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Singh D, Mittal N, Mittal P, Siddiqui MH. Transcriptome sequencing of medical herb Salvia Rosmarinus (Rosemary) revealed the phenylpropanoid biosynthesis pathway genes and their phylogenetic relationships. Mol Biol Rep 2024; 51:757. [PMID: 38874856 DOI: 10.1007/s11033-024-09685-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Accepted: 05/30/2024] [Indexed: 06/15/2024]
Abstract
BACKGROUND The Salvia rosmarinus spenn. (rosemary) is considered an economically important ornamental and medicinal plant and is widely utilized in culinary and for treating several diseases. However, the procedure behind synthesizing secondary metabolites-based bioactive compounds at the molecular level in S. rosmarinus is not explored completely. METHODS AND RESULTS We performed transcriptomic sequencing of the pooled sample from leaf and stem tissues on the Illumina HiSeqTM X10 platform. The transcriptomics analysis led to the generation of 29,523,608 raw reads, followed by data pre-processing which generated 23,208,592 clean reads, and de novo assembly of S. rosmarinus obtained 166,849 unigenes. Among them, nearly 75.1% of unigenes i.e., 28,757 were interpreted against a non-redundant protein database. The gene ontology-based annotation classified them into 3 main categories and 55 sub-categories, and clusters of orthologous genes annotation categorized them into 23 functional categories. The Kyoto Encyclopedia of Genes and Genomes database-based pathway analysis confirmed the involvement of 13,402 unigenes in 183 biochemical pathways, among these unigenes, 1,186 are involved in the 17 secondary metabolite production pathways. Several key enzymes involved in producing aromatic amino acids and phenylpropanoids were identified from the transcriptome database. Among the identified 48 families of transcription factors from coding unigenes, bHLH, MYB, WRKYs, NAC, C2H2, C3H, and ERF are involved in flavonoids and other secondary metabolites biosynthesis. CONCLUSION The phylogenetic analysis revealed the evolutionary relationship between the phenylpropanoid pathway genes of rosemary with other members of Lamiaceae. Our work reveals a new molecular mechanism behind the biosynthesis of phenylpropanoids and their regulation in rosemary plants.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Kursi Road, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Faculty of Biosciences, Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Pooja Mittal
- Chitkara College of Pharmacy, Chitkara University, Rajpura, Punjab, 140401, India
| | - Mohammed Haris Siddiqui
- Department of Bioengineering, Integral University, Kursi Road, Lucknow, Uttar Pradesh, 226026, India.
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Tyagi P, Prasad M, Mathur S, Ranjan R. Diosgenin biosynthesis investigation in medicinal herb (Tribulus terrestris) by transcriptome analysis. Gene 2024; 893:147937. [PMID: 38381509 DOI: 10.1016/j.gene.2023.147937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 10/16/2023] [Accepted: 10/26/2023] [Indexed: 02/22/2024]
Abstract
Next-generation sequencing (NGS) has revolutionized the analysis of specific genes, pathways, and their regulation in various species. Tribulus terrestris L., an annual medicinal herb of Zygophyllaceae family, has gained significant attention due to its diverse medicinal properties, including anti-inflammatory, antimicrobial, and anti-cancer effects. Diosgenin, a steroidal saponin, is the major bioactive compound responsible for the medicinal importance of T. terrestris. However, there is a paucity of information regarding the genes involved in the diosgenin biosynthetic pathway in T. terrestris. To address this gap, this study aimed to identify candidate genes associated with diosgenin biosynthesis through whole transcriptome profiling. A total of ∼7.9 GB of data, comprising 482 million reads, was obtained and assembled into 148,871 unigenes. Subsequently, functional annotations were assigned to 50 % of the unigenes using sequence similarity searches against the NCBI non-redundant (NR), Uniprot, KEGG, Pfam, GO, and COG databases, primarily based on Gene Ontology and KEGG-KAAS pathways. The majority of unigenes associated with the biosynthesis of the steroidal diosgenin backbone exhibited up-regulation in the fruit, leaf, and root tissues, except the SQE gene in root. The differential expression of selected genes was further validated through quantitative real-time polymerase chain reaction (qRT-PCR). Additionally, the study identified 21,026 unigenes related to transcription factors and 15,551 unigenes containing simple sequence repeats (SSR). Notably, di-nucleotide SSR motifs exhibited a high repeat frequency. These findings greatly enhance our understanding of the diosgenin biosynthesis pathway and provide a basis for future research in molecular investigation and metabolic engineering, specifically for boosting diosgenin content.
