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Zhang X, Chen W, Yang Z, Luo C, Zhang W, Xu F, Ye J, Liao Y. Genetic diversity analysis and DNA fingerprint construction of Zanthoxylum species based on SSR and iPBS markers. BMC PLANT BIOLOGY 2024; 24:843. [PMID: 39244564 PMCID: PMC11380355 DOI: 10.1186/s12870-024-05373-1] [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: 03/01/2024] [Accepted: 07/03/2024] [Indexed: 09/09/2024]
Abstract
Zanthoxylum is a versatile economic tree species utilized for its spice, seasoning, oil, medicinal, and industrial raw material applications, and it has a lengthy history of cultivation and domestication in China. This has led to the development of numerous cultivars. However, the phenomenon of mixed cultivars and confusing names has significantly obstructed the effective utilization of Zanthoxylum resources and industrial development. Consequently, conducting genetic diversity studies and cultivar identification on Zanthoxylum are crucial. This research analyzed the genetic traits of 80 Zanthoxylum cultivars using simple sequence repeat (SSR) and inter-Primer Binding Site (iPBS) molecular markers, leading to the creation of a DNA fingerprint. This study identified 206 and 127 alleles with 32 SSR markers and 10 iPBS markers, respectively, yielding an average of 6.4 and 12.7 alleles (Na) per marker. The average polymorphism information content (PIC) for the SSR and iPBS markers was 0.710 and 0.281, respectively. The genetic similarity coefficients for the 80 Zanthoxylum accessions ranged from 0.0947 to 0.9868 and from 0.2206 to 1.0000, with mean values of 0.3864 and 0.5215, respectively, indicating substantial genetic diversity. Cluster analysis, corroborated by principal coordinate analysis (PCoA), categorized these accessions into three primary groups. Analysis of the genetic differentiation among the three Zanthoxylum (Z. bungeanum, Z. armatum, and Z. piperitum) populations using SSR markers revealed a mean genetic differentiation coefficient (Fst) of 0.335 and a gene flow (Nm) of 0.629, suggesting significant genetic divergence among the populations. Molecular variance analysis (AMOVA) indicated that 65% of the genetic variation occurred within individuals, while 35% occurred among populations. Bayesian model-based analysis of population genetic structure divided all materials into two groups. The combined PI and PIsibs value of the 32 SSR markers were 4.265 × 10- 27 and 1.282 × 10- 11, respectively, showing strong fingerprinting power. DNA fingerprints of the 80 cultivars were established using eight pairs of SSR primers, each assigned a unique numerical code. In summary, while both markers were effective at assessing the genetic diversity and relationships of Zanthoxylum species, SSR markers demonstrated superior polymorphism and cultivar discrimination compared to iPBS markers. These findings offer a scientific foundation for the conservation and sustainable use of Zanthoxylum species.
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Affiliation(s)
- Xiaoxi Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Wei Chen
- Sichuan Academy of Forestry, Chengdu, Sichuan, 610081, China
| | - Zhiwu Yang
- Sichuan Academy of Forestry, Chengdu, Sichuan, 610081, China
| | - Chengrong Luo
- Sichuan Academy of Forestry, Chengdu, Sichuan, 610081, China
| | - Weiwei Zhang
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China.
| | - Feng Xu
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China.
| | - Jiabao Ye
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China
| | - Yongling Liao
- College of Horticulture and Gardening, Yangtze University, Jingzhou, Hubei, 434025, China
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Wen J, Xiang Q, Guo J, Zhang J, Yang N, Huang Y, Chen Y, Hu T, Rao C. Pharmacological activities of Zanthoxylum L. plants and its exploitation and utilization. Heliyon 2024; 10:e33207. [PMID: 39022083 PMCID: PMC11252797 DOI: 10.1016/j.heliyon.2024.e33207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 05/10/2024] [Accepted: 06/17/2024] [Indexed: 07/20/2024] Open
Abstract
The study aims to provide an up-to-date review at the advancements of the investigations on the ethnopharmacology, phytochemistry, pharmacological effect and exploitation and utilizations of Zanthoxylum L. Besides, the possible tendency and perspective for future research of this plant are discussed, as well. This article uses "Zanthoxylum L." "Zanthorylum bungeanum" as the keywords and collects relevant information on Zanthoxylum L. plants through electronic searches (Elsevier, PubMed, ACS, Web of Science, Science Direct, CNKI, Google Scholar), relevant books, and classic literature about Chinese herb. The plants of this genus are rich in volatile oils, alkaloids, amides, lignans, coumarins and organic acids, and has a wide range of pharmacological activities, including but not limited to anti-inflammatory, analgesic, anti-tumor, hypoglycemic, hypolipidemic, antioxidant and anti-infectious. This article reviewed both Chinese and international research progress on the active ingredients and pharmacological activities of Zanthoxylum L. as well as the applications of this genus in the fields of food, medicinal and daily chemicals, and clarified the material basis of its pharmacological activities. Based on traditional usage, phytochemicals, and pharmacological properties, of Zanthoxylum L. species, which indicate that they possess diverse bioactive metabolites with interesting bioactivities. Zanthoxylum L. is a potential medicinal and edible plant with diverse pharmacological effects. Due to its various advantages, it may have vast application potential in the food and medicinal industries and daily chemicals. Nonetheless, the currently available data has several gaps in understanding the herbal utilization of Zanthoxylum L. Thus, further research into their toxicity, mechanisms of actions of the isolated bioactive metabolites, as well as scientific connotations between the traditional medicinal uses and pharmacological properties is required to unravel their efficacy in therapeutic potential for safe clinical application.
