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Lai Y, Ma J, Zhang X, Xuan X, Zhu F, Ding S, Shang F, Chen Y, Zhao B, Lan C, Unver T, Huo G, Li X, Wang Y, Liu Y, Lu M, Pan X, Yang D, Li M, Zhang B, Zhang D. High-quality chromosome-level genome assembly and multi-omics analysis of rosemary (Salvia rosmarinus) reveals new insights into the environmental and genome adaptation. PLANT BIOTECHNOLOGY JOURNAL 2024; 22:1833-1847. [PMID: 38363812 PMCID: PMC11182591 DOI: 10.1111/pbi.14305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 12/27/2023] [Accepted: 01/18/2024] [Indexed: 02/18/2024]
Abstract
High-quality genome of rosemary (Salvia rosmarinus) represents a valuable resource and tool for understanding genome evolution and environmental adaptation as well as its genetic improvement. However, the existing rosemary genome did not provide insights into the relationship between antioxidant components and environmental adaptability. In this study, by employing Nanopore sequencing and Hi-C technologies, a total of 1.17 Gb (97.96%) genome sequences were mapped to 12 chromosomes with 46 121 protein-coding genes and 1265 non-coding RNA genes. Comparative genome analysis reveals that rosemary had a closely genetic relationship with Salvia splendens and Salvia miltiorrhiza, and it diverged from them approximately 33.7 million years ago (MYA), and one whole-genome duplication occurred around 28.3 MYA in rosemary genome. Among all identified rosemary genes, 1918 gene families were expanded, 35 of which are involved in the biosynthesis of antioxidant components. These expanded gene families enhance the ability of rosemary adaptation to adverse environments. Multi-omics (integrated transcriptome and metabolome) analysis showed the tissue-specific distribution of antioxidant components related to environmental adaptation. During the drought, heat and salt stress treatments, 36 genes in the biosynthesis pathways of carnosic acid, rosmarinic acid and flavonoids were up-regulated, illustrating the important role of these antioxidant components in responding to abiotic stresses by adjusting ROS homeostasis. Moreover, cooperating with the photosynthesis, substance and energy metabolism, protein and ion balance, the collaborative system maintained cell stability and improved the ability of rosemary against harsh environment. This study provides a genomic data platform for gene discovery and precision breeding in rosemary. Our results also provide new insights into the adaptive evolution of rosemary and the contribution of antioxidant components in resistance to harsh environments.
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Affiliation(s)
- Yong Lai
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Jinghua Ma
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Xuebin Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi‐Omics Research, School of Life SciencesHenan UniversityKaifengHenanChina
| | - Xiaobo Xuan
- Key Laboratory of Water Management and Water Security for Yellow River BasinMinistry of Water ResourcesZhengzhouHenanChina
| | - Fengyun Zhu
- School of Biological and Food Processing EngineeringHuanghuai UniversityZhumadianHenanChina
| | - Shen Ding
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Fude Shang
- College of Life ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Yuanyuan Chen
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Bing Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi‐Omics Research, School of Life SciencesHenan UniversityKaifengHenanChina
| | - Chen Lan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Henan Joint International Laboratory for Crop Multi‐Omics Research, School of Life SciencesHenan UniversityKaifengHenanChina
| | | | - George Huo
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Ximei Li
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Yihan Wang
- College of Life ScienceHenan Agricultural UniversityZhengzhouHenanChina
| | - Yufang Liu
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Mengfei Lu
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Xiaoping Pan
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Deshuang Yang
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Mingwan Li
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
| | - Baohong Zhang
- Department of BiologyEast Carolina UniversityGreenvilleNorth CarolinaUSA
| | - Dangquan Zhang
- College of ForestryHenan Agricultural UniversityZhengzhouHenanChina
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Wang J, Song B, Yang M, Hu F, Qi H, Zhang H, Jia Y, Li Y, Wang Z, Wang X. Deciphering recursive polyploidization in Lamiales and reconstructing their chromosome evolutionary trajectories. PLANT PHYSIOLOGY 2024; 195:2143-2157. [PMID: 38482951 DOI: 10.1093/plphys/kiae151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 02/20/2024] [Indexed: 06/30/2024]
Abstract