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Affiliation(s)
- Parul Tyagi
- Plant Molecular Biology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India
| | - Mrinalini Prasad
- Plant Molecular Biology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India
| | - Shivangi Mathur
- Plant Molecular Biology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India
| | - Rajiv Ranjan
- Plant Molecular Biology Lab, Department of Botany, Faculty of Science, Dayalbagh Educational Institute, Dayalbagh, Agra-282005, India.
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Ren WJ, Io CC, Jiang R, Ng KF, Liu JZ, Bai LP, Zhang W, Jiang ZH, Liu YH, Zhu GY. Di- and Triterpenoids from the Rhizomes of Isodon amethystoides and Their Anti-inflammatory Activities. JOURNAL OF NATURAL PRODUCTS 2023; 86:1230-1239. [PMID: 37146221 DOI: 10.1021/acs.jnatprod.2c01136] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
Amethystoidesic acid (1), a triterpenoid with an unprecedented 5/6/6/6 tetracyclic skeleton, and six undescribed diterpenoids, amethystoidins A-F (2-7), were isolated from the rhizomes of Isodon amethystoides along with 31 known di- and triterpenoids (8-38). Their structures were fully elucidated via extensive spectroscopic analysis including 1D and 2D NMR, high-resolution electrospray ionization mass spectrometry (HRESIMS), and electronic circular dichroism (ECD) calculations. Compound 1 is the first example of a triterpenoid possessing a rare ring system (5/6/6/6) derived from a contracted A-ring and the 18,19-seco-E-ring of ursolic acid. Compounds 6, 16, 21, 22, 24, and 27 significantly inhibited nitric oxide (NO) production in lipopolysaccharide (LPS)-stimulated RAW264.7 cells, which could be partly mediated by the downregulation of LPS-induced inducible nitric oxide synthase (iNOS) protein expression.
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Affiliation(s)
- Wen-Jing Ren
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Chi-Cheng Io
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Rong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Kei-Fong Ng
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Jia-Zheng Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Li-Ping Bai
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Zhi-Hong Jiang
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
| | - Yu-Hong Liu
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
- School of Pharmaceutical Sciences, Shandong University of Traditional Chinese Medicine, Jinan 250355, People's Republic of China
| | - Guo-Yuan Zhu
- State Key Laboratory of Quality Research in Chinese Medicine, Guangdong-Hong Kong-Macao Joint Laboratory of Respiratory Infectious Disease, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Macau 999078, People's Republic of China
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Combined analysis of transcriptomics and metabolomics revealed complex metabolic genes for diterpenoids biosynthesis in different organs of Anoectochilus roxburghii. CHINESE HERBAL MEDICINES 2022. [DOI: 10.1016/j.chmed.2022.11.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Comparative Transcriptome Analyses of Different Rheum officinale Tissues Reveal Differentially Expressed Genes Associated with Anthraquinone, Catechin, and Gallic Acid Biosynthesis. Genes (Basel) 2022; 13:genes13091592. [PMID: 36140760 PMCID: PMC9498579 DOI: 10.3390/genes13091592] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 08/30/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022] Open
Abstract
Rheum officinale Baill. is an important traditional Chinese medicinal herb, its dried roots and rhizomes being widely utilized to cure diverse diseases. However, previous studies mainly focused on the active compounds and their pharmacological effects, and the molecular mechanism underlying the biosynthesis of these ingredients in R. officinale is still elusive. Here, we performed comparative transcriptome analyses to elucidate the differentially expressed genes (DEGs) in the root, stem, and leaf of R. officinale. A total of 236,031 unigenes with N50 of 769 bp was generated, 136,329 (57.76%) of which were annotated. A total of 5884 DEGs was identified after the comparative analyses of different tissues; 175 and 126 key enzyme genes with tissue-specific expression were found in the anthraquinone, catechin/gallic acid biosynthetic pathway, respectively, and some of these key enzyme genes were verified by qRT-PCR. The phylogeny of the PKS III family in Polygonaceae indicated that probably only PL_741 PKSIII1, PL_11549 PKSIII5, and PL_101745 PKSIII6 encoded PKSIII in the polyketide pathway. These results will shed light on the molecular basis of the tissue-specific accumulation and regulation of secondary metabolites in R. officinale, and lay a foundation for the future genetic diversity, molecular assisted breeding, and germplasm resource improvement of this essential medicinal plant.
