT transcripts into eight functional subclasses, indicating that they are functionally diverse. The expression pattern analysis of 218 PgGT transcripts revealed that their expression was tissue-specific and spatiotemporally-specific in 14 different tissues of 4-year-old ginseng, 4 different ages of ginseng roots, and 42 farmers' cultivars of 4-year-old ginseng roots. Despite the differences in the expression patterns of these transcripts, coexpression network analysis revealed that these transcripts could be expressed synergistically in ginseng. In addition, two randomly selected PgGT transcripts in each of the five different subfamilies were subjected to methyl jasmonate treatment at different times, and PgGT was able to respond to the regulation of methy1 jasmonate. These results provide a theoretical basis and gene resources for an in-depth study of the function of trihelix genes in other plants.

Transcriptome-Wide Integrated Analysis of the PgGT25-04 Gene in Controlling Ginsenoside Biosynthesis in Panax ginseng

Panax ginseng is a valuable medicinal herb of the Araliaceae family with various pharmacological activities. The Trihelix transcription factors family is involved in growth and secondary metabolic processes in plants, but no studies have been reported on the involvement of Trihelix genes in secondary metabolic processes in ginseng. In this study, weighted co-expression network analysis, correlation analysis between PgGTs and ginsenosides and key enzyme genes, and interaction network analysis between PgGTs and key enzyme genes were used to screen out the PgGT25-04 gene, which was negatively correlated with ginsenoside synthesis. Using ABA treatment of ginseng hair roots, PgGT genes were found to respond to ABA signals. Analysis of the sequence characteristics and expression pattern of the PgGT25-04 gene in ginseng revealed that its expression is spatiotemporally specific. The interfering vector pBI121-PgGT25-04 containing the PgGT25-04 gene was constructed, and the ginseng adventitious roots were transformed using the Agrobacterium-mediated method to obtain the pBI121-PgGT25-04 positive hairy root monocot line. The saponin contents of positive ginseng hair roots were measured by HPLC, and the changes in PgGT25-04 and key enzyme genes in positive ginseng hair roots were detected via fluorescence quantitative RT-PCR. These results preliminarily identified the role of the PgGT25-04 gene in the secondary metabolism of ginseng in Jilin to provide a theoretical basis for the study of Trihelix transcription factors in Panax ginseng.

Large-scale analysis of putative Euphorbiaceae R2R3-MYB transcription factors identifies a MYB involved in seed oil biosynthesis

BACKGROUND

MYB transcription factors are widely distributed in the plant kingdom and play key roles in regulatory networks governing plant metabolism and biochemical and physiological processes.

RESULTS

Here, we first determined the R2R3-MYB genes in five Euphorbiaceae genomes. The three Trp (W) residues from the first MYB domain (R2) were absolutely conserved, whereas the first W residue from the second MYB domain (R3) was preferentially mutated. The R2R3-MYBs were clustered into 48 functional subfamilies, of which 34 had both R2R3-MYBs of Euphorbiaceae species and AtMYBs, and four contained only Euphorbiaceae R2R3-MYBs. The whole-genome duplication (WGD) and/or segmental duplication (SD) played key roles in the expansion of the R2R3-MYB family. Unlike paralogous R2R3-MYB family members, orthologous R2R3-MYB members contained a higher selective pressure and were subject to a constrained evolutionary rate. VfMYB36 was specifically expressed in fruit, and its trend was consistent with the change in oil content, indicating that it might be involved in oil biosynthesis. Overexpression experiments showed that VfMYB36 could significantly provide linolenic acid (C18:3) content, which eventually led to a significant increase in oil content.

CONCLUSION

Our study first provides insight into understanding the evolution and expression of R2R3-MYBs in Euphorbiaceae species, and also provides a target for the production of biomass diesel and a convenient way for breeding germplasm resources with high linolenic acid content in the future.

Identification and Functional Characterization of WRKY, PHD and MYB Three Salt Stress Responsive Gene Families in Mungbean (Vigna radiata L.)

WRKY-, PHD-, and MYB-like proteins are three important types of transcription factors in mungbeans, and play an important role in development and stress resistance. The genes' structures and characteristics were clearly reported and were shown to contain the conservative WRKYGQK heptapeptide sequence, Cys4-His-cys3 zinc binding motif, and HTH (helix) tryptophan cluster W structure, respectively. Knowledge on the response of these genes to salt stress is largely unknown. To address this issue, 83 VrWRKYs, 47 VrPHDs, and 149 VrMYBs were identified by using comparative genomics, transcriptomics, and molecular biology methods in mungbeans. An intraspecific synteny analysis revealed that the three gene families had strong co-linearity and an interspecies synteny analysis showed that mungbean and Arabidopsis were relatively close in genetic relationship. Moreover, 20, 10, and 20 genes showed significantly different expression levels after 15 days of salt treatment (p < 0.05; Log2 FC > 0.5), respectively. Additionally, in the qRT-PCR analysis, VrPHD14 had varying degrees of response to NaCl and PEG treatments after 12 h. VrWRKY49 was upregulated by ABA treatment, especially in the beginning (within 24 h). VrMYB96 was significantly upregulated in the early stages of ABA, NaCl, and PEG stress treatments (during the first 4 h). VrWRKY38 was significantly upregulated by ABA and NaCl treatments, but downregulated by PEG treatment. We also constructed a gene network centered on the seven DEGs under NaCl treatment; the results showed that VrWRKY38 was in the center of the PPI network and most of the homologous Arabidopsis genes of the interacted genes were reported to have response to biological stress. Candidate genes identified in this study provide abundant gene resources for the study of salt tolerance in mungbeans.