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Hou Z, Yang S, He W, Lu T, Feng X, Zang L, Bai W, Chen X, Nie B, Li C, Wei M, Ma L, Han Z, Zou Q, Li W, Wang L. The haplotype-resolved genome of diploid Chrysanthemum indicum unveils new acacetin synthases genes and their evolutionary history. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38864745 DOI: 10.1111/tpj.16854] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Revised: 03/31/2024] [Accepted: 05/03/2024] [Indexed: 06/13/2024]
Abstract
Acacetin, a flavonoid compound, possesses a wide range of pharmacological effects, including antimicrobial, immune regulation, and anticancer effects. Some key steps in its biosynthetic pathway were largely unknown in flowering plants. Here, we present the first haplotype-resolved genome of Chrysanthemum indicum, whose dried flowers contain abundant flavonoids and have been utilized as traditional Chinese medicine. Various phylogenetic analyses revealed almost equal proportion of three tree topologies among three Chrysanthemum species (C. indicum, C. nankingense, and C. lavandulifolium), indicating that frequent gene flow among Chrysanthemum species or incomplete lineage sorting due to rapid speciation might contribute to conflict topologies. The expanded gene families in C. indicum were associated with oxidative functions. Through comprehensive candidate gene screening, we identified five flavonoid O-methyltransferase (FOMT) candidates, which were highly expressed in flowers and whose expressional levels were significantly correlated with the content of acacetin. Further experiments validated two FOMTs (CI02A009970 and CI03A006662) were capable of catalyzing the conversion of apigenin into acacetin, and these two genes are possibly responsible acacetin accumulation in disc florets and young leaves, respectively. Furthermore, combined analyses of ancestral chromosome reconstruction and phylogenetic trees revealed the distinct evolutionary fates of the two validated FOMT genes. Our study provides new insights into the biosynthetic pathway of flavonoid compounds in the Asteraceae family and offers a model for tracing the origin and evolutionary routes of single genes. These findings will facilitate in vitro biosynthetic production of flavonoid compounds through cellular and metabolic engineering and expedite molecular breeding of C. indicum cultivars.
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Affiliation(s)
- Zhuangwei Hou
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Song Yang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Weijun He
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Tingting Lu
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xunmeng Feng
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Lanlan Zang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Wenhui Bai
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Xueqing Chen
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Min Wei
- China Resources Sanjiu Medical and Pharmaceutical Co., Ltd, Shenzhen, 518110, China
| | - Liangju Ma
- China Resources Sanjiu Medical and Pharmaceutical Co., Ltd, Shenzhen, 518110, China
| | - Zhengzhou Han
- China Resources Sanjiu Medical and Pharmaceutical Co., Ltd, Shenzhen, 518110, China
| | - Qingjun Zou
- China Resources Sanjiu Medical and Pharmaceutical Co., Ltd, Shenzhen, 518110, China
- National Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, Chinese Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Wei Li
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, China
- State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, Beijing, 100700, China
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Zhao R, Yu Y, Gao M, Xing Y, Xue J, Xu L, Kang T. The conversion of monolignans to sesquilignans and dilignans is closely correlated to the regulation of Arctium lappa seed germination. PLANTA 2024; 260:9. [PMID: 38795149 DOI: 10.1007/s00425-024-04445-8] [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: 12/12/2023] [Accepted: 05/17/2024] [Indexed: 05/27/2024]
Abstract
MAIN CONCLUSION The secondary metabolic conversion of monolignans to sesquilignans/dilignans was closely related to seed germination and seedling establishment in Arctium lappa. Arctium lappa plants are used as a kind of traditional Chinese medicines for nearly 1500 years, and so far, only a few studies have put focus on the key secondary metabolic changes during seed germination and seedling establishment. In the current study, a combined approach was used to investigate the correlation among secondary metabolites, plant hormone signaling, and transcriptional profiles at the early critical stages of A. lappa seed germination and seedling establishment. Of 50 metabolites in methonolic extracts of A. lappa samples, 35 metabolites were identified with LC-MS/MS and 15 metabolites were identified with GC-MS. Their qualitative properties were examined according to the predicted chemical structures. The quantitative analysis was performed for deciphering their metabolic profiles, discovering that the secondary metabolic conversion from monolignans to sesquilignans/dilignans was closely correlated to the initiation of A. lappa seed germination and seedling establishment. Furthermore, the critical transcriptional changes in primary metabolisms, translational regulation at different cellular compartments, and multiple plant hormone signaling pathways were revealed. In addition, the combined approach provides unprecedented insights into key regulatory mechanisms in both gene transcription and secondary metabolites besides many known primary metabolites during seed germination of an important traditional Chinese medicinal plant species. The results not only provide new insights to understand the regulation of key medicinal components of 'ARCTII FRUCTUS', arctiin and arctigenin at the stages of seed germination and seedling establishment, but also potentially spur the development of seed-based cultivation in A. lappa plants.
