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Tu M, Liu N, He Z, Dong X, Gao T, Zhu A, Yang J, Zhang S. Integrative omics reveals mechanisms of biosynthesis and regulation of floral scent in Cymbidium tracyanum. PLANT BIOTECHNOLOGY JOURNAL 2025; 23:2162-2181. [PMID: 40091604 PMCID: PMC12120893 DOI: 10.1111/pbi.70025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2024] [Revised: 01/20/2025] [Accepted: 02/10/2025] [Indexed: 03/19/2025]
Abstract
Flower scent is a crucial determiner in pollinator attraction and a significant horticultural trait in ornamental plants. Orchids, which have long been of interest in evolutionary biology and horticulture, exhibit remarkable diversity in floral scent type and intensity. However, the mechanisms underlying floral scent biosynthesis and regulation in orchids remain largely unexplored. In this study, we focus on floral scent in Cymbidium tracyanum, a wild species known for its strong floral fragrance and as a primary breeding parent of commercial Cymbidium hybrids. We present a chromosome-level genome assembly of C. tracyanum, totaling 3.79 Gb in size. Comparative genomic analyses reveal significant expansion of gene families associated with terpenoid biosynthesis and related metabolic pathways in C. tracyanum. Integrative analysis of genomic, volatolomic and transcriptomic data identified terpenoids as the predominant volatile components in the flowers of C. tracyanum. We characterized the spatiotemporal patterns of these volatiles and identified CtTPS genes responsible for volatile terpenoid biosynthesis, validating their catalytic functions in vitro. Dual-luciferase reporter assays, yeast one-hybrid assays and EMSA experiments confirmed that CtTPS2, CtTPS3, and CtTPS8 could be activated by various transcription factors (i.e., CtAP2/ERF1, CtbZIP1, CtMYB2, CtMYB3 and CtAP2/ERF4), thereby regulating the production of corresponding monoterpenes and sesquiterpenes. Our study elucidates the biosynthetic and regulatory mechanisms of floral scent in C. tracyanum, which is of great significance for the breeding of fragrant Cymbidium varieties and understanding the ecological adaptability of orchids. This study also highlights the importance of integrating multi-omics data in deciphering key horticultural traits in orchids.
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Affiliation(s)
- Mengling Tu
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Ningyawen Liu
- University of Chinese Academy of SciencesBeijingChina
- National Key Laboratory of Genetic Evolution & Animal Models, Kunming Natural History Museum of Zoology, Kunming Institute of ZoologyChinese Academy of SciencesKunmingYunnanChina
| | - Zheng‐Shan He
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Xiu‐Mei Dong
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Tian‐Yang Gao
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
- University of Chinese Academy of SciencesBeijingChina
| | - Andan Zhu
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Jun‐Bo Yang
- Germplasm Bank of Wild Species & Yunnan Key Laboratory of Crop Wild Relatives Omics, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
| | - Shi‐Bao Zhang
- Key Laboratory for Economic Plants and Biotechnology, Kunming Institute of BotanyChinese Academy of SciencesKunmingYunnanChina
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Tavu LEJ, Redillas MCFR. Oxidative Stress in Rice ( Oryza sativa): Mechanisms, Impact, and Adaptive Strategies. PLANTS (BASEL, SWITZERLAND) 2025; 14:1463. [PMID: 40431027 PMCID: PMC12114693 DOI: 10.3390/plants14101463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/14/2025] [Revised: 05/08/2025] [Accepted: 05/09/2025] [Indexed: 05/29/2025]
Abstract
Oxidative stress, arising from environmental challenges such as drought, salinity, extreme temperatures, and pathogen attack, significantly impairs rice (Oryza sativa) growth, yield, and grain quality. This review provides a comprehensive synthesis of the mechanisms underlying oxidative stress in rice, with a focus on the generation of reactive oxygen species (ROS), their physiological and molecular impacts, and the antioxidant defense systems employed for mitigation. The roles of enzymatic and non-enzymatic antioxidants, along with key transcription factors, signaling pathways, and stress-responsive genes, are explored in detail. This study further highlights varietal differences in oxidative stress tolerance, emphasizing traditional, modern, and genetically engineered rice cultivars. Recent advances in breeding strategies, gene editing technologies, and multi-omics integration are discussed as promising approaches for enhancing stress resilience. The regulatory influence of epigenetic modifications and small RNAs in modulating oxidative stress responses is also examined. Finally, this paper identifies critical research gaps-including the need for multi-stress tolerance, long-term field validation, and deeper insights into non-coding RNA functions-and offers recommendations to inform the development of climate-resilient rice varieties through integrative, sustainable strategies.