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Affiliation(s)
- Jiayu Wen
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Qiwen Xiang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Jiafu Guo
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Jian Zhang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Nannan Yang
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Yan Huang
- Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Yan Chen
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
- Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Tingting Hu
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
| | - Chaolong Rao
- School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
- Key Laboratory of Southwestern Chinese Medicine Resources, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
- R&D Center for Efficiency, Safety and Application in Chinese Materia Medica with Medical and Edible Values, School of Public Health, Chengdu University of Traditional Chinese Medicine, Chengdu, Sichuan, 611137, China
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Afzal M, Qais FA, Abduh NA, Christy M, Ayub R, Alarifi A. Identification of bioactive compounds of Zanthoxylum armatum as potential inhibitor of pyruvate kinase M2 (PKM2): Computational and virtual screening approaches. Heliyon 2024; 10:e27361. [PMID: 38495183 PMCID: PMC10943388 DOI: 10.1016/j.heliyon.2024.e27361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2023] [Revised: 02/26/2024] [Accepted: 02/28/2024] [Indexed: 03/19/2024] Open
Abstract
PKM2 (Pyruvate kinase M2) is the isoform of pyruvate kinase which is known to catalyse the last step of glycolysis that is responsible for energy production. This specific isoform is known to be highly expressed in certain cancerous conditions. Considering the role of this protein in various cancer conditions, we used PKM2 as a target protein to identify the potential compounds against this target. In this study, we have examined 96 compounds of Zanthoxylum armatum using an array of computational and in silico tools. The compounds were assessed for toxicity then their anticancer potential was predicted. The virtual screening was done with molecular docking followed by a detailed examination using molecular dynamics simulation. The majority of the compounds showed a higher probability of being antineoplastic. Based on toxicity, predicted anticancer potential, binding affinity, and binding site, three compounds (nevadensin, asarinin, and kaempferol) were selected as hit compounds. The binding energy of these compounds with PKM2 ranged from -7.7 to -8.3 kcal/mol and all hit compounds interact at the active site of the protein. The selected hit compounds formed a stable complex with PKM2 when simulated under physiological conditions. The dynamic analysis showed that these compounds remained attached to the active site till the completion of molecular simulation. MM-PBSA analysis showed that nevadensin exhibited a higher affinity towards PKM2 compared to asarinin and kaempferol. These compounds need to be assessed properties in vivo and in vitro to validate their efficacy.
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Affiliation(s)
- Mohd Afzal
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Faizan Abul Qais
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, UP, 202002, India
| | - Naaser A.Y. Abduh
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Maria Christy
- Department of Energy Engineering, Hanyang University, 222 Wangsimni-ro, Seongdong-gu, Seoul, 04763, South Korea
| | - Rashid Ayub
- Department of Science Technology and Innovation, King Saud University, Riyadh, 11451, Saudi Arabia
| | - Abdullah Alarifi
- Department of Chemistry, College of Science, King Saud University, Riyadh, 11451, Saudi Arabia
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Deng Y, He Z, Li Y, Ye M, Xiang L. Six Express Sequence Tag-Simple Sequence Repeat Primers Reveal Genetic Diversity in the Cultivars of Three Zanthoxylum Species. Curr Issues Mol Biol 2023; 45:7183-7196. [PMID: 37754238 PMCID: PMC10529843 DOI: 10.3390/cimb45090454] [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: 07/28/2023] [Revised: 08/21/2023] [Accepted: 08/24/2023] [Indexed: 09/28/2023] Open
Abstract
Zanthoxylum (Sichuan pepper), with its rich cultivars, has long been widely cultivated in China for its unique seasoning and medicinal uses, but most of its cultivars have similar morphological characteristics. Therefore, we hypothesized that the genetic diversity of Zanthoxylum cultivars is low because of their apomixis and long cultivation history. In this study, we aimed to investigate the genetic diversity of three Zanthoxylum species on the cultivar level based on express sequence tag-simple sequence repeat (EST-SSR) primers. In total, 121 samples of three Zanthoxylum species (Z. bungeanum, Z. armatum and Z. piperitum) were collected from different areas in China for genetic diversity analysis. A total of six specificity and polymorphism EST-SSR primers, which we selected from among 120 primers based on two transcriptomes (Z. bungeanum, Z. armatum) in our earlier study, were used to evaluate genetic diversity based on capillary electrophoresis technology. The results of our analysis using the unweighted pair group method with arithmetic mean (UPGMA) indicated that most of the samples are clustered in one clade in the UPGMA dendrogram, and the average genetic distance was 0.6409. Principal component analysis (PCA) showed that Z. piperitum may have a closer genetic relationship with Z. bungeanum than with Z. armatum. An analysis of molecular variation (AMOVA) showed that the genetic variation mainly stemmed from individuals within populations; the genetic differentiation coefficient (PhiPT) was 0.429, the gene flow (Nm) between populations was 0.333, and the differences among populations were not significant (p > 0.001). For the intraspecific populations of ZB, the percentage of genetic variation was 53% among populations and 47% within populations, with non-significant differences between populations (p > 0.001). The genetic differentiation coefficient (PhiT) was 0.529, and the gene flow (Nm) was 0.223. For the intraspecific populations of ZA, the results indicated that the percentage of genetic variation was 29% among populations and 71% within populations, with non-significant differences between populations (p > 0.001); the genetic differentiation coefficient (PhiPT) was 0.293, and the gene flow (Nm) was 0.223. Through genetic structure analysis (GSA), we predicted that these 121 samples belonged to two optimal subgroups, which means that all the samples probably originated from two gene pools. Above all, this indicated that the genetic diversity of the 121 Zanthoxylum samples was relatively low at both the species and cultivar levels, a finding which was consistent with our initial assumptions. This study provides a reference, with molecular-level data, for the further identification of Zanthoxylum species.