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Affiliation(s)
- Rong Zhao
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, Liaoning Province, People's Republic of China
| | - Ying Yu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, Liaoning Province, People's Republic of China
| | - Mingze Gao
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, Liaoning Province, People's Republic of China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, Liaoning Province, People's Republic of China
| | - Jianing Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, Liaoning Province, People's Republic of China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, Liaoning Province, People's Republic of China.
| | - Tingguo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, Liaoning Province, People's Republic of China.
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Dang Z, Xu Y, Zhang X, Mi W, Chi Y, Tian Y, Liu Y, Ren W. Chromosome-level genome assembly provides insights into the genome evolution and functional importance of the phenylpropanoid-flavonoid pathway in Thymus mongolicus. BMC Genomics 2024; 25:291. [PMID: 38504151 PMCID: PMC10949689 DOI: 10.1186/s12864-024-10202-8] [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: 12/02/2023] [Accepted: 03/08/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Thymus mongolicus (family Lamiaceae) is a Thyme subshrub with strong aroma and remarkable environmental adaptability. Limited genomic information limits the use of this plant. RESULTS Chromosome-level 605.2 Mb genome of T. mongolicus was generated, with 96.28% anchored to 12 pseudochromosomes. The repetitive sequences were dominant, accounting for 70.98%, and 32,593 protein-coding genes were predicted. Synteny analysis revealed that Lamiaceae species generally underwent two rounds of whole genome duplication; moreover, species-specific genome duplication was identified. A recent LTR retrotransposon burst and tandem duplication might play important roles in the formation of the Thymus genome. Using comparative genomic analysis, phylogenetic tree of seven Lamiaceae species was constructed, which revealed that Thyme plants evolved recently in the family. Under the phylogenetic framework, we performed functional enrichment analysis of the genes on nodes that contained the most gene duplication events (> 50% support) and of relevant significant expanded gene families. These genes were highly associated with environmental adaptation and biosynthesis of secondary metabolites. Combined transcriptome and metabolome analyses revealed that Peroxidases, Hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferases, and 4-coumarate-CoA ligases genes were the essential regulators of the phenylpropanoid-flavonoid pathway. Their catalytic products (e.g., apigenin, naringenin chalcone, and several apigenin-related compounds) might be responsible for the environmental tolerance and aromatic properties of T. mongolicus. CONCLUSION This study enhanced the understanding of the genomic evolution of T. mongolicus, enabling further exploration of its unique traits and applications, and contributed to the understanding of Lamiaceae genomics and evolutionary biology.
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Affiliation(s)
- Zhenhua Dang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Ying Xu
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Xin Zhang
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Wentao Mi
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Yuan Chi
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China
| | - Yunyun Tian
- Ministry of Education Key Laboratory of Herbage & Endemic Crop Biotechnology, School of Life Sciences, Inner Mongolia University, Hohhot, 010070, China
| | - Yaling Liu
- Key Laboratory of Forage Breeding and Seed Production of Inner Mongolia, Inner Mongolia M-Grass Ecology and Environment (Group) Co., National Center of Pratacultural Technology Innovation (under preparation), Ltd, Hohhot, 010060, China
| | - Weibo Ren
- Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau & Inner Mongolia Key Laboratory of Grassland Ecology, School of Ecology and Environment, Inner Mongolia University, Hohhot, 010070, China.