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Full-length transcriptome analysis provides new insights into the early bolting occurrence in medicinal Angelica sinensis. Sci Rep 2021; 11:13000. [PMID: 34155325 PMCID: PMC8217430 DOI: 10.1038/s41598-021-92494-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Accepted: 06/08/2021] [Indexed: 02/05/2023] Open
Abstract
Angelica sinensis (Oliv.) Diels root part is an integral component of traditional Chinese medicine, widely prescribed to improve blood circulation and blood stasis. However, early bolting of A. sinensis compromises the quality of the roots and hence is a major limitation for yield of medicinal materials. To date, little information about the molecular mechanisms underlying bolting is available for this important medicinal plant. To identify genes putatively involved in early bolting, we have conducted the transcriptome analysis of the shoot tips of the early-bolting plants and non-bolting (normal) plants of A. sinensis, respectively, using a combination of third-generation sequencing and next-generation sequencing. A total of 43,438 non-redundant transcripts were collected and 475 unique differentially expressed genes (DEGs) were identified. Gene annotation and functional analyses revealed that DEGs were highly involved in plant hormone signaling and biosynthesis pathways, three main flowering pathways, pollen formation, and very-long-chain fatty acids biosynthesis pathways. The levels of endogenous hormones were also changed significantly in the early bolting stage of A. sinensis. This study provided new insights into the transcriptomic control of early bolting in A. sinensis, which could be further applied to enhance the yield of medicinally important raw materials.
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Sun M, Dong Z, Yang J, Wu W, Zhang C, Zhang J, Zhao J, Xiong Y, Jia S, Ma X. Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers. BMC PLANT BIOLOGY 2021; 21:264. [PMID: 34098903 PMCID: PMC8186225 DOI: 10.1186/s12870-021-03037-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2021] [Accepted: 05/11/2021] [Indexed: 05/27/2023]
Abstract
BACKGROUND Prairie grass (Bromus catharticus) is a typical cool-season forage crop with high biomass production and fast growth rate during winter and spring. However, its genetic research and breeding has remained stagnant due to limited available genomic resources. The aim of this study was to generate large-scale genomic data using high-throughput transcriptome sequencing, and perform a preliminary validation of EST-SSR markers of B. catharticus. RESULTS Eleven tissue samples including seeds, leaves, and stems were collected from a new high-yield strain of prairie grass BCS1103. A total of 257,773 unigenes were obtained, of which 193,082 (74.90%) were annotated. Comparison analysis between tissues identified 1803, 3030, and 1570 genes specifically and highly expressed in seed, leaf, and stem, respectively. A total of 37,288 EST-SSRs were identified from unigene sequences, and more than 80,000 primer pairs were designed. We synthesized 420 primer pairs and selected 52 ones with high polymorphisms to estimate genetic diversity and population structure in 24 B. catharticus accessions worldwide. Despite low diversity indicated by an average genetic distance of 0.364, the accessions from South America and Asia and wild accessions showed higher genetic diversity. Moreover, South American accessions showed a pure ancestry, while Asian accessions demonstrated mixed internal relationships, which indicated a different probability of gene flow. Phylogenetic analysis clustered the studied accessions into four clades, being consistent with phenotypic clustering results. Finally, Mantel analysis suggested the total phenotypic variation was mostly contributed by genetic component. Stem diameter, plant height, leaf width, and biomass yield were significantly correlated with genetic data (r > 0.6, P < 0.001), and might be used in the future selection and breeding. CONCLUSION A genomic resource was generated that could benefit genetic and taxonomic studies, as well as molecular breeding for B. catharticus and its relatives in the future.
