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A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Plant Genetics and Genomics".

Deadline for manuscript submissions: 15 March 2025 | Viewed by 10849

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Dr. Qi Tang

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Guest Editor

College of Horticulture, Hunan Agricultural University, Changsha 410128, China
Interests: molecular biology in medicinal plants; biosynthetic pathway; genome, transcriptome and proteome; synthetic biology
Special Issues, Collections and Topics in MDPI journals

Dr. Rufeng Wang

E-Mail Website
Guest Editor

Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai 201203, China
Interests: molecular biology in medicinal plants; biosynthetic pathway; biocatalysis; metabolic engineering; synthetic biology

Special Issue Information

Dear Colleagues,

Medicinal plants are an important resource for humans. However, compared with the research on model systems and crops, the number of studies on medicinal plants has fallen far behind. Recently, with the increase in demand for medicinal plants and the development and application of high-throughput technologies, the research field of medicinal plants has rapidly expanded. Significant progress has been made in studying the genomics, transcriptomics, proteomics, and metabolomics of medicinal plants. Numerous studies have contributed to elucidating the biosynthetic pathway of secondary metabolites, genes encoding key enzymes of the pathway, and regulatory mechanisms of secondary metabolites. This has enabled the production of secondary metabolites through metabolic engineering and synthetic biology. Moreover, novel technologies and strategies are being developed and applied to this research field. This open-access Special Issue of Genes is devoted to publishing original research and review articles on medicinal plant studies that highlight recent advances in the biosynthesis and regulatory mechanisms of secondary metabolites, particularly significant discoveries from intensive studies, and the development and application of novel technologies. This Special Issue aims to provide an accessible collection of research sharing innovative results from the research field of medicinal plants to aid further studies on secondary metabolism, medicinal plant improvement, and the production of functionally important secondary metabolites.

Topics of interest for this Special Issue include, but are not limited to:

The genomics, transcriptomics, proteomics, and metabolomics of medicinal plants;
Biosynthetic pathway of secondary metabolites;
Key enzyme genes involved in the biosynthesis of secondary metabolites;
Transcription factor and regulatory network in medicinal plants;
Metabolic engineering and synthetic biology of secondary metabolites;
Application of high-throughput sequencing technologies;
Databases associated with the biosynthesis and regulation of secondary metabolites;
Novel technologies and strategies for secondary metabolism studies.

Dr. Qi Tang
Dr. Rufeng Wang
Guest Editors

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Keywords

medicinal plants
biosynthetic pathway
molecular regulatory mechanisms
gene annotation
transcription factor
high-throughput sequencing
metabolic engineering
secondary metabolites
gene editing
multi-omics
genome, transcriptome, and proteome
metabolomics
synthetic biology
metabolic analysis
metabolic outline

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Published Papers (8 papers)

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Research

17 pages, 4606 KiB

Open AccessArticle

Multi-Omics Revealed Regulatory Mechanisms Underlying the Flowering of Ferula sinkiangensis across Three Dimensions

by Congzhao Fan, Yanfei Li, Jizhao Zhang, Yaqin Zhao, Yigong Zhang, Jun Zhu, Xingwang Gao, Yan Liang, Yuanjin Qiu, Jingyuan Song and Guoping Wang

Genes 2024, 15(10), 1275; https://doi.org/10.3390/genes15101275 - 28 Sep 2024

Viewed by 605

Abstract

Backgroud/Objectives: Ferula spp. is an essential crop in Central Asia with pronounced economic benefits governed by its flowering process. However, the mechanisms of the flowering phenotype remain unclear. Methods: In this study, using F. sinkiangensis as a model plant, we integrated transcriptome, proteome, and metabolome analyses to compare the multilayer differences in leaves and roots of plants with flowering and unflowering phenotypes. Results: We found that several variations in the transcriptome, proteome, and metabolome were closely associated with flowering. The Photosynthesis and Phenylpropanoid biosynthesis pathways in plants with the flowering phenotype were more active. Additionally, three flowering genes, named FL2–FL4, were upregulated in the leaves of flowering plants. Notably, six transcription factors were potentially responsible for regulating the expression of FL2–FL4 in the leaves to mediate flowering process of F. sinkiangensis. Moreover, genes relevant to Photosynthesis and Phenylpropanoid biosynthesis were also involved in regulating the expression of FL2–FL4 in flowering plants. Conclusions: The active regulation network together with Photosynthesis and Phenylpropanoid biosynthesis were essential for inducing the expression of flowering-related genes in leaves to promote the flowering process of F. sinkiangensis. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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19 pages, 8631 KiB