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Singh D, Mittal N, Verma S, Singh A, Siddiqui MH. Applications of some advanced sequencing, analytical, and computational approaches in medicinal plant research: a review. Mol Biol Rep 2023; 51:23. [PMID: 38117315 DOI: 10.1007/s11033-023-09057-1] [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: 05/18/2023] [Accepted: 11/27/2023] [Indexed: 12/21/2023]
Abstract
The potential active chemicals found in medicinal plants, which have long been employed as natural medicines, are abundant. Exploring the genes responsible for producing these compounds has given new insights into medicinal plant research. Previously, the authentication of medicinal plants was done via DNA marker sequencing. With the advancement of sequencing technology, several new techniques like next-generation sequencing, single molecule sequencing, and fourth-generation sequencing have emerged. These techniques enshrined the role of molecular approaches for medicinal plants because all the genes involved in the biosynthesis of medicinal compound(s) could be identified through RNA-seq analysis. In several research insights, transcriptome data have also been used for the identification of biosynthesis pathways. miRNAs in several medicinal plants and their role in the biosynthesis pathway as well as regulation of the disease-causing genes were also identified. In several research articles, an in silico study was also found to be effective in identifying the inhibitory effect of medicinal plant-based compounds against virus' gene(s). The use of advanced analytical methods like spectroscopy and chromatography in metabolite proofing of secondary metabolites has also been reported in several recent research findings. Furthermore, advancement in molecular and analytic methods will give new insight into studying the traditionally important medicinal plants that are still unexplored.
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Affiliation(s)
- Dhananjay Singh
- Department of Biosciences, Integral University, Lucknow, Uttar Pradesh, 226026, India
| | - Nishu Mittal
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
| | - Swati Verma
- College of Horticulture and Forestry Thunag, Dr. Y. S. Parmar University of Horticulture and Forestry, Nauni, Solan, Himachal Pradesh, 173230, India
| | - Anjali Singh
- Institute of Biosciences and Technology, Shri Ramswaroop Memorial University, Barabanki, Uttar Pradesh, 225003, India
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Bejerman N, Dietzgen R, Debat H. Novel Tri-Segmented Rhabdoviruses: A Data Mining Expedition Unveils the Cryptic Diversity of Cytorhabdoviruses. Viruses 2023; 15:2402. [PMID: 38140643 PMCID: PMC10747219 DOI: 10.3390/v15122402] [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: 11/07/2023] [Revised: 12/07/2023] [Accepted: 12/08/2023] [Indexed: 12/24/2023] Open
Abstract
Cytorhabdoviruses (genus Cytorhabdovirus, family Rhabdoviridae) are plant-infecting viruses with enveloped, bacilliform virions. Established members of the genus Cytorhabdovirus have unsegmented single-stranded negative-sense RNA genomes (ca. 10-16 kb) which encode four to ten proteins. Here, by exploring large publicly available metatranscriptomics datasets, we report the identification and genomic characterization of 93 novel viruses with genetic and evolutionary cues of cytorhabdoviruses. Strikingly, five unprecedented viruses with tri-segmented genomes were also identified. This finding represents the first tri-segmented viruses in the family Rhabdoviridae, and they should be classified in a novel genus within this family for which we suggest the name "Trirhavirus". Interestingly, the nucleocapsid and polymerase were the only typical rhabdoviral proteins encoded by those tri-segmented viruses, whereas in three of them, a protein similar to the emaravirus (family Fimoviridae) silencing suppressor was found, while the other predicted proteins had no matches in any sequence databases. Genetic distance and evolutionary insights suggest that all these novel viruses may represent members of novel species. Phylogenetic analyses, of both novel and previously classified plant rhabdoviruses, provide compelling support for the division of the genus Cytorhabdovirus into three distinct genera. This proposed reclassification not only enhances our understanding of the evolutionary dynamics within this group of plant rhabdoviruses but also illuminates the remarkable genomic diversity they encompass. This study not only represents a significant expansion of the genomics of cytorhabdoviruses that will enable future research on the evolutionary peculiarity of this genus but also shows the plasticity in the rhabdovirus genome organization with the discovery of tri-segmented members with a unique evolutionary trajectory.