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Affiliation(s)
- Ming Sun
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Zhixiao Dong
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jian Yang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Wendan Wu
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Chenglin Zhang
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jianbo Zhang
- Sichuan Academy of Grassland Science, Chengdu, 611731, Sichuan, China
| | - Junming Zhao
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi Xiong
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Shangang Jia
- College of Grassland Science and Technology, China Agricultural University, Beijing, 100193, China.
- Key Laboratory of Pratacultural Science, Beijing Municipality, China Agricultural University, Beijing, 100193, China.
| | - Xiao Ma
- Department of Grassland Science, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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Wang X, Hu H, Wu Z, Fan H, Wang G, Chai T, Wang H. Tissue-specific transcriptome analyses reveal candidate genes for stilbene, flavonoid and anthraquinone biosynthesis in the medicinal plant Polygonum cuspidatum. BMC Genomics 2021; 22:353. [PMID: 34000984 PMCID: PMC8127498 DOI: 10.1186/s12864-021-07658-3] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2020] [Accepted: 04/28/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Polygonum cuspidatum Sieb. et Zucc. is a well-known medicinal plant whose pharmacological effects derive mainly from its stilbenes, anthraquinones, and flavonoids. These compounds accumulate differentially in the root, stem, and leaf; however, the molecular basis of such tissue-specific accumulation remains poorly understood. Because tissue-specific accumulation of compounds is usually associated with tissue-specific expression of the related biosynthetic enzyme genes and regulators, we aimed to clarify and compare the transcripts expressed in different tissues of P. cuspidatum in this study. RESULTS High-throughput RNA sequencing was performed using three different tissues (the leaf, stem, and root) of P. cuspidatum. In total, 80,981 unigenes were obtained, of which 40,729 were annotated, and 21,235 differentially expressed genes were identified. Fifty-four candidate synthetase genes and 12 transcription factors associated with stilbene, flavonoid, and anthraquinone biosynthetic pathways were identified, and their expression levels in the three different tissues were analyzed. Phylogenetic analysis of polyketide synthase gene families revealed two novel CHS genes in P. cuspidatum. Most phenylpropanoid pathway genes were predominantly expressed in the root and stem, while methylerythritol 4-phosphate and isochorismate pathways for anthraquinone biosynthesis were dominant in the leaf. The expression patterns of synthase genes were almost in accordance with metabolite profiling in different tissues of P. cuspidatum as measured by high-performance liquid chromatography or ultraviolet spectrophotometry. All predicted transcription factors associated with regulation of the phenylpropanoid pathway were expressed at lower levels in the stem than in the leaf and root, but no consistent trend in their expression was observed between the leaf and the root. CONCLUSIONS The molecular knowledge of key genes involved in the biosynthesis of P. cuspidatum stilbenes, flavonoids, and anthraquinones is poor. This study offers some novel insights into the biosynthetic regulation of bioactive compounds in different P. cuspidatum tissues and provides valuable resources for the potential metabolic engineering of this important medicinal plant.
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Affiliation(s)
- Xiaowei Wang
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Hongyan Hu
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Zhijun Wu
- School of Life Sciences and Biotechnology, Heilongjiang Bayi Agricultural University, Daqing, 163319, China
| | - Haili Fan
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Guowei Wang
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China
| | - Tuanyao Chai
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China.
- Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Hong Wang
- College of Life Sciences, University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing, 100049, People's Republic of China.