Open AccessArticle

Integrated Transcriptomics and Metabolomics Reveal Key Insights into Iridoid Biosynthesis in Gentiana crassicaulis Seeds during Germination

by Lechen Xuan, Hongyang Xiao, Zhili Zhao, Jingxian Feng, Lianghong Ni and Jinrong Wu

Genes 2024, 15(10), 1255; https://doi.org/10.3390/genes15101255 - 26 Sep 2024

Viewed by 549

Abstract

Background: Gentiana crassicaulis Duthie ex Burk., a key species used in traditional Chinese medicine for treating rheumatic pain and stroke, contains iridoids as its primary active component. However, the biosynthetic mechanisms underlying iridoid production are not fully understood. Methods: This study focused on iridoid biosynthesis during the germination of G. crassicaulis seeds, integrating metabolomic and transcriptomic analyses to uncover the underlying pathways and key candidate genes. Results: 196,132 unigenes and 10 iridoid compounds were identified through RNA-seq and ultra performance liquid chromatography-quadrupole time of flight-mass spectrometer (UPLC-Q-TOF-MS), respectively. The intersection of results from Pearson correlation analysis and weighted gene co-expression network analysis (WGCNA) revealed a significant correlation between 26 genes and iridoid levels, suggesting their potential role in the iridoid metabolism. Notably, six highly expressed candidate genes (DL7H, SLS, CYP76, CYP72A2, CYP84A1, and 13-LOX3) and five iridoids (loganic acid, sweroside, swertiamarin, gentiopicroside, and 6′-O-β-D-glucosyl-gentiopicroside) responded to methyl jasmonate stimulation in G. crassicaulis seedlings. Conclusions: by combining the known functions of candidate gene families, It is hypothesized that the CYP716 and LOX families exert indirect influences on iridoid metabolism, while the CYP71, CYP81, CYP72, CYP76, CYP710 families, 2OG-FeII family, and the glucosyltransferase family are likely to play direct roles in the biosynthetic transformations of the five iridoids. This study provides a theoretical basis for further functional gene validation and metabolic engineering aimed at enhancing iridoid production. The insights gained could lead to improved iridoid production efficiency in medicinal plants, ultimately benefiting the quality and efficacy of medicinal materials. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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14 pages, 12283 KiB

Open AccessArticle

The Complete Chloroplast Genome Sequence of the Medicinal Moss Rhodobryum giganteum (Bryaceae, Bryophyta): Comparative Genomics and Phylogenetic Analyses

by Zhengyuan Shen, Qin Liu, Jiewei Hao, Sheng Bi, Yezhen Fu and Lina Zhang

Genes 2024, 15(7), 900; https://doi.org/10.3390/genes15070900 - 10 Jul 2024

Viewed by 1212

Abstract

Rhodobryum giganteum (Bryaceae, Bryophyta), a rare medicinal bryophyte, is valued for its cardiovascular therapeutic properties in traditional Chinese medicine. This study presents the first complete chloroplast genome sequence of R. giganteum, including its assembly and annotation. The circular chloroplast genome of R. giganteum is 124,315 bp in length, displaying a typical quadripartite structure with 128 genes: 83 protein-coding genes, 37 tRNAs, and 8 rRNAs. Analyses of codon usage bias, repetitive sequences, and simple sequence repeats (SSRs) revealed an A/U-ending codon preference, 96 repetitive sequences, and 385 SSRs in the R. giganteum chloroplast genome. Nucleotide diversity analysis identified 10 high mutational hotspots. Ka/Ks ratio analysis suggested potential positive selection in rpl20, rps18, petG, and psbM genes. Phylogenetic analysis of whole chloroplast genomes from 38 moss species positioned R. giganteum within Bryales, closely related to Rhodobryum laxelimbatum. This study augments the chloroplast genomic data for Bryales and provides a foundation for molecular marker development and genetic diversity analyses in medicinal bryophytes. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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13 pages, 2607 KiB