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Affiliation(s)
- Nicolas Bejerman
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
| | - Ralf Dietzgen
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, St. Lucia, QLD 4072, Australia
| | - Humberto Debat
- Instituto de Patología Vegetal—Centro de Investigaciones Agropecuarias—Instituto Nacional de Tecnología Agropecuaria (IPAVE—CIAP—INTA), Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
- Unidad de Fitopatología y Modelización Agrícola, Consejo Nacional de Investigaciones Científicas y Técnicas, Camino 60 Cuadras Km 5,5, Córdoba X5020ICA, Argentina
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Ma K, Sheng W, Song X, Song J, Li Y, Huang W, Liu Y. Chlorogenic Acid from Burdock Roots Ameliorates Oleic Acid-Induced Steatosis in HepG2 Cells through AMPK/ACC/CPT-1 Pathway. Molecules 2023; 28:7257. [PMID: 37959676 PMCID: PMC10647434 DOI: 10.3390/molecules28217257] [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: 07/26/2023] [Revised: 08/30/2023] [Accepted: 10/13/2023] [Indexed: 11/15/2023] Open
Abstract
Hepatic steatosis can cause liver dysfunction and cell injury, on which natural functional factors are expected to be an effective approach for long-term intervention. However, the cellular molecular mechanisms are unclear. Chlorogenic acid is a phenolic compound, which can regulate lipid metabolism and is abundant in burdock root. The aim of this study was to investigate the potential molecular mechanism of the effect of chlorogenic acid from burdock root (ACQA) on steatosis in HepG2 cells. In this study, we found that ACQA reduced the number of lipid droplets and lipid levels in oleic acid-treated HepG2 cells. Molecular mechanistic results showed that ACQA enhanced CPT-1 expression by activating AMPK-related signaling pathways, and the concentrations of Ca2+ and cAMP were increased with the intervention of ACQA. In addition, ACQA enhanced the β-oxidation of fatty acids, reduced alanine transaminase and aspartate transaminase, and inhibited apoptosis in oleic acid-treated HepG2 cells. Our studies elucidate a novel mechanism that ACQA enhances the β-oxidation of fatty acids through the AMPK/ACC/CPT-1 pathway to protect against steatosis in HepG2 cells, which provides insight into its molecular mechanism as well as intervention strategies for chlorogenic acid against fatty liver diseases.
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Affiliation(s)
- Kaiyang Ma
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.M.); (X.S.)
- Institute of Agro-product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.S.)
| | - Weixi Sheng
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.M.); (X.S.)
| | - Xinxin Song
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.M.); (X.S.)
| | - Jiangfeng Song
- Institute of Agro-product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.S.)
| | - Ying Li
- College of Food Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (K.M.); (X.S.)
- Institute of Agro-product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.S.)
| | - Wuyang Huang
- Institute of Agro-product Processing, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China; (J.S.)