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A comparison of shared patterns of differential gene expression and gene ontologies in response to water-stress in roots and leaves of four diverse genotypes of Lolium and Festuca spp. temperate pasture grasses. PLoS One 2021; 16:e0249636. [PMID: 33831050 PMCID: PMC8031407 DOI: 10.1371/journal.pone.0249636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 03/22/2021] [Indexed: 12/13/2022] Open
Abstract
Ryegrasses (Lolium spp.) and fescues (Festuca spp.) are closely related and widely cultivated perennial forage grasses. As such, resilience in the face of abiotic stresses is an important component of their traits. We have compared patterns of differentially expressed genes (DEGs) in roots and leaves of two perennial ryegrass genotypes and a single genotype of each of a festulolium (predominantly Italian ryegrass) and meadow fescue with the onset of water stress, focussing on overall patterns of DEGs and gene ontology terms (GOs) shared by all four genotypes. Plants were established in a growing medium of vermiculite watered with nutrient solution. Leaf and root material were sampled at 35% (saturation) and, as the medium dried, at 15%, 5% and 1% estimated water contents (EWCs) and RNA extracted. Differential gene expression was evaluated comparing the EWC sampling points from RNAseq data using a combination of analysis methods. For all genotypes, the greatest numbers of DEGs were identified in the 35/1 and 5/1 comparisons in both leaves and roots. In total, 566 leaf and 643 root DEGs were common to all 4 genotypes, though a third of these leaf DEGs were not regulated in the same up/down direction in all 4 genotypes. For roots, the equivalent figure was 1% of the DEGs. GO terms shared by all four genotypes were often enriched by both up- and down-regulated DEGs in the leaf, whereas generally, only by either up- or down-regulated DEGs in the root. Overall, up-regulated leaf DEGs tended to be more genotype-specific than down-regulated leaf DEGs or root DEGs and were also associated with fewer GOs. On average, only 5–15% of the DEGs enriching common GO terms were shared by all 4 genotypes, suggesting considerable variation in DEGs between related genotypes in enacting similar biological processes.
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Identification and characterization of potential antioxidant components in Isodon amethystoides (Benth.) Hara tea leaves by UPLC-LTQ-Orbitrap-MS. Food Chem Toxicol 2021; 148:111961. [DOI: 10.1016/j.fct.2020.111961] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/20/2020] [Accepted: 12/24/2020] [Indexed: 12/19/2022]
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Liu Y, Li M, Li T, Chen Y, Zhang L, Zhao G, Zhuang J, Zhao W, Gao L, Xia T. Airborne fungus-induced biosynthesis of anthocyanins in Arabidopsis thaliana via jasmonic acid and salicylic acid signaling. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 300:110635. [PMID: 33180713 DOI: 10.1016/j.plantsci.2020.110635] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2019] [Revised: 08/09/2020] [Accepted: 08/11/2020] [Indexed: 06/11/2023]
Abstract
Anthocyanins are plant-specific pigments, the biosynthesis of which is stimulated by pathogen infection in several plant species. A. thaliana seedlings injected with airborne fungi can accumulate a high content of anthocyanins. The mechanism involved in fungus-induced anthocyanin accumulation in plants has not been fully described. In this study, the fungus Penicillium corylophilum (P. corylophilum), isolated from an Arabidopsis culture chamber, triggered jasmonic acid (JA), salicylic acid (SA), and anthocyanin accumulation in A. thaliana. Inhibitors of JA and SA biosynthesis suppressed the anthocyanin accumulation induced by P. corylophilum. The anthocyanin content was minimal in both the null mutant of JA-receptor coi1 and the null mutant of SA-receptor npr1 under P. corylophilum stimulation. The results indicate that JA and SA signaling mediated fungus-induced anthocyanin biosynthesis in A. thaliana. P. corylophilum led to different levels of anthocyanin generation in null mutants for MYB75, bHLH, EGL3, and GL3 transcription factors and WD40 protein, demonstrating that multiple MYB-bHLH-WD40 transcription factor complexes participated in fungus-induced anthocyanin accumulation in A. thaliana. The present study will help further elucidate the mechanism of plant resistance to pathogen infection.