Lamiales is an order of core eudicots with abundant diversity, and many Lamiales plants have important medicinal and ornamental values. Here, we comparatively reanalyzed 11 Lamiales species with well-assembled genome sequences and found evidence that Lamiales plants, in addition to a hexaploidization or whole-genome triplication (WGT) shared by core eudicots, experienced further polyploidization events, establishing new groups in the order. Notably, we identified a whole-genome duplication (WGD) occurred just before the split of Scrophulariaceae from the other Lamiales families, such as Acanthaceae, Bignoniaceae, and Lamiaceae, suggesting its likely being the causal reason for the establishment and fast divergence of these families. We also found that a WGT occurred ∼68 to 78 million years ago (Mya), near the split of Oleaceae from the other Lamiales families, implying that it may have caused their fast divergence and the establishment of the Oleaceae family. Then, by exploring and distinguishing intra- and intergenomic chromosomal homology due to recursive polyploidization and speciation, respectively, we inferred that the Lamiales ancestral cell karyotype had 11 proto-chromosomes. We reconstructed the evolutionary trajectories from these proto-chromosomes to form the extant chromosomes in each Lamiales plant under study. We must note that most of the inferred 11 proto-chromosomes, duplicated during a WGD thereafter, have been well preserved in jacaranda (Jacaranda mimosifolia) genome, showing the credibility of the present inference implementing a telomere-centric chromosome repatterning model. These efforts are important to understand genome repatterning after recursive polyploidization, especially shedding light on the origin of new plant groups and angiosperm cell karyotype evolution.
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Affiliation(s)
- Jiangli Wang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Bowen Song
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Minran Yang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Fubo Hu
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Huilong Qi
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Huizhe Zhang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yuelong Jia
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Yingjie Li
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Zhenyi Wang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
| | - Xiyin Wang
- School of Public Health, School of Life Science, and College of Mathematics and Sciences, North China University of Science and Technology, Tangshan 063210, China
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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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de Assis EB, de Andrade RS, Silva JPRE, Martorano LH, Amorim GMW, Loureiro PBA, Abreu LS, Sobral MV, Scotti MT, dos Santos Junior FM, Agra MDF, Tavares JF, da Silva MS. Abietane Diterpenes from Medusantha martiusii and Their Anti-Neuroinflammatory Activity. Molecules 2024; 29:2723. [PMID: 38930790 PMCID: PMC11207065 DOI: 10.3390/molecules29122723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Revised: 05/23/2024] [Accepted: 05/27/2024] [Indexed: 06/28/2024] Open
Abstract
Seven new abietane diterpenoids, comprising medusanthol A-G (1-3, 5, 7-9) and two previously identified analogs (4 and 6), were isolated from the hexane extract of the aerial parts of Medusantha martiusii. The structures of the compounds were elucidated by HRESIMS, 1D/2D NMR spectroscopic data, IR spectroscopy, NMR calculations with DP4+ probability analysis, and ECD calculations. The anti-neuroinflammatory potential of compounds 1-7 was evaluated by determining their ability to inhibit the production of nitric oxide (NO) and the proinflammatory cytokine TNF-α in BV2 microglia stimulated with LPS and IFN-γ. Compounds 1-4 and 7 exhibited decreased NO levels at a concentration of 12.5 µM. Compound 1 demonstrated strong activity with an IC50 of 3.12 µM, and compound 2 had an IC50 of 15.53 µM; both compounds effectively reduced NO levels compared to the positive control quercetin (IC50 11.8 µM). Additionally, both compounds significantly decreased TNF-α levels, indicating their potential as promising anti-neuroinflammatory agents.
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Affiliation(s)
- Edileuza B. de Assis
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Rodrigo S. de Andrade
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Joanda P. R. e Silva
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Lucas H. Martorano
- Department of Organic Chemistry, Fluminense Federal University, Niterói 24020-141, Brazil; (L.H.M.); (L.S.A.); (F.M.d.S.J.)
| | - Geraldo M. W. Amorim
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Paulo B. A. Loureiro
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Lucas S. Abreu
- Department of Organic Chemistry, Fluminense Federal University, Niterói 24020-141, Brazil; (L.H.M.); (L.S.A.); (F.M.d.S.J.)
| | - Marianna V. Sobral
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Marcus T. Scotti
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Fernando M. dos Santos Junior
- Department of Organic Chemistry, Fluminense Federal University, Niterói 24020-141, Brazil; (L.H.M.); (L.S.A.); (F.M.d.S.J.)
| | - Maria de Fátima Agra
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Josean F. Tavares
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
| | - Marcelo S. da Silva
- Postgraduate Program in Natural and Synthetic Bioactive Products, Federal University of Paraiba, João Pessoa 58051-900, Brazil; (E.B.d.A.); (R.S.d.A.); (J.P.R.e.S.); (G.M.W.A.); (P.B.A.L.); (M.V.S.); (M.T.S.); (M.d.F.A.)