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Affiliation(s)
- Yangchuan Deng
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Zhoujian He
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Yanlin Li
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Meng Ye
- College of Forestry, Sichuan Agricultural University, Huimin Road 211, Wenjiang District, Chengdu 611130, China; (Y.D.); (Z.H.); (Y.L.)
| | - Li Xiang
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, No. 16 Nanxiaojie, Dongzhimennei Ave., Beijing 100700, China
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Shams S, Ismaili A, Firouzabadi FN, Mumivand H, Sorkheh K. Comparative transcriptome analysis to identify putative genes involved in carvacrol biosynthesis pathway in two species of Satureja, endemic medicinal herbs of Iran. PLoS One 2023; 18:e0281351. [PMID: 37418504 PMCID: PMC10328369 DOI: 10.1371/journal.pone.0281351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 01/22/2023] [Indexed: 07/09/2023] Open
Abstract
Satureja is rich in phenolic monoterpenoids, mainly carvacrol, that is of interest due to diverse biological activities including antifungal and antibacterial. However, limited information is available regarding the molecular mechanisms underlying carvacrol biosynthesis and its regulation for this wonderful medicinal herb. To identify the putative genes involved in carvacrol and other monoterpene biosynthesis pathway, we generated a reference transcriptome in two endemic Satureja species of Iran, containing different yields (Satureja khuzistanica and Satureja rechingeri). Cross-species differential expression analysis was conducted between two species of Satureja. 210 and 186 transcripts related to terpenoid backbone biosynthesis were identified for S. khuzistanica and S. rechingeri, respectively. 29 differentially expressed genes (DEGs) involved in terpenoid biosynthesis were identified, and these DEGs were significantly enriched in monoterpenoid biosynthesis, diterpenoid biosynthesis, sesquiterpenoid and triterpenoid biosynthesis, carotenoid biosynthesis and ubiquinone and other terpenoid-quinone biosynthesis pathways. Expression patterns of S. khuzistanica and S. rechingeri transcripts involved in the terpenoid biosynthetic pathway were evaluated. In addition, we identified 19 differentially expressed transcription factors (such as MYC4, bHLH, and ARF18) that may control terpenoid biosynthesis. We confirmed the altered expression levels of DEGs that encode carvacrol biosynthetic enzymes using quantitative real-time PCR (qRT-PCR). This study is the first report on de novo assembly and transcriptome data analysis in Satureja which could be useful for an understanding of the main constituents of Satureja essential oil and future research in this genus.
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Affiliation(s)
- Somayeh Shams
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Lorestan University, Khorramabad, Iran
| | - Ahmad Ismaili
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Lorestan University, Khorramabad, Iran
| | - Farhad Nazarian Firouzabadi
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Lorestan University, Khorramabad, Iran
| | - Hasan Mumivand
- Faculty of Agriculture, Department of Horticultural Science, Lorestan University, Khorramabad, Iran
| | - Karim Sorkheh
- Faculty of Agriculture, Department of Plant Production and Genetic Engineering, Shahid Chamran University of Ahvaz, Ahvaz, Iran
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Singh R, Singh A, Mahato AK, Paliwal R, Tiwari G, Kumar A. De Novo Transcriptome Profiling for the Generation and Validation of Microsatellite Markers, Transcription Factors, and Database Development for Andrographis paniculata. Int J Mol Sci 2023; 24:ijms24119212. [PMID: 37298166 DOI: 10.3390/ijms24119212] [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: 02/27/2023] [Revised: 03/24/2023] [Accepted: 03/27/2023] [Indexed: 06/12/2023] Open
Abstract
Andrographis paniculata belongs to the family Acanthaceae and is known for its medicinal properties owing to the presence of unique constituents belonging to the lactones, diterpenoids, diterpene glycosides, flavonoids, and flavonoid glycosides groups of chemicals. Andrographolide, a major therapeutic constituent of A. paniculata, is extracted primarily from the leaves of this plant and exhibits antimicrobial and anti-inflammatory activities. Using 454 GS-FLX pyrosequencing, we have generated a whole transcriptome profile of entire leaves of A. paniculata. A total of 22,402 high-quality transcripts were generated, with an average transcript length and N50 of 884 bp and 1007 bp, respectively. Functional annotation revealed that 19,264 (86%) of the total transcripts showed significant similarity with the NCBI-Nr database and were successfully annotated. Out of the 19,264 BLAST hits, 17,623 transcripts were assigned GO terms and distributed into three major functional categories: molecular function (44.62%), biological processes (29.19%), and cellular component (26.18%) based on BLAST2GO. Transcription factor analysis showed 6669 transcripts, belonging to 57 different transcription factor families. Fifteen TF genes that belong to the NAC, MYB, and bHLH TF categories were validated by RT PCR amplification. In silico analysis of gene families involved in the synthesis of biochemical compounds having medicinal values, such as cytochrome p450, protein kinases, heat shock proteins, and transporters, was completed and a total of 102 different transcripts encoding enzymes involved in the biosynthesis of terpenoids were predicted. Out of these, 33 transcripts belonged to terpenoid backbone biosynthesis. This study also identified 4254 EST-SSRs from 3661 transcripts, representing 16.34% of the total transcripts. Fifty-three novel EST-SSR markers generated from our EST dataset were used to assess the genetic diversity among eighteen A. paniculata accessions. The genetic diversity analysis revealed two distinct sub-clusters and all accessions based on the genetic similarity index were distinct from each other. A database based on EST transcripts, EST-SSR markers, and transcription factors has been developed using data generated from the present study combined with available transcriptomic resources from a public database using Meta transcriptome analysis to make genomic resources available in one place to the researchers working on this medicinal plant.