Open AccessArticle

Isolation and Characterization of Phenylalanine Ammonia Lyase (PAL) Genes in Ferula pseudalliacea: Insights into the Phenylpropanoid Pathway

by Pegah Shahidi, Bahman Bahramnejad, Yavar Vafaee, Dara Dastan and Parviz Heidari

Genes 2024, 15(6), 771; https://doi.org/10.3390/genes15060771 - 12 Jun 2024

Cited by 2 | Viewed by 1129

Abstract

Phenylalanine ammonia lyase (PAL) is a key enzyme regulating the biosynthesis of the compounds of the phenylpropanoid pathway. This study aimed to isolate and characterize PAL genes from Ferula pseudalliacea Rech.f. (Apiales: Apiaceae) to better understand the regulation of metabolite production. Three PAL gene isoforms (FpPAL1-3) were identified and cloned using the 3′-RACE technique and confirmed by sequencing. Bioinformatics analysis revealed important structural features, such as phosphorylation sites, physicochemical properties, and evolutionary relationships. Expression analysis by qPCR demonstrated the differential transcription profiles of each FpPAL isoform across roots, stems, leaves, flowers, and seeds. FpPAL1 showed the highest expression in stems, FpPAL2 in roots and flowers, and FpPAL3 in flowers. The presence of three isoforms of PAL in F. pseudalliacea, along with the diversity of PAL genes and their tissue-specific expression profiles, suggests that complex modes of regulation exist for phenylpropanoid biosynthesis in this important medicinal plant. The predicted interaction network revealed associations with key metabolic pathways, emphasizing the multifaceted roles of these PAL genes. In silico biochemical analyses revealed the hydrophilicity of the FpPAL isozyme; however, further analysis of substrate specificity and enzyme kinetics can clarify the specific role of each FpPAL isozyme. These comprehensive results increase the understanding of PAL genes in F. pseudalliacea, helping to characterize their contributions to secondary metabolite biosynthesis. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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11 pages, 6285 KiB

Open AccessArticle

Genetic Identification of Medicinal Citrus Cultivar ‘Local Juhong’ Using Molecular Markers and Genomics

by Peng Chen, Jingbo Liu, Qi Tang, Tie Zhou, Lingxia Guo, Yuanyuan Xu, Lijun Chai, Qiang Xu, Ziniu Deng and Xianxin Li

Genes 2024, 15(6), 719; https://doi.org/10.3390/genes15060719 - 1 Jun 2024

Viewed by 941

Abstract

The citrus cultivar ‘Local Juhong’, which has historically been used as a traditional Chinese medicinal material, originated in Yuanjiang County, Hunan Province.Its parental type and genetic background are indistinct as of yet. Morphological observation shows that ‘Local Juhong’ has a slight oblateness in fruit shape, a relatively smooth pericarp, a fine and slightly raised oil vacuole, and an inward concave at the blossom end. The tree form and fruit and leaf morphology of ‘Local Juhong’ are similar to those of ‘Huangpi’ sour orange. To reveal the genetic background of ‘Local Juhong’, 21 citrus accessions were evaluated using nuclear and chloroplast SSR markers and whole-genome SNP information. ‘Local Juhong’ was grouped with mandarins and sub-grouped with ‘Miyagawa Wase’ and ‘Yanxi Wanlu’ in a nuclear SSR analysis, which indicated that its pollen parent might be mandarins. It was closely clustered with orange and pummelo in the chloroplast SSR analysis. The genomic sequence similarity rate of ‘Local Juhong’ with mandarin and pummelo heterozygosity was 70.88%; the main part was the heterozygosity, except for the unknown (19.66%), mandarin (8.73%), and pummelo (3.9%) parts. Thus, ‘Local Juhong’ may be an F₁ hybrid with pummelo as the female parent and mandarin as the male parent, sharing sisterhood with ‘Huangpi’ sour orange. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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22 pages, 9382 KiB