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Affiliation(s)
- Yajun Liu
- School of Life Science, Anhui Agricultural University, Hefei 230036, China; State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Ming Li
- School of Life Science, Anhui Agricultural University, Hefei 230036, China; Guangdong Provincial Key Laboratory of Protein Function and Regulation in Agricultural Organisms, College of Life Sciences, South China Agricultural University, Guangzhou 510642, China
| | - Tongtong Li
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Yujie Chen
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Lingjie Zhang
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Guifu Zhao
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China
| | - Juhua Zhuang
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Wenyan Zhao
- School of Life Science, Anhui Agricultural University, Hefei 230036, China
| | - Liping Gao
- School of Life Science, Anhui Agricultural University, Hefei 230036, China.
| | - Tao Xia
- State Key Laboratory of Tea Plant Biology and Utilization, Anhui Agricultural University, Hefei 230036, China.
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Mitu SA, Cummins SF, Reddell PW, Ogbourne SM. Transcriptome analysis of the medicinally significant plant Fontainea picrosperma (Euphorbiaceae) reveals conserved biosynthetic pathways. Fitoterapia 2020; 146:104680. [DOI: 10.1016/j.fitote.2020.104680] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2020] [Revised: 06/17/2020] [Accepted: 06/21/2020] [Indexed: 01/27/2023]
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Comparative transcriptome analysis of root, stem, and leaf tissues of Entada phaseoloides reveals potential genes involved in triterpenoid saponin biosynthesis. BMC Genomics 2020; 21:639. [PMID: 32933468 PMCID: PMC7493163 DOI: 10.1186/s12864-020-07056-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 09/06/2020] [Indexed: 12/15/2022] Open
Abstract
Background Entada phaseoloides (L.) Merr. is an important traditional medicinal plant. The stem of Entada phaseoloides is popularly used as traditional medicine because of its significance in dispelling wind and dampness and remarkable anti-inflammatory activities. Triterpenoid saponins are the major bioactive compounds of Entada phaseoloides. However, genomic or transcriptomic technologies have not been used to study the triterpenoid saponin biosynthetic pathway in this plant. Results We performed comparative transcriptome analysis of the root, stem, and leaf tissues of Entada phaseoloides with three independent biological replicates and obtained a total of 53.26 Gb clean data and 116,910 unigenes, with an average N50 length of 1218 bp. Putative functions could be annotated to 42,191 unigenes (36.1%) based on BLASTx searches against the Non-redundant, Uniprot, KEGG, Pfam, GO, KEGG and COG databases. Most of the unigenes related to triterpenoid saponin backbone biosynthesis were specifically upregulated in the stem. A total of 26 cytochrome P450 and 17 uridine diphosphate glycosyltransferase candidate genes related to triterpenoid saponin biosynthesis were identified. The differential expressions of selected genes were further verified by qPT-PCR. Conclusions The dataset reported here will facilitate the research about the functional genomics of triterpenoid saponin biosynthesis and genetic engineering of Entada phaseoloides.
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Yang X, Zhang L, Xiang Y, Du L, Huang X, Liu Y. Comparative transcriptome analysis of Sclerotinia sclerotiorum revealed its response mechanisms to the biological control agent, Bacillus amyloliquefaciens. Sci Rep 2020; 10:12576. [PMID: 32724140 PMCID: PMC7387486 DOI: 10.1038/s41598-020-69434-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 07/12/2020] [Indexed: 11/08/2022] Open
Abstract
Biological control mechanisms of plant diseases have been intensively studied. However, how plant pathogens respond to and resist or alleviate biocontrol agents remains largely unknown. In this study, a comparative transcriptome analysis was performed to elucidate how the pathogen of sclerotinia stem rot, Sclerotinia sclerotiorum, responds and resists to the biocontrol agent, Bacillus amyloliquefaciens. Results revealed that a total of 2,373 genes were differentially expressed in S. sclerotiorum samples treated with B. amyloliquefaciens fermentation broth (TS) when compared to control samples (CS). Among these genes, 2,017 were upregulated and 356 were downregulated. Further analyses indicated that various genes related to fungal cell wall and cell membrane synthesis, antioxidants, and the autophagy pathway were significantly upregulated, including glucan synthesis, ergosterol biosynthesis pathway, fatty acid synthase, heme-binding peroxidase related to oxidative stress, glutathione S-transferase, ABC transporter, and autophagy-related genes. These results suggest that S. sclerotiorum recruits numerous genes to respond to or resist the biocontrol of B. amyloliquefaciens. Thus, this study serves as a valuable resource regarding the mechanisms of fungal pathogen resistance to biocontrol agents.