| | - Yuanfa Liu
- Future Food (Bai Ma) Research Institute, Nanjing 211225, China
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Kong X, Zhang Y, Wang Z, Bao S, Feng Y, Wang J, Yu Z, Long F, Xiao Z, Hao Y, Gao X, Li Y, Ding Y, Wang J, Lei T, Xu C, Wang J. Two-step model of paleohexaploidy, ancestral genome reshuffling and plasticity of heat shock response in Asteraceae. HORTICULTURE RESEARCH 2023; 10:uhad073. [PMID: 37303613 PMCID: PMC10251138 DOI: 10.1093/hr/uhad073] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 04/10/2023] [Indexed: 06/13/2023]
Abstract
An ancient hexaploidization event in the most but not all Asteraceae plants, may have been responsible for shaping the genomes of many horticultural, ornamental, and medicinal plants that promoting the prosperity of the largest angiosperm family on the earth. However, the duplication process of this hexaploidy, as well as the genomic and phenotypic diversity of extant Asteraceae plants caused by paleogenome reorganization, are still poorly understood. We analyzed 11 genomes from 10 genera in Asteraceae, and redated the Asteraceae common hexaploidization (ACH) event ~70.7-78.6 million years ago (Mya) and the Asteroideae specific tetraploidization (AST) event ~41.6-46.2 Mya. Moreover, we identified the genomic homologies generated from the ACH, AST and speciation events, and constructed a multiple genome alignment framework for Asteraceae. Subsequently, we revealed biased fractionations between the paleopolyploidization produced subgenomes, suggesting the ACH and AST both are allopolyplodization events. Interestingly, the paleochromosome reshuffling traces provided clear evidence for the two-step duplications of ACH event in Asteraceae. Furthermore, we reconstructed ancestral Asteraceae karyotype (AAK) that has 9 paleochromosomes, and revealed a highly flexible reshuffling of Asteraceae paleogenome. Of specific significance, we explored the genetic diversity of Heat Shock Transcription Factors (Hsfs) associated with recursive whole-genome polyploidizations, gene duplications, and paleogenome reshuffling, and revealed that the expansion of Hsfs gene families enable heat shock plasticity during the genome evolution of Asteraceae. Our study provides insights on polyploidy and paleogenome remodeling for the successful establishment of Asteraceae, and is helpful for further communication and exploration of the diversification of plant families and phenotypes.
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Affiliation(s)
| | | | | | | | - Yishan Feng
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jiaqi Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zijian Yu
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Feng Long
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Zejia Xiao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yanan Hao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Xintong Gao
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yinfeng Li
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Yue Ding
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
| | - Jianyu Wang
- Department of Bioinformatics, School of Life Sciences, and Center for Genomics and Computational Biology, North China University of Science and Technology, Tangshan, Hebei 063000, China
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Song Y, Yang Y, Xu L, Bian C, Xing Y, Xue H, Hou W, Men W, Dou D, Kang T. The burdock database: a multi-omic database for Arctium lappa, a food and medicinal plant. BMC PLANT BIOLOGY 2023; 23:86. [PMID: 36759759 PMCID: PMC9909940 DOI: 10.1186/s12870-023-04092-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 01/27/2023] [Indexed: 06/18/2023]
Abstract
BACKGROUND Burdock is a biennial herb of Asteraceae found in Northern Europe, Eurasia, Siberia, and China. Its mature dry fruits, called Niu Bang Zi, are recorded in various traditional Chinese medicine books. With the development of sequencing technology, the mitochondrial, chloroplast, and nuclear genomes, transcriptome, and sequence-related amplified polymorphism (SRAP) fingerprints of burdock have all been reported. To make better use of this data for further research and analysis, a burdock database was constructed. RESULTS This burdock multi-omics database contains two burdock genome datasets, two transcriptome datasets, eight burdock chloroplast genomes, one burdock mitochondrial genome, one A. tomentosum chloroplast genome, one A. tomentosum mitochondrial genome, 26 phenotypes of burdock varieties, burdock rhizosphere-associated microorganisms, and chemical constituents of burdock fruit, pericarp, and kernel at different growth stages (using UPLC-Q-TOF-MS). The wild and cultivation distribution of burdock in China was summarized, and the main active components and pharmacological effects of burdock currently reported were concluded. The database contains ten central functional modules: Home, Genome, Transcriptome, Jbrowse, Search, Tools, SRAP fingerprints, Associated microorganisms, Chemical, and Publications. Among these, the "Tools" module can be used to perform sequence homology alignment (Blast), multiple sequence alignment analysis (Muscle), homologous protein prediction (Genewise), primer design (Primer), large-scale genome analysis (Lastz), and GO and KEGG enrichment analyses (GO Enrichment and KEGG Enrichment). CONCLUSIONS The database URL is http://210.22.121.250:41352/ . This burdock database integrates molecular and chemical data to provide a comprehensive information and analysis platform for interested researchers and can be of immense help to the cultivation, breeding, and molecular pharmacognosy research of burdock.