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Gupta P, Geniza M, Elser J, Al-Bader N, Baschieri R, Phillips JL, Haq E, Preece J, Naithani S, Jaiswal P. Reference genome of the nutrition-rich orphan crop chia ( Salvia hispanica) and its implications for future breeding. FRONTIERS IN PLANT SCIENCE 2023; 14:1272966. [PMID: 38162307 PMCID: PMC10757625 DOI: 10.3389/fpls.2023.1272966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2023] [Accepted: 10/23/2023] [Indexed: 01/03/2024]
Abstract
Chia (Salvia hispanica L.) is one of the most popular nutrition-rich foods and pseudocereal crops of the family Lamiaceae. Chia seeds are a rich source of proteins, polyunsaturated fatty acids (PUFAs), dietary fibers, and antioxidants. In this study, we present the assembly of the chia reference genome, which spans 303.6 Mb and encodes 48,090 annotated protein-coding genes. Our analysis revealed that ~42% of the chia genome harbors repetitive content, and identified ~3 million single nucleotide polymorphisms (SNPs) and 15,380 simple sequence repeat (SSR) marker sites. By investigating the chia transcriptome, we discovered that ~44% of the genes undergo alternative splicing with a higher frequency of intron retention events. Additionally, we identified chia genes associated with important nutrient content and quality traits, such as the biosynthesis of PUFAs and seed mucilage fiber (dietary fiber) polysaccharides. Notably, this is the first report of in-silico annotation of a plant genome for protein-derived small bioactive peptides (biopeptides) associated with improving human health. To facilitate further research and translational applications of this valuable orphan crop, we have developed the Salvia genomics database (SalviaGDB), accessible at https://salviagdb.org.
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Affiliation(s)
- Parul Gupta
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Matthew Geniza
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Justin Elser
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Noor Al-Bader
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
- Molecular and Cellular Biology Graduate Program, Oregon State University, Corvallis, OR, United States
| | - Rachel Baschieri
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Jeremy Levi Phillips
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Ebaad Haq
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Justin Preece
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Sushma Naithani
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
| | - Pankaj Jaiswal
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR, United States
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Chen X, Li Y, Pang Y, Shen W, Chen Q, Liu L, Luo X, Chen Z, Li X, Li Y, Zhang Y, Huang M, Yuan C, Wang D, Guan L, Liu Y, Yang Q, Chen H, Wu H, Yu F. A comparative analysis of morphology, microstructure, and volatile metabolomics of leaves at varied developmental stages in Ainaxiang ( Blumea balsamifera (Linn.) DC.). FRONTIERS IN PLANT SCIENCE 2023; 14:1285616. [PMID: 38034556 PMCID: PMC10682096 DOI: 10.3389/fpls.2023.1285616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Accepted: 10/26/2023] [Indexed: 12/02/2023]
Abstract
Introduction Ainaxiang (Blumea balsamifera (Linn.) DC.) is cultivated for the extraction of (-)-borneol and other pharmaceutical raw materials due to its abundant volatile oil. However, there is limited knowledge regarding the structural basis and composition of volatile oil accumulation in fresh B. balsamifera leaves. Methods To address this problem, we compare the fresh leaves' morphology, microstructure, and volatile metabonomic at different development stages, orderly defined from the recently unfolded young stage (S1) to the senescent stage (S4). Results and discussion Distinct differences were observed in the macro-appearance and microstructure at each stage, particularly in the B. balsamifera glandular trichomes (BbGTs) distribution. This specialized structure may be responsible for the accumulation of volatile matter. 213 metabolites were identified through metabolomic analysis, which exhibited spatiotemporal accumulation patterns among different stages. Notably, (-)-borneol was enriched at S1, while 10 key odor metabolites associated with the characteristic balsamic, borneol, fresh, and camphor aromas of B. balsamifera were enriched in S1 and S2. Ultra-microstructural examination revealed the involvement of chloroplasts, mitochondria, endoplasmic reticulum, and vacuoles in the synthesizing, transporting, and storing essential oils. These findings confirm that BbGTs serve as the secretory structures in B. balsamifera, with the population and morphology of BbGTs potentially serving as biomarkers for (-)-borneol accumulation. Overall, young B. balsamifera leaves with dense BbGTs represent a rich (-)-borneol source, while mesophyll cells contribute to volatile oil accumulation. These findings reveal the essential oil accumulation characteristics in B. balsamifera, providing a foundation for further understanding.