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Affiliation(s)
- Xiaoxiang Yang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China
| | - Lei Zhang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China
| | - Yunjia Xiang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
| | - Lei Du
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China
| | - Xiaoqin Huang
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China.
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China.
| | - Yong Liu
- Institute of Plant Protection, Sichuan Academy of Agricultural Sciences, Chengdu, 610066, Sichuan, People's Republic of China.
- Key Laboratory of Integrated Pest Management on Crops in Southwest, Ministry of Agriculture and Rural Affairs, Chengdu, 610066, Sichuan, People's Republic of China.
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Thakur V, Bains S, Pathania S, Sharma S, Kaur R, Singh K. Comparative transcriptomics reveals candidate transcription factors involved in costunolide biosynthesis in medicinal plant-Saussurea lappa. Int J Biol Macromol 2020; 150:52-67. [DOI: 10.1016/j.ijbiomac.2020.01.312] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 01/28/2020] [Accepted: 01/28/2020] [Indexed: 01/01/2023]
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Xue T, Zhang H, Zhang Y, Wei S, Chao Q, Zhu Y, Teng J, Zhang A, Sheng W, Duan Y, Xue J. Full-length transcriptome analysis of shade-induced promotion of tuber production in Pinellia ternata. BMC PLANT BIOLOGY 2019; 19:565. [PMID: 31852442 PMCID: PMC6921527 DOI: 10.1186/s12870-019-2197-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Accepted: 12/10/2019] [Indexed: 06/10/2023]
Abstract
BACKGROUND Pinellia ternata is native to China and has been used as a traditional herb due to its antiemetic, antitussive, analgesic, and anxiolytic effects. When exposed to strong light intensity and high temperature during the reproductive growth process, P. ternata withers in a phenomenon known as "sprout tumble", which largely limits tuber production. Shade was previously found to delay sprout tumble formation (STF); however, no information exists regarding this process at the molecular level. Hence, we determined the genes involved in tuber development and STF in P. ternata. RESULTS Compared to that with natural sun-light (control), shade significantly induced chlorophyll accumulation, increased chlorophyll fluorescence parameters including initial fluorescence, maximal fluorescence, and qP, and dramatically repressed chlorophyll a:b and NPQ. Catalase (CAT) activity was largely induced by shade, and tuber products were largely increased in this environment. Transcriptome profiles of P. ternata grown in natural sun-light and shaded environments were analyzed by a combination of next generation sequencing (NGS) and third generation single-molecule real-time (SMRT) sequencing. Corrections of SMRT long reads based on NGS short reads yielded 136,163 non-redundant transcripts, with an average N50 length of 2578 bp. In total, 6738 deferentially-expressed genes (DEGs) were obtained from the comparisons, specifically D5S vs D5CK, D20S vs D20CK, D20S vs D5S, and D20CK vs D5CK, of which, 6384 DEGs (94.8%) were generated from the D20S vs D20CK comparison. Gene annotation and functional analyses revealed that these genes were related to auxin signal transduction, polysaccharide and sugar metabolism, phenylpropanoid biosynthesis, and photosynthesis. Moreover, the expression of genes enriched in photosynthesis appeared to be significantly altered by shade. The expression patterns of 16 candidate genes were consistent with changes in their transcript abundance as identified by RNA-Seq, and these might contribute to STF and tuber production. CONCLUSION The full-length transcripts identified in this study have provided a more accurate depiction of P. ternata gene transcription. Further, we identified potential genes involved in STF and tuber growth. Such data could serve as a genetic resource and a foundation for further research on this important traditional herb.