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Meng J, Wang Y, Guo R, Liu J, Jing K, Zuo J, Yuan Y, Jiang F, Dong N. Integrated genomic and transcriptomic analyses reveal the genetic and molecular mechanisms underlying hawthorn peel color and seed hardness diversity. J Genet Genomics 2025:S1673-8527(25)00097-9. [PMID: 40220858 DOI: 10.1016/j.jgg.2025.04.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2024] [Revised: 03/30/2025] [Accepted: 04/01/2025] [Indexed: 04/14/2025]
Abstract
Hawthorn (Crataegus pinnatifida) fruit peel color and seed hardness are key traits that significantly impact economic value. We present here the high-quality chromosome-scale genomes of two cultivars, including the hard-seed, yellow-peel C. pinnatifida "Jinruyi" (JRY) and the soft-seed, red-peel C. pinnatifida "Ruanzi" (RZ). The assembled genomes comprising 17 chromosomes are 809.1 Mb and 760.5 Mb in size, achieving scaffold N50 values of 48.5 Mb and 46.8 Mb for JRY and RZ, respectively. Comparative genomic analysis identifies 3.6-3.8 million single nucleotide polymorphisms, 8.5-9.3 million insertions/deletions, and approximately 30 Mb of presence/absence variations across different hawthorn genomes. Through integrating differentially expressed genes and accumulated metabolites, we filter candidate genes CpMYB114 and CpMYB44 associated with differences in hawthorn fruit peel color and seed hardness, respectively. Functional validation confirms that the CpMYB114-CpANS regulates anthocyanin biosynthesis in hawthorn peels, contributing to the observed variation in peel color. CpMYB44-CpCOMT is significantly upregulated in JRY and is verified to promote lignin biosynthesis, resulting in the distinction in seed hardness. Overall, this study reveals the new insights into understanding of distinct peel pigmentation and seed hardness in hawthorn and provides an abundant resource for molecular breeding.
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Affiliation(s)
- Jiaxin Meng
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Yan Wang
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Rongkun Guo
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Jianyi Liu
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Kerui Jing
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Jiaqi Zuo
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China
| | - Yanping Yuan
- College of Landscape Architecture and Arts, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fengchao Jiang
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China.
| | - Ningguang Dong
- Beijing Engineering Research Center for Deciduous Fruit Trees, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops (North China), Ministry of Agriculture and Rural Affairs, Institute of Forestry and Pomology, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100093, China.