Open AccessArticle

Isolation, Characterization, and Expression Analysis of NAC Transcription Factor from Andrographis paniculata (Burm. f.) Nees and Their Role in Andrographolide Production

by Ramesh Kumar, Chavlesh Kumar, Debjani Roy Choudhury, Aashish Ranjan, Ritesh Kumar Raipuria, Kaushik Kumar Dhar Dubey, Ayushi Mishra, Chetan Kumar, Malik Muzafar Manzoor, Ashok Kumar, Abha Kumari, Kuldeep Singh, Gyanendra Pratap Singh and Rakesh Singh

Genes 2024, 15(4), 422; https://doi.org/10.3390/genes15040422 - 28 Mar 2024

Cited by 1 | Viewed by 2443

Abstract

Andrographis paniculata (Burm. f.) Nees is an important medicinal plant known for its bioactive compound andrographolide. NAC transcription factors (NAM, ATAF1/2, and CUC2) play a crucial role in secondary metabolite production, stress responses, and plant development through hormonal signaling. In this study, a putative partial transcript of three NAC family genes (ApNAC83, ApNAC21 22 and ApNAC02) was used to isolate full length genes using RACE. Bioinformatics analyses such as protein structure prediction, cis-acting regulatory elements, and gene ontology analysis were performed. Based on in silico predictions, the diterpenoid profiling of the plant’s leaves (five-week-old) and the real-time PCR-based expression analysis of isolated NAC genes under abscisic acid (ABA) treatment were performed. Additionally, the expression analysis of isolated NAC genes under MeJA treatment and transient expression in Nicotiana tabacum was performed. Full-length sequences of three members of the NAC transcription factor family, ApNAC83 (1102 bp), ApNAC21 22 (996 bp), and ApNAC02 (1011 bp), were isolated and subjected to the promoter and gene ontology analysis, which indicated their role in transcriptional regulation, DNA binding, ABA-activated signaling, and stress management. It was observed that ABA treatment leads to a higher accumulation of andrographolide and 14-deoxyandrographolide content, along with the upregulation of ApNAC02 (9.6-fold) and the downregulation of ApNAC83 and ApNAC21 22 in the leaves. With methyl jasmonate treatment, ApNAC21 22 expression decreased, while ApNAC02 increased (1.9-fold), with no significant change being observed in ApNAC83. The transient expression of the isolated NAC genes in a heterologous system (Nicotiana benthamiana) demonstrated their functional transcriptional activity, leading to the upregulation of the NtHMGR gene, which is related to the terpene pathway in tobacco. The expression analysis and heterologous expression of ApNAC21 22 and ApNAC02 indicated their role in andrographolide biosynthesis. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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15 pages, 9252 KiB

Open AccessArticle

Study of Dandelion (Taraxacum mongolicum Hand.-Mazz.) Salt Response and Caffeic Acid Metabolism under Saline Stress by Transcriptome Analysis

by Zhe Wu, Ran Meng, Wei Feng, Tassnapa Wongsnansilp, Zhaojia Li, Xuelin Lu and Xiuping Wang