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Affiliation(s)
- Tao Xue
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Han Zhang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yuanyuan Zhang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Shuqin Wei
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Qiujie Chao
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yanfang Zhu
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Jingtong Teng
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Aimin Zhang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Wei Sheng
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China
| | - Yongbo Duan
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
| | - Jianping Xue
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, 235000, China.
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Wen C, Chen S, Yuan F, Liu X, Song F, Mei Z, Yang X, Yang G. Diterpenoids from Isodon rubescens and their nitric oxide production inhibitory activity. RSC Adv 2019; 9:40628-40635. [PMID: 35542677 PMCID: PMC9076279 DOI: 10.1039/c9ra08831h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 12/02/2019] [Indexed: 11/25/2022] Open
Abstract
Six new ent-kaurane diterpenoids, isodonrubescins A-F (1-6), together with twenty-five known ent-kaurane diterpenoids (7-31), a known ent-atisane diterpenoid (32), and two known ent-abietane diterpenoids (33-34), were isolated from Isodon rubescens. Their structures were established by means of extensive MS and NMR data analysis. Among the all isolates, compound 7 was found in a natural product for the first time, and ent-atisane diterpenoid was discovered from I. rubescens in Hubei Province, P. R. China for the first time. Furthermore, all the isolated compounds were tested for their NO production inhibitory activity in LPS stimulated RAW264.7 cells. Compounds 7-9, 12, 13, 16, and 17 displayed NO production inhibitory activities with IC50 values ranging from 1.36 to 18.25 μM, respectively.
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Affiliation(s)
- Chumao Wen
- College of Biomedical Engineering, South-Central University for Nationalities Wuhan 430074 P. R. China +86 27 6784 1196 +86 27 6784 1196
| | - Su Chen
- College of Biomedical Engineering, South-Central University for Nationalities Wuhan 430074 P. R. China +86 27 6784 1196 +86 27 6784 1196
| | - Fang Yuan
- College of Biomedical Engineering, South-Central University for Nationalities Wuhan 430074 P. R. China +86 27 6784 1196 +86 27 6784 1196
| | - Xiangming Liu
- College of Biomedical Engineering, South-Central University for Nationalities Wuhan 430074 P. R. China +86 27 6784 1196 +86 27 6784 1196
| | - Fajun Song
- College of Life Science, South Central University for Nationalities Wuhan 430074 P. R. China
| | - Zhinan Mei
- School of Pharmaceutical Sciences, South-Central University for Nationalities Wuhan 430074 P. R. China
| | - Xiaofei Yang
- College of Biomedical Engineering, South-Central University for Nationalities Wuhan 430074 P. R. China +86 27 6784 1196 +86 27 6784 1196
| | - Guangzhong Yang
- School of Pharmaceutical Sciences, South-Central University for Nationalities Wuhan 430074 P. R. China
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Zhao F, Zhang W, Meng X, Yang X, Yang L, Teng J, Xue J, Duan Y, Sheng W. Antioxidant and antimicrobial properties of Isodon amethystoides (Benth.) CY Wu et Hsuan leaf extracts against agriculturally important pathogenic fungi. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1695542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
Affiliation(s)
- Fenglan Zhao
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Wanjun Zhang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Xue Meng
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Xue Yang
- Laboratory for Risk Assessment of Quality and Safety of Agro-Products, MOA, Institute of Plant Protection, Anhui Academy of Agricultural Sciences, Hefei, Anhui, P.R. China
| | - Lianzhi Yang
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Jingtong Teng
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Jianping Xue
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Yongbo Duan
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
| | - Wei Sheng
- Key Laboratory of Resource Plant Biology of Anhui Province, College of Life Sciences, Huaibei Normal University, Huaibei, Anhui, P.R. China
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