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Affiliation(s)
- Yueyue Song
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Yanyun Yang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Liang Xu
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China.
| | - Che Bian
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Yanping Xing
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Hefei Xue
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Wenjuan Hou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Wenxiao Men
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Deqiang Dou
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China
| | - Tingguo Kang
- School of Pharmacy, Liaoning University of Traditional Chinese Medicine, Dalian, 116600, China.
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Luo D, Zeng Z, Wu Z, Chen C, Zhao T, Du H, Miao Y, Liu D. Intraspecific variation in genome size in Artemisia argyi determined using flow cytometry and a genome survey. 3 Biotech 2023; 13:57. [PMID: 36698769 PMCID: PMC9868218 DOI: 10.1007/s13205-022-03412-y] [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: 07/20/2022] [Accepted: 11/26/2022] [Indexed: 01/23/2023] Open
Abstract
Different collections and accessions of Artemisia argyi (Chinese mugwort) harbour considerable diversity in morphology and bioactive compounds, but no mechanisms have been reported that explain these variations. We studied genome size in A. argyi accessions from different regions of China by flow cytometry. Genome size was significantly distinct among origins of these 42 Chinese mugwort accessions, ranging from 8.428 to 11.717 pg. There were no significant intraspecific differences among the 42 accessions from the five regions of China. The clustering analysis showed that these 42 A. argyi accessions could be divided into three groups, which had no significant relationship with geographical location. In a genome survey, the total genome size of A. argyi (A15) was estimated to be 7.852 Gb (or 8.029 pg) by K-mer analysis. This indicated that the results from the two independent methods are consistent, and that the genome survey can be used as an adjunct to flow cytometry to compensate for its deficiencies. In addition, genome survey can provide the information about heterozygosity, repeat sequences, GC content and ploidy of A. argyi genome. The nuclear DNA contents determined here provide a new reference for intraspecific variation in genome size in A. argyi, and may also be a potential resource for the study of genetic diversity and for breeding new cultivar.
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Affiliation(s)
- Dandan Luo
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Zeyi Zeng
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Zongqi Wu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Changjie Chen
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Tingting Zhao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Hongzhi Du
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Yuhuan Miao
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
| | - Dahui Liu
- College of Pharmacy, Hubei University of Chinese Medicine, Wuhan, 430065 China
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10
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Yang P, Zhao HY, Wei JS, Zhao YY, Lin XJ, Su J, Li FP, Li M, Ma DM, Tan XK, Liang HL, Sun YW, Zhan RT, He GZ, Zhou XF, Yang JF. Chromosome-level genome assembly and functional characterization of terpene synthases provide insights into the volatile terpenoid biosynthesis of Wurfbainia villosa. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:630-645. [PMID: 36071028 DOI: 10.1111/tpj.15968] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 09/04/2022] [Indexed: 06/15/2023]
Abstract
Wurfbainia villosa is a well-known medicinal and edible plant that is widely cultivated in the Lingnan region of China. Its dried fruits (called Fructus Amomi) are broadly used in traditional Chinese medicine for curing gastrointestinal diseases and are rich in volatile terpenoids. Here, we report a high-quality chromosome-level genome assembly of W. villosa with a total size of approximately 2.80 Gb, 42 588 protein-coding genes, and a very high percentage of repetitive sequences (87.23%). Genome analysis showed that W. villosa likely experienced a recent whole-genome duplication event prior to the W. villosa-Zingiber officinale divergence (approximately 11 million years ago), and a recent burst of long terminal repeat insertions afterward. The W. villosa genome enabled the identification of 17 genes involved in the terpenoid skeleton biosynthesis pathway and 66 terpene synthase (TPS) genes. We found that tandem duplication events have an important contribution to the expansion of WvTPSs, which likely drove the production of volatile terpenoids. In addition, functional characterization of 18 WvTPSs, focusing on the TPS-a and TPS-b subfamilies, showed that most of these WvTPSs are multi-product TPS and are predominantly expressed in seeds. The present study provides insights into the genome evolution and the molecular basis of the volatile terpenoids diversity in W. villosa. The genome sequence also represents valuable resources for the functional gene research and molecular breeding of W. villosa.