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Affiliation(s)
- Xiaolu Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Yanqun Li
- Medicinal Plants Research Center, South China Agricultural University, Guangzhou, China
| | - Yuxin Pang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Wanyun Shen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Qilei Chen
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China
| | - Liwei Liu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xueting Luo
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
- College of Tropical Crops, Yunnan Agricultural University, Puer, China
| | - Zhenxia Chen
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Xingfei Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Yulan Li
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Yingying Zhang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Mei Huang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Chao Yuan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Dan Wang
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Lingliang Guan
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
| | - Yuchen Liu
- School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guiyang, China
| | - Quan Yang
- School of Traditional Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
| | - Hubiao Chen
- School of Chinese Medicine, Hong Kong Baptist University, Hong Kong, Hong Kong SAR, China
| | - Hong Wu
- Medicinal Plants Research Center, South China Agricultural University, Guangzhou, China
| | - Fulai Yu
- Tropical Crops Genetic Resources Institute, Chinese Academy of Tropical Agricultural Sciences/Key Laboratory of Biology and Cultivation of Herb Medicine (Haikou), Ministry of Agriculture and Rural Affairs/Hainan Provincial Engineering Research Center for Blumea balsamifera, Haikou, China
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Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
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Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
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Hu J, Qiu S, Wang F, Li Q, Xiang CL, Di P, Wu Z, Jiang R, Li J, Zeng Z, Wang J, Wang X, Zhang Y, Fang S, Qiao Y, Ding J, Jiang Y, Xu Z, Chen J, Chen W. Functional divergence of CYP76AKs shapes the chemodiversity of abietane-type diterpenoids in genus Salvia. Nat Commun 2023; 14:4696. [PMID: 37542034 PMCID: PMC10403556 DOI: 10.1038/s41467-023-40401-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 07/26/2023] [Indexed: 08/06/2023] Open
Abstract
The genus Salvia L. (Lamiaceae) comprises myriad distinct medicinal herbs, with terpenoids as one of their major active chemical groups. Abietane-type diterpenoids (ATDs), such as tanshinones and carnosic acids, are specific to Salvia and exhibit taxonomic chemical diversity among lineages. To elucidate how ATD chemical diversity evolved, we carried out large-scale metabolic and phylogenetic analyses of 71 Salvia species, combined with enzyme function, ancestral sequence and chemical trait reconstruction, and comparative genomics experiments. This integrated approach showed that the lineage-wide ATD diversities in Salvia were induced by differences in the oxidation of the terpenoid skeleton at C-20, which was caused by the functional divergence of the cytochrome P450 subfamily CYP76AK. These findings present a unique pattern of chemical diversity in plants that was shaped by the loss of enzyme activity and associated catalytic pathways.
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Affiliation(s)
- Jiadong Hu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Shi Qiu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Feiyan Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Qing Li
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China
| | - Chun-Lei Xiang
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Peng Di
- State Local Joint Engineering Research Center of Ginseng Breeding and Application, College of Chinese Medicinal Materials, Jilin Agricultural University, Changchun, 130118, China
| | - Ziding Wu
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Rui Jiang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jinxing Li
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Zhen Zeng
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jing Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Xingxing Wang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuchen Zhang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Shiyuan Fang
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Yuqi Qiao
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China
| | - Jie Ding
- Urban Horticulture Research and Extension Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Yun Jiang
- Urban Horticulture Research and Extension Center, Shanghai Chenshan Botanical Garden, Shanghai, 201602, China
| | - Zhichao Xu
- College of Life Sciences, Northeast Forestry University, Harbin, 150040, China.
| | - Junfeng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
| | - Wansheng Chen
- The SATCM Key Laboratory for New Resources & Quality Evaluation of Chinese Medicine, Institute of Chinese Materia Medica, Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, China.
- Department of Pharmacy, Second Affiliated Hospital of Navy Medical University, Shanghai, 200003, China.
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