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Sun R, Wang Y, Zhu R, Li L, Xi Q, Dai Y, Li J, Cao Y, Guo X, Pan X, Wang Q, Zhang B. Genome-wide identification of CA genes in cotton and the functional analysis of GhαCA4-D, GhβCA6-D and GhγCA2-D in response to drought and salt stresses. Int J Biol Macromol 2025; 304:140872. [PMID: 39938833 DOI: 10.1016/j.ijbiomac.2025.140872] [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: 06/17/2024] [Revised: 01/25/2025] [Accepted: 02/08/2025] [Indexed: 02/14/2025]
Abstract
Carbonic anhydrases (CAs) are critical metalloenzymes, widely exist in organisms, which involve in many physiological processes, including response to adverse environmental conditions. Although CA genes have been comprehensive identified and analyzed in numerous plants, there are a few of reports in cotton. Therefore, we conducted an exhaustive research for CA genes from two tetraploid cotton species and their ancestral species. A total of 138 CA genes were found, and 45 of them belonged to Gossypium hirsutum. Phylogenetic relationships and sequences analysis showed that CA genes were categorized into three distinct subtypes: α-type, β-type and γ-type. The exon numbers of β-type members were highly variable. Various types of cis-elements, including drought inducibility, were identified in CA genes, suggesting that CA genes might be involved in the regulation of drought stress response. qRT-PCR was applied to assess the gene expression level in various tissues under drought stress. The results indicated that the expression levels of GhαCA4-D, GhβCA1-A, GhβCA1-D, GhβCA3-D and GhβCA6-D were significantly higher in leaves than that in stems and roots. The expression of GhαCA4-A, GhαCA8-A, GhαCA4-D, GhβCA3-D, GhβCA6-D and GhγCAL1-D was significantly upregulated in roots at severe drought treatment. The functions of GhαCA4-D, GhβCA6-D and GhγCA2-D were analyzed using virus-induced gene silencing (VIGS) technology. Compared to the controls, GhγCA2-D-silenced upland cotton seedlings were more sensitive to salt stress. However, the drought tolerance of GhαCA4-D and GhβCA6-D silenced plants was significantly decreased. Stomatal density, width and area were significantly higher in TRV:GhβCA6-D compared to TRV:00 inoculated plants. GhαCA4-D silenced plants were susceptible to oxidative stress, and silencing GhαCA4-D induced leave cell death. Our results will assist to make clear the regulatory mechanism of CA genes under abiotic stress.
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Affiliation(s)
- Runrun Sun
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Yuanyuan Wang
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Ruihao Zhu
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Lijie Li
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China; Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qianhui Xi
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Yunpeng Dai
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Jiahui Li
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Yuanyuan Cao
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Xinlei Guo
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Xiaoping Pan
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
| | - Qinglian Wang
- Henan International Joint Laboratory of Functional Genomics and Molecular Breeding of Cotton, Henan Collaborative Innovation Center of Modern Biological Breeding, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China.
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA.
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Liang X, Han J, Cui Y, Shu X, Lei M, Wang B, Jia D, Peng W, He X, Liu X. Whole-Genome Sequencing of Flammulina filiformis and Multi-Omics Analysis in Response to Low Temperature. J Fungi (Basel) 2025; 11:229. [PMID: 40137266 PMCID: PMC11942922 DOI: 10.3390/jof11030229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2025] [Revised: 03/11/2025] [Accepted: 03/14/2025] [Indexed: 03/27/2025] Open
Abstract
The growth of Flammulina filiformis is strongly dependent on low-temperature cues for the initiation of primordia formation. To obtain a comprehensive understanding of the molecular mechanisms that govern the mycelial response to cold stress, de novo genome sequencing of the F. filiformis monokaryon and multi-omics data (transcriptome and metabolome) analyses of the mycelia, primordia, and fruiting bodies were conducted in the present study. Genome sequencing based on PacBio HiFi and Hi-C resulted in a 36.3 Mb genome sequence that mapped to 12 chromosomes, comprising 11,886 protein-coding genes. A total of 25 cold-responsive (COR) genes and 520 cold-adapted enzymes were identified in the genome. Multi-omics analyses showed that the pathways related to carbohydrate metabolism in the mycelia under low temperature (10 °C) were significantly enriched. Further examination of the expression profiles of carbohydrate-active enzymes (CAZymes) involved in carbohydrate metabolism revealed that out of 515 CAZyme genes in F. filiformis, 58 were specifically upregulated in mycelia under low-temperature conditions. By contrast, the expression levels of these genes in primordia and fruiting bodies reverted to those prior to low-temperature exposure. These indicate that CAZyme genes are important for the low-temperature adaptation of F. filiformis. This research contributes to the targeted breeding of F. filiformis.