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Affiliation(s)
- Peng Yang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Hunan Provincial Key Laboratory for Synthetic Biology of Traditional Chinese Medicine, School of Pharmaceutical Sciences, Hunan University of Medicine, Huaihua, 418000, China
| | - Hai-Ying Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- The Second Clinical Medical College of Guangxi University of Science and Technology, Louzhou, 5450000, China
| | - Jie-Shu Wei
- School of Pharmacy, Guangzhou Xinhua University, Guangzhou, 510520, China
| | - Yuan-Yuan Zhao
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xiao-Jing Lin
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Jing Su
- Agricultural Experimental Station of Yangchun City (Amomum villosum Testing farm of Yangchun City), Yangchun, 529600, China
| | - Fang-Ping Li
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Meng Li
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Dong-Ming Ma
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xu-Kai Tan
- Grandomics Biosciences, Beijing, 102200, China
| | - Hui-Lin Liang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ye-Wen Sun
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Ruo-Ting Zhan
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Guo-Zhen He
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
| | - Xiao-Fan Zhou
- Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, 510642, China
| | - Jin-Fen Yang
- School of Pharmaceutical Science, Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
- Key Laboratory of Chinese Medicinal Resource from Lingnan (Ministry of Education), Guangzhou University of Chinese Medicine, Guangzhou, 510006, China
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11
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Liu X, Gong X, Liu Y, Liu J, Zhang H, Qiao S, Li G, Tang M. Application of High-Throughput Sequencing on the Chinese Herbal Medicine for the Data-Mining of the Bioactive Compounds. FRONTIERS IN PLANT SCIENCE 2022; 13:900035. [PMID: 35909744 PMCID: PMC9331165 DOI: 10.3389/fpls.2022.900035] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 06/10/2022] [Indexed: 05/11/2023]
Abstract
The Chinese Herbal Medicine (CHM) has been used worldwide in clinic to treat the vast majority of human diseases, and the healing effect is remarkable. However, the functional components and the corresponding pharmacological mechanism of the herbs are unclear. As one of the main means, the high-throughput sequencing (HTS) technologies have been employed to discover and parse the active ingredients of CHM. Moreover, a tremendous amount of effort is made to uncover the pharmacodynamic genes associated with the synthesis of active substances. Here, based on the genome-assembly and the downstream bioinformatics analysis, we present a comprehensive summary of the application of HTS on CHM for the synthesis pathways of active ingredients from two aspects: active ingredient properties and disease classification, which are important for pharmacological, herb molecular breeding, and synthetic biology studies.
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Affiliation(s)
- Xiaoyan Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Xun Gong
- Department of Rheumatology and Immunology, Affiliated Hospital of Jiangsu University, Zhenjiang, China
| | - Yi Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- Institute of Animal Husbandry, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Junlin Liu
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Hantao Zhang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Sen Qiao
- School of Life Sciences, Jiangsu University, Zhenjiang, China
| | - Gang Li
- Department of Vascular Surgery, The Second Affiliated Hospital of Shandong First Medical University, Taian, China
- Gang Li,
| | - Min Tang
- School of Life Sciences, Jiangsu University, Zhenjiang, China
- *Correspondence: Min Tang,
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