Genes 2024, 15(2), 220; https://doi.org/10.3390/genes15020220 - 9 Feb 2024

Viewed by 1576

Abstract

Utilizing salt-tolerant plants is a cost-effective strategy for agricultural production on salinized land. However, little is known about the mechanism of dandelion (Taraxacum mongolicum Hand.-Mazz.) in response to saline stress and caffeic acid biosynthesis. We investigated the morphological and physiological variations of two dandelions, namely, “BINPU2” (dandelion A) and “TANGHAI” (dandelion B) under gradient NaCl concentrations (0, 0.3%, 0.5%, 0.7%, and 0.9%), and analyzed potential mechanisms through a comparison analysis of transcriptomes in the two dandelions. Dandelion A had a high leaf weight; high ρ-coumaric acid, caffeic acid, ferulic acid, and caffeoyl shikimic acid contents; and high activities of POD and Pro. The maximum content of four kinds of phenolic acids mostly occurred in the 0.7% NaCl treatment. In this saline treatment, 2468 and 3238 differentially expressed genes (DEGs) in dandelion A and B were found, of which 1456 and 1369 DEGs in the two dandelions, respectively, showed up-regulation, indicating that more up-regulated DEGs in dandelion A may cause its high salt tolerance. Further, Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis showed that dandelion salt response and caffeic acid metabolism were mainly enriched in the phenylpropanoid biosynthesis pathway (ko00940) and response to ethylene (GO: 0009723). The caffeic acid biosynthesis pathway was reconstructed based on DEGs which were annotated to PAL, C4H, 4CL, HCT, C3′H, and CSE. Most of these genes showed a down-regulated mode, except for parts of DEGs of 4CL (TbA05G077650 and TbA07G073600), HCT (TbA03G009110, TbA03G009080, and novel.16880), and COMT (novel.13839). In addition, more up-regulated transcription factors (TFs) of ethylene TFs in dandelion A were found, but the TFs of ERF104, CEJ1, and ERF3 in the two dandelions under saline stress showed an opposite expression pattern. These up-regulated genes could enhance dandelion salt tolerance, and down-regulated DEGs in the caffeic acid biosynthesis pathway, especially CSE (TbA08G014310) and COMT (TbA04G07330), could be important candidate genes in the synthesis of caffeic acid under saline stress. The above findings revealed the potential mechanisms of salt response and caffeic acid metabolism in dandelion under saline stress, and provide references for salt-tolerant plant breeding and cultivation on saline–alkali land in the future. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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16 pages, 2062 KiB

Open AccessArticle

Selection and Verification of Standardized Reference Genes of Angelica dahurica under Various Abiotic Stresses by Real-Time Quantitative PCR

by Jing Zhang, Xinyi He, Jun Zhou, Zhuang Dong, Han Yu, Qi Tang, Lei Yuan, Siqing Peng, Xiaohong Zhong and Yuedong He

Genes 2024, 15(1), 79; https://doi.org/10.3390/genes15010079 - 7 Jan 2024

Cited by 1 | Viewed by 1582

Abstract

In traditional Chinese medicine, Angelica dahurica is a valuable herb with numerous therapeutic applications for a range of ailments. There have not yet been any articles on the methodical assessment and choice of the best reference genes for A. dahurica gene expression studies. Real-time quantitative PCR (RT-qPCR) is widely employed as the predominant method for investigating gene expression. In order to ensure the precise determination of target gene expression outcomes in RT-qPCR analysis, it is imperative to employ stable reference genes. In this study, a total of 11 candidate reference genes including SAND family protein (SAND), polypyrimidine tract-binding protein (PTBP), glyceraldehyde-3-phosphate dehydrogenase (GAPDH), actin (ACT), TIP41-like protein (TIP41), cyclophilin 2 (CYP2), elongation factor 1 α (EF1α), ubiquitin-protein ligase 9 (UBC9), tubulin β-6 (TUB6), thioredoxin-like protein YLS8 (YLS8), and tubulin-α (TUBA) were selected from the transcriptome of A. dahurica. Subsequently, three statistical algorithms (geNorm, NormFinder, and BestKeeper) were employed to assess the stability of their expression patterns across seven distinct stimulus treatments. The outcomes obtained from these analyses were subsequently amalgamated into a comprehensive ranking using RefFinder. Additionally, one target gene, phenylalanine ammonia-lyase (PAL), was used to confirm the effectiveness of the selected reference genes. According to the findings of this study, the two most stable reference genes for normalizing the expression of genes in A. dahurica are TIP41 and UBC9. Overall, our research has determined the appropriate reference genes for RT-qPCR in A. dahurica and provides a crucial foundation for gene screening and identifying genes associated with the biosynthesis of active ingredients in A. dahurica. Full article

(This article belongs to the Special Issue Genomics and Genetics of Medicinal Plants)

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