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Affiliation(s)
- Xinmin Liang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
| | - Jing Han
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
| | - Yuqin Cui
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Xueqin Shu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
| | - Mengting Lei
- College of Resources, Sichuan Agricultural University, Chengdu 611130, China
| | - Bo Wang
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
| | - Dinghong Jia
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
| | - Weihong Peng
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
- Key Laboratory of Coarse Cereal Processing, Ministry of Agriculture and Rural Affairs, College of Food and Biological Engineering, Chengdu University, Chengdu 610106, China
| | - Xiaolan He
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
| | - Xun Liu
- Sichuan Institute of Edible Fungi, Sichuan Academy of Agricultural Sciences, Chengdu 610066, China (X.H.)
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Shi W, Li Q, Li X, Luo L, Gan J, Ma Y, Wang J, Chen T, Zhang Y, Su P, Ma X, Guo J, Huang L. Transcriptome Analysis of Stephania yunnanensis and Functional Validation of CYP80s Involved in Benzylisoquinoline Alkaloid Biosynthesis. Molecules 2025; 30:259. [PMID: 39860129 PMCID: PMC11767795 DOI: 10.3390/molecules30020259] [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: 12/12/2024] [Revised: 12/30/2024] [Accepted: 12/31/2024] [Indexed: 01/27/2025] Open
Abstract
The medicinal plant Stephania yunnanensis is rich in aporphine alkaloids, a type of benzylisoquinoline alkaloid (BIA), with aporphine being the representative and most abundant compound, but our understanding of the biosynthesis of BIAs in this plant has been relatively limited. Previous research reported the genome of S. yunnanensis and preliminarily identified the norcoclaurine synthase (NCS), which is involved in the early stages of the BIA biosynthetic pathways. However, the key genes promoting the formation of the aporphine skeleton have not yet been reported. In this study, based on the differences in the content of crebanine and several other BIAs in different tissues, we conducted transcriptome sequencing of roots, stems, and leaves. We then identified candidate genes through functional annotation and sequence alignment and further analyzed them in combination with the genome. Based on this analysis, we identified three CYP80 enzymes (SyCYP80Q5-1, SyCYP80Q5-3, and SyCYP80G6), which exhibited different activities toward (S)- and (R)-configured substrates in S. yunnanensis and demonstrated strict stereoselectivity enroute to aporphine. This study provides metabolomic and transcriptomic information on the biosynthesis of BIAs in S. yunnanensis, offers valuable insights into the elucidation of BIA biosynthesis, and lays the foundation for the complete analysis of pathways for more aporphine alkaloids.
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Affiliation(s)
- Wenlong Shi
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Qishuang Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Xinyi Li
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Linglong Luo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Jingyi Gan
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
- Yunnan Key Laboratory of Southern Medicinal Utilization, College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China;
| | - Ying Ma
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Jian Wang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Tong Chen
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Yifeng Zhang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Ping Su
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Xiaohui Ma
- Yunnan Key Laboratory of Southern Medicinal Utilization, College of Chinese Materia Medica, Yunnan University of Chinese Medicine, Kunming 650500, China;
| | - Juan Guo
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
| | - Luqi Huang
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China; (W.S.); (Q.L.); (X.L.); (L.L.); (J.G.); (Y.M.); (J.W.); (T.C.); (Y.Z.); (P.S.); (L.H.)