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Affiliation(s)
- Rakesh Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Akshay Singh
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Ajay Kumar Mahato
- The Centre for DNA Fingerprinting and Diagnostics, Hyderabad 500039, India
| | - Ritu Paliwal
- Division of Genomic Resources, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
| | - Gunjan Tiwari
- CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India
| | - Ashok Kumar
- Division of Germplasm Evaluation, ICAR-National Bureau of Plant Genetic Resources, New Delhi 110012, India
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Mutinda ES, Kimutai F, Mkala EM, Waswa EN, Odago WO, Nanjala C, Ndungu CN, Gichua MK, Njire MM, Gituru RW, Hu GW. Ethnobotanical uses, phytochemistry and pharmacology of pantropical genus Zanthoxylum L. (Rutaceae): An update. JOURNAL OF ETHNOPHARMACOLOGY 2023; 303:115895. [DOI: https:/doi.org/10.1016/j.jep.2022.115895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/21/2023]
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Mutinda ES, Kimutai F, Mkala EM, Waswa EN, Odago WO, Nanjala C, Ndungu CN, Gichua MK, Njire MM, Gituru RW, Hu GW. Ethnobotanical uses, phytochemistry and pharmacology of pantropical genus Zanthoxylum L. (Rutaceae): An update. JOURNAL OF ETHNOPHARMACOLOGY 2023; 303:115895. [PMID: 36513263 DOI: 10.1016/j.jep.2022.115895] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2022] [Revised: 10/24/2022] [Accepted: 10/30/2022] [Indexed: 06/17/2023]
Abstract
ETHNOPHARMACOLOGICAL RELEVANCE Plants have been used in various parts of the world to treat various diseases. The genus Zanthoxylum L. (Rutaceae) is the second largest genus of this family and comprises approximately 225-549 species distributed in the tropical and temperate regions of the world. Plants of this genus are trees and shrubs with various applications in folklore medicine for food, medicine, construction, and other uses. AIM OF THE REVIEW The goal of this review is to give an updated data on the ethnobotanical applications, phytochemistry, and pharmacology of the Zanthoxylum species to investigate their medicinal potential and identify research gaps for future research studies. MATERIALS AND METHODS Data was obtained through a systematic search of published literature and online databases such as Google Scholar, Web of Science, PubMed, Science Direct, and Sci-Finder. The botanical names were confirmed using the World Flora Online and chemical structures were drawn using the ChemBio Draw Ultra Version 14.0 Software. RESULTS The Zanthoxylum species have a wide use in different parts of the continents as a remedy for various diseases such as digestive diseases, gastrointestinal disorders, venereal diseases, respiratory diseases, rheumatism, bacterial diseases, viral, and other diseases. Various parts of the plant comprising fruits, seeds, twigs, leaves, oils, and stems are administered singly or in the form of decoction, infusion, powder, paste, poultice, juice, or mixed with other medicinal plants to cure the disease. More than 400 secondary metabolites have been isolated and characterized in this genus with various biological activities, which comprise alkaloids, flavonoids, coumarins, lignans, alcohols, fatty acids, amides, sesquiterpenes, monoterpenes, and hydrocarbons. The crude extracts, fractions, and chemical compounds isolated from the genus have demonstrated a wide range of biological activities both in vivo and in vitro, including; anti-cancer, antimicrobial, anti-sickling, hepatoprotective, antipyretic, antitumor, and other pharmacological activities. CONCLUSION This genus has demonstrated an array of phytoconstituents with therapeutic potential. The ethnobotanical uses of this genus have been confirmed in modern pharmacological research. This genus is a potential source for modern drug discovery and health care products. Further and extensive research is therefore required on the safety approval and therapeutic application of the species of this genus as well as clinical trials and pharmacokinetic studies.
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Affiliation(s)
- Elizabeth Syowai Mutinda
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Festus Kimutai
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Elijah Mbandi Mkala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Emmanuel Nyongesa Waswa
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Wyclif Ochieng Odago
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Consolata Nanjala
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Caroline Njambi Ndungu
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya.
| | - Moses Kirega Gichua
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya.
| | - Moses Muguci Njire
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya.
| | - Robert Wahiti Gituru
- Jomo Kenyatta University of Agriculture and Technology, P.O. Box 62000-00200, Nairobi, Kenya.
| | - Guang-Wan Hu
- CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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Hui W, Zheng H, Fan J, Wang J, Saba T, Wang K, Wu J, Wu H, Zhong Y, Chen G, Gong W. Genome-wide characterization of the MBF1 gene family and its expression pattern in different tissues and stresses in Zanthoxylum armatum. BMC Genomics 2022; 23:652. [PMID: 36104767 PMCID: PMC9472409 DOI: 10.1186/s12864-022-08863-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 08/31/2022] [Indexed: 11/18/2022] Open
Abstract
Background Multiprotein bridging factor 1 (MBF1) is a crucial transcriptional coactivator in animals, plants, and some microorganisms, that plays a necessary role in growth development and stress tolerance. Zanthoxylum armatum is an important perennial plant for the condiments and pharmaceutical industries, whereas the potential information in the genes related to stress resistance remains poorly understood in Z. armatum. Results Herein, six representative species were selected for use in a genome-wide investigation of the MBF1 family, including Arabidopsis thaliana, Oryza sativa, Populus trichocarpa, Citrus sinensis, Ginkgo biloba, and Z. armatum. The results showed that the MBF1 genes could be divided into two groups: Group I contained the MBF1a and MBF1b subfamilies, and group II was independent of the MBF1c subfamily.. Most species have at least two different MBF1 genes, and MBF1c is usually an essential member. The three ZaMBF1 genes were respectively located on ZaChr26, ZaChr32, and ZaChr4 of Zanthoxylum chromosomes. The collinearity were occurred between three ZaMBF1 genes, and ZaMBF1c showed the collinearity between Z. armatum and both P. trichocarpa and C. sinensis. Moreover, many cis-elements associated with abiotic stress and phytohormone pathways were detected in the promoter regions of MBF1 of six representative species. The ERF binding sites were the most abundant targets in the sequences of the ZaMBF1 family, and some transcription factor sites related to floral differentiation were also identified in ZaMBF1c, such as MADS, LFY, Dof, and AP2. ZaMBF1a was observed to be very highly expressed in 25 different samples except in the seeds, and ZaMBF1c may be associated with the male and female floral initiation processes. In addition, expression in all the ZaMBF1 genes could be significantly induced by water-logging, cold stress, ethephon, methyl jasmonate, and salicylic acid treatments, especially in ZaMBF1c. Conclusion The present study carried out a comprehensive bioinformatic investigation related to the MBF1 family in six representative species, and the responsiveness of ZaMBF1 genes to various abiotic stresses and phytohormone inductions was also revealed. This work not only lays a solid foundation to uncover the biological roles of the ZaMBF1 family in Z. armatum, but also provides some broad references for conducting the MBF1 research in other plants. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08863-4.
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Liao LB, Chen XX, Xiang J, Zhang NN, Wang ET, Shi FS. Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil. PeerJ 2022; 10:e13808. [PMID: 35945942 PMCID: PMC9357373 DOI: 10.7717/peerj.13808] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 07/07/2022] [Indexed: 01/18/2023] Open
Abstract
Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.
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Affiliation(s)
- Li Bin Liao
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - Xiao Xia Chen
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,University of Chinese Academy of Sciences, Beijing, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - Jun Xiang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China
| | - Nan Nan Zhang
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
| | - En Tao Wang
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, Ciudad de México, México
| | - Fu Sun Shi
- Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, China,CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration and Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chendu, China
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11
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Feng T, Jiang Y, Jia Q, Han R, Wang D, Zhang X, Liang Z. Transcriptome Analysis of Different Sections of Rhizome in Polygonatum sibiricum Red. and Mining Putative Genes Participate in Polysaccharide Biosynthesis. Biochem Genet 2022; 60:1547-1566. [DOI: 10.1007/s10528-022-10183-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
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12
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Vidya V, Prasath D, Snigdha M, Gobu R, Sona C, Maiti CS. Development of EST-SSR markers based on transcriptome and its validation in ginger (Zingiber officinale Rosc.). PLoS One 2021; 16:e0259146. [PMID: 34705868 PMCID: PMC8550423 DOI: 10.1371/journal.pone.0259146] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 10/13/2021] [Indexed: 12/20/2022] Open
Abstract
Ginger (Zingiber officinale Rosc.) is an economically important and valuable spice crop around the world. It is used as food, spice, condiment, and medicine. A considerable extent of genetic diversity in ginger occurs in the Western Ghats and North-Eastern India. However, genetic diversity studies at the molecular level in ginger is limited due to limited availability of genetic and genomic information. In the present study, for the first time, we have identified and validated expressed sequence tag (EST)-simple sequence repeat (SSR) markers from ginger. We obtained 16,790 EST-SSR loci from 78987 unigenes, and 4597 SSR loci in the predicted 76929 coding sequences from RNA-Seq assembled contigs of ginger through Illumina paired-end sequencing. Gene ontology results indicate that the unigenes with SSR loci participate in various biological processes such as metabolism, growth, and development in ginger. One hundred and twenty-five primer pairs were designed from unigenes and coding sequences. These primers were tested for PCR optimization, characterization, and amplification and identified 12 novel EST-SSR markers. Twelve flanking polymorphic EST-SSR primers were validated using 48 ginger genotypes representing North-Eastern India and different eco-geographical adaptations by PCR amplification and allele sizing through capillary electrophoresis. Twelve EST-SSR primers generated a total of 111 alleles with an average of 9.25 alleles per locus and allele sizes ranging between 115-189bp. This study implies that the SSR markers designed from transcriptome sequences provides ample EST-SSR resources, which are helpful for genetic diversity analysis of Zingiberaceae species and molecular verification of ginger genotypes.
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Affiliation(s)
- Venugopal Vidya
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India
| | | | - Mohandas Snigdha
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India
| | - Ramasamy Gobu
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India
| | - Charles Sona
- ICAR-Indian Institute of Spices Research, Kozhikode, Kerala, India
| | - Chandan Suravi Maiti
- School of Agricultural Sciences and Rural Development (SASARD), Nagaland University, Nagaland, India
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13
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Anil-Inevi M, Delikoyun K, Mese G, Tekin HC, Ozcivici E. Magnetic levitation assisted biofabrication, culture, and manipulation of 3D cellular structures using a ring magnet based setup. Biotechnol Bioeng 2021; 118:4771-4785. [PMID: 34559409 DOI: 10.1002/bit.27941] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Revised: 09/03/2021] [Accepted: 09/19/2021] [Indexed: 12/13/2022]
Abstract
Diamagnetic levitation is an emerging technology for remote manipulation of cells in cell and tissue level applications. Low-cost magnetic levitation configurations using permanent magnets are commonly composed of a culture chamber physically sandwiched between two block magnets that limit working volume and applicability. This work describes a single ring magnet-based magnetic levitation system to eliminate physical limitations for biofabrication. Developed configuration utilizes sample culture volume for construct size manipulation and long-term maintenance. Furthermore, our configuration enables convenient transfer of liquid or solid phases during the levitation. Before biofabrication, we first calibrated/ the platform for levitation with polymeric beads, considering the single cell density range of viable cells. By taking advantage of magnetic focusing and cellular self-assembly, millimeter-sized 3D structures were formed and maintained in the system allowing easy and on-site intervention in cell culture with an open operational space. We demonstrated that the levitation protocol could be adapted for levitation of various cell types (i.e., stem cell, adipocyte and cancer cell) representing cells of different densities by modifying the paramagnetic ion concentration that could be also reduced by manipulating the density of the medium. This technique allowed the manipulation and merging of separately formed 3D biological units, as well as the hybrid biofabrication with biopolymers. In conclusion, we believe that this platform will serve as an important tool in broad fields such as bottom-up tissue engineering, drug discovery and developmental biology.
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Affiliation(s)
- Muge Anil-Inevi
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Kerem Delikoyun
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Gulistan Mese
- Department of Molecular Biology and Genetics, Izmir Institute of Technology, Izmir, Turkey
| | - H Cumhur Tekin
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
| | - Engin Ozcivici
- Department of Bioengineering, Izmir Institute of Technology, Izmir, Turkey
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14
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Feng S, Liu Z, Cheng J, Li Z, Tian L, Liu M, Yang T, Liu Y, Liu Y, Dai H, Yang Z, Zhang Q, Wang G, Zhang J, Jiang H, Wei A. Zanthoxylum-specific whole genome duplication and recent activity of transposable elements in the highly repetitive paleotetraploid Z. bungeanum genome. HORTICULTURE RESEARCH 2021; 8:205. [PMID: 34480029 PMCID: PMC8417289 DOI: 10.1038/s41438-021-00665-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/29/2021] [Accepted: 07/30/2021] [Indexed: 05/14/2023]
Abstract
Zanthoxylum bungeanum is an important spice and medicinal plant that is unique for its accumulation of abundant secondary metabolites, which create a characteristic aroma and tingling sensation in the mouth. Owing to the high proportion of repetitive sequences, high heterozygosity, and increased chromosome number of Z. bungeanum, the assembly of its chromosomal pseudomolecules is extremely challenging. Here, we present a genome sequence for Z. bungeanum, with a dramatically expanded size of 4.23 Gb, assembled into 68 chromosomes. This genome is approximately tenfold larger than that of its close relative Citrus sinensis. After the divergence of Zanthoxylum and Citrus, the lineage-specific whole-genome duplication event η-WGD approximately 26.8 million years ago (MYA) and the recent transposable element (TE) burst ~6.41 MYA account for the substantial genome expansion in Z. bungeanum. The independent Zanthoxylum-specific WGD event was followed by numerous fusion/fission events that shaped the genomic architecture. Integrative genomic and transcriptomic analyses suggested that prominent species-specific gene family expansions and changes in gene expression have shaped the biosynthesis of sanshools, terpenoids, and anthocyanins, which contribute to the special flavor and appearance of Z. bungeanum. In summary, the reference genome provides a valuable model for studying the impact of WGDs with recent TE activity on gene gain and loss and genome reconstruction and provides resources to accelerate Zanthoxylum improvement.
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Affiliation(s)
- Shijing Feng
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Zhenshan Liu
- College of Life Science, Northwest A&F University, Yangling, Shaanxi, China
| | - Jian Cheng
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China
| | - Zihe Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an, Shanxi, China
| | - Lu Tian
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Min Liu
- Biomarker Technologies Corporation, Beijing, China
| | - Tuxi Yang
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Yulin Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - Yonghong Liu
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China
| | - He Dai
- Biomarker Technologies Corporation, Beijing, China
| | - Zujun Yang
- Center for Information in Biology, College of Life Science and Technology, University of Electronic Science and Technology of China, Chengdu, China
| | - Qing Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gang Wang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jisen Zhang
- Center for Genomics and Biotechnology, Haixia Institute of Science and Technology, Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Huifeng Jiang
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, China.
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, Shaanxi, China.
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, Shaanxi, China.
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15
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Dong S, Tian Q, Zhu T, Wang K, Lei G, Liu Y, Xiong H, Shen L, Wang M, Zhao R, Wu H, Li B, Zhang Q, Yao Y, Guo H, Xia K, Xia L, Hu Z. SLC39A5 dysfunction impairs extracellular matrix synthesis in high myopia pathogenesis. J Cell Mol Med 2021; 25:8432-8441. [PMID: 34302427 PMCID: PMC8419198 DOI: 10.1111/jcmm.16803] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Revised: 05/13/2021] [Accepted: 07/06/2021] [Indexed: 12/23/2022] Open
Abstract
High myopia is one of the leading causes of visual impairment worldwide with high heritability. We have previously identified the genetic contribution of SLC39A5 to nonsyndromic high myopia and demonstrated that disease‐related mutations of SLC39A5 dysregulate the TGF‐β pathway. In this study, the mechanisms underlying SLC39A5 involvement in the pathogenesis of high myopia are determined. We observed the morphogenesis and migration abnormalities of the SLC39A5 knockout (KO) human embryonic kidney cells (HEK293) and found a significant injury of ECM constituents. RNA‐seq and qRT‐PCR revealed the transcription decrease in COL1A1, COL2A1, COL4A1, FN1 and LAMA1 in the KO cells. Further, we demonstrated that TGF‐β signalling, the regulator of ECM, was inhibited in SLC39A5 depletion situation, wherein the activation of receptor Smads (R‐Smads) via phosphorylation was greatly blocked. SLC39A5 re‐expression reversed the phenotype of TGF‐β signalling and ECM synthesis in the KO cells. The fact that TGF‐β signalling was zinc‐regulated and that SLC39A5 was identified as a zinc transporter urged us to check the involvement of intracellular zinc in TGF‐β signalling impairment. Finally, we determined that insufficient zinc chelation destabilized Smad proteins, which naturally inhibited TGF‐β signalling. Overall, the SLC39A5 depletion–induced zinc deficiency destabilized Smad proteins, which inhibited the TGF‐β signalling and downstream ECM synthesis, thus contributing to the pathogenesis of high myopia. This discovery provides a deep insight into myopic development.
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Affiliation(s)
- Shanshan Dong
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Qi Tian
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Tengfei Zhu
- Department of Critical Care Medicine, Shenzhen Third People's Hospital, Shenzhen, Guangdong, China
| | - Kangli Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Ganting Lei
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yanling Liu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Haofeng Xiong
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Lu Shen
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Meng Wang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Rongjuan Zhao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Huidan Wu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Bin Li
- National Clinical Research Center for Geriatric Disorders, Department of Geriatrics, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qiumeng Zhang
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Yujun Yao
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Hui Guo
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Kun Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Molecular Precisional Medicine, Central South University, Changsha, Hunan, China
| | - Lu Xia
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China
| | - Zhengmao Hu
- Center for Medical Genetics & Hunan Key Laboratory of Medical Genetics, School of Life Sciences, Central South University, Changsha, Hunan, China.,Hunan Key Laboratory of Animal Models for Human Diseases, Central South University, Changsha, Hunan, China
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16
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Wang M, Tong S, Ma T, Xi Z, Liu J. Chromosome-level genome assembly of Sichuan pepper provides insights into apomixis, drought tolerance, and alkaloid biosynthesis. Mol Ecol Resour 2021; 21:2533-2545. [PMID: 34145765 DOI: 10.1111/1755-0998.13449] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2021] [Revised: 06/11/2021] [Accepted: 06/14/2021] [Indexed: 11/27/2022]
Abstract
Sichuan pepper is a commonly used spice in Asian cuisine. Sanshools and wgx-50/gx-50 isolated from it have been shown to possess a wide spectrum of medicinal properties. Here we generated a chromosome-level genome assembly of one Sichuan pepper species Zanthoxylum armatum characterized by drought tolerance and apomixis. Analyses of functionally related genes suggested that increased gene copy number and expression level of drought-tolerant genes might play an important role in improving drought tolerance of Z. armatum. Moreover, a gene encoding an RWP-RK domain-containing protein was shown to contribute to apomixis in Z. armatum, which was further characterized by overexpression in Arabidopsis thaliana. Furthermore, based on gene homology searching and co-expression patterns of metabolite concentration and gene expressions, we identified a number of candidate genes involved in the biosynthesis of sanshools and wgx-50/gx-50. Taken together, our results yield valuable insights for understanding the evolution of apomixis, drought tolerance, and alkaloid biosynthesis in Z. armatum.
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Affiliation(s)
- Mingcheng Wang
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China.,Institute for Advanced Study, Chengdu University, Chengdu, China
| | - Shaofei Tong
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Tao Ma
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Zhenxiang Xi
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
| | - Jianquan Liu
- Key Laboratory of Bio-Resource and Eco-Environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, China
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17
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Genome survey of Zanthoxylum bungeanum and development of genomic-SSR markers in congeneric species. Biosci Rep 2021; 40:225368. [PMID: 32558907 PMCID: PMC7322109 DOI: 10.1042/bsr20201101] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Revised: 06/11/2020] [Accepted: 06/18/2020] [Indexed: 01/13/2023] Open
Abstract
Zanthoxylum bungeanum, a spice and medicinal plant, is cultivated in many parts of China and some countries in Southeast Asia; however, data on its genome are lacking. In the present study, we performed a whole-genome survey and developed novel genomic-SSR markers of Z. bungeanum. Clean data (∼197.16 Gb) were obtained and assembled into 11185221 scaffolds with an N50 of 183 bp. K-mer analysis revealed that Z. bungeanum has an estimated genome size of 3971.92 Mb, and the GC content, heterozygous rate, and repeat sequence rate are 37.21%, 1.73%, and 86.04%, respectively. These results indicate that the genome of Z. bungeanum is complex. Furthermore, 27153 simple sequence repeat (SSR) loci were identified from 57288 scaffolds with a minimum length > 1 kb. Mononucleotide repeats (19706) were the most abundant type, followed by dinucleotide repeats (5154). The most common motifs were A/T, followed by AT/AT; these SSRs accounted for 71.42% and 11.84% of all repeats, respectively. A total of 21243 non-repeating primer pairs were designed, and 100 were randomly selected and validated by PCR analysis using DNA from 10 Z. bungeanum individuals and 5 Zanthoxylum armatum individuals. Finally, 36 polymorphic SSR markers were developed with polymorphism information content (PIC) values ranging from 0.16 to 0.75. Cluster analysis revealed that Z. bungeanum and Z. armatum could be divided into two major clusters, suggesting that these newly developed SSR markers are useful for genetic diversity and germplasm resource identification in Z. bungeanum and Z. armatum.
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18
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De novo transcriptome assembly and mining of EST-SSR markers in Gloriosa superba. J Genet 2020. [DOI: 10.1007/s12041-020-01235-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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19
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Feng S, Liu Z, Hu Y, Tian J, Yang T, Wei A. Genomic analysis reveals the genetic diversity, population structure, evolutionary history and relationships of Chinese pepper. HORTICULTURE RESEARCH 2020; 7:158. [PMID: 33082965 PMCID: PMC7527552 DOI: 10.1038/s41438-020-00376-z] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Revised: 07/07/2020] [Accepted: 07/13/2020] [Indexed: 05/26/2023]
Abstract
Chinese pepper, mainly including Zanthoxylum bungeanum and Zanthoxylum armatum, is an economically important crop popular in Asian countries due to its unique taste characteristics and potential medical uses. Numerous cultivars of Chinese pepper have been developed in China through long-term domestication. To better understand the population structure, demographic history, and speciation of Chinese pepper, we performed a comprehensive analysis at a genome-wide level by analyzing 38,395 genomic SNPs that were identified in 112 cultivated and wild accessions using a high-throughput genome-wide genotyping-by-sequencing (GBS) approach. Our analysis provides genetic evidence of multiple splitting events occurring between and within species, resulting in at least four clades in Z. bungeanum and two clades in Z. armatum. Despite no evidence of recent admixture between species, we detected substantial gene flow within species. Estimates of demographic dynamics and species distribution modeling suggest that climatic oscillations during the Pleistocene (including the Penultimate Glaciation and the Last Glacial Maximum) and recent domestication events together shaped the demography and evolution of Chinese pepper. Our analyses also suggest that southeastern Gansu province is the most likely origin of Z. bungeanum in China. These findings provide comprehensive insights into genetic diversity, population structure, demography, and adaptation in Zanthoxylum.
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Affiliation(s)
- Shijing Feng
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- College of Life Science, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Zhenshan Liu
- College of Life Science, Northwest A&F University, Yangling, 712100 Shaanxi China
| | - Yang Hu
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Jieyun Tian
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Tuxi Yang
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
| | - Anzhi Wei
- College of Forestry, Northwest A&F University, Yangling, 712100 Shaanxi China
- Research Centre for Engineering and Technology of Zanthoxylum State Forestry Administration, Yangling, 712100 Shaanxi China
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20
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Li Z, Tariq A, Pan K, Graciano C, Sun F, Song D, Abiodun Olatunji O. Role of Glycine max in improving drought tolerance in Zanthoxylum bungeanum. PeerJ 2020; 8:e9040. [PMID: 32411523 PMCID: PMC7207205 DOI: 10.7717/peerj.9040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Accepted: 04/01/2020] [Indexed: 01/13/2023] Open
Abstract
Intercropping may improve community stability and yield under climate change. Here, we set up a field experiment to evaluate the advantages of cultivating Z anthoxylum bungeanum with Capsicum annum, and Z. bungeanum with Glycine max as intercrops, compared with cultivating Z. bungeanum in monoculture. Effects of extreme drought stress conditions on morphological, physiological