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Uncu AT, Patat AS, Uncu AO. Whole-genome sequencing and identification of antimicrobial peptide coding genes in parsley (Petroselinum crispum), an important culinary and medicinal Apiaceae species. Funct Integr Genomics 2024; 24:142. [PMID: 39187716 DOI: 10.1007/s10142-024-01423-x] [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: 07/04/2024] [Revised: 08/09/2024] [Accepted: 08/14/2024] [Indexed: 08/28/2024]
Abstract
Parsley is a commonly cultivated Apiaceae species of culinary and medicinal importance. Parsley has several recognized health benefits and the species has been utilized in traditional medicine since ancient times. Although parsley is among the most commonly cultivated members of Apiaceae, no systematic genomic research has been conducted on parsley. In the present work, parsley genome was sequenced using the long-read HiFi (high fidelity) sequencing technology and a draft contig assembly of 1.57 Gb that represents 80.9% of the estimated genome size was produced. The assembly was highly repeat-rich with a repetitive DNA content of 81%. The assembly was phased into a primary and alternate assembly in order to minimize redundant contigs. Scaffolds were constructed with the primary assembly contigs, which were used for the identification of AMP (antimicrobial peptide) genes. Characteristic AMP domains and 3D structures were used to detect and verify antimicrobial peptides. As a result, 23 genes (PcAMP1-23) representing defensin, snakin, thionin, lipid transfer protein and vicilin-like AMP classes were identified. Bioinformatic analyses for the characterization of peptide physicochemical properties indicated that parsley AMPs are extracellular peptides, therefore, plausibly exert their antimicrobial effects through the most commonly described AMP action mechanism of membrane attack. AMPs are attracting increasing attention since they display their fast antimicrobial effects in small doses on both plant and animal pathogens with a significantly reduced risk of resistance development. Therefore, identification and characterization of AMPs is important for their incorporation into plant disease management protocols as well as medicinal research for the treatment of multi-drug resistant infections.
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Affiliation(s)
- Ali Tevfik Uncu
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey
| | - Aysenur Soyturk Patat
- Department of Molecular Biology and Genetics, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey
| | - Ayse Ozgur Uncu
- Department of Biotechnology, Faculty of Science, Necmettin Erbakan University, Meram, Konya, 42090, Turkey.
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Liu XY, Wang WZ, Yao SP, Li XY, Han RM, Zhang D, Zhao Z, Wang Y, Zhang JP. Antioxidation Activity Enhancement by Intramolecular Hydrogen Bond and Non-Browning Mechanism of Active Ingredients in Rosemary: Carnosic Acid and Carnosol. J Phys Chem B 2024. [PMID: 39073136 DOI: 10.1021/acs.jpcb.4c02949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/30/2024]
Abstract
Rosemary is one of the most promising, versatile, and studied natural preservatives. Carnosic acid (CA) and carnosol (CARN), as the primary active ingredients of rosemary extracts, have little difference in structure, but their antioxidant activities vary significantly, depending on the system studied. The underlying molecular mechanisms remain unclear. By means of optical spectroscopies, stopped-flow, laser photolysis, and density functional theory (DFT) calculations, we have compared CA and CARN between their reaction dynamics of radical scavenging, metal ion chelation, and oxidation inhibition in lipid emulsion and beef, as well as between their interactions with β-carotene (β-Car). For reference, 3-isopropyl catechol (IC), which is structurally similar to the active groups of CA and CARN, was studied in parallel. It is found for CA that the intramolecular hydrogen bond can boost the acidity of its phenol hydroxyl and that the synergistic effect with β-Car can substantially enhance its antioxidation activity in the model systems of lipid and meat via the CA-to-β-Car electron transfer reaction. The substitution of A and B rings on the catechol group in both CA and CARN limits browning caused by their formation of oxidative products as antioxidants.
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Affiliation(s)
- Xin-Yu Liu
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Wen-Zhu Wang
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Song-Po Yao
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Xue-Ying Li
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Rui-Min Han
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Dangquan Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou 450002, China
| | - Zhijun Zhao
- Lab of Biorefinery, Shanghai Advanced Research Institute, Chinese Academy of Sciences, Shanghai 201210, China
| | - Yapei Wang
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, China
| | - Jian-Ping Zhang
- Key Laboratory of Advanced Light Conversion Materials and Biophotonics, School of Chemistry and Life Resources, Renmin University of China, Beijing 100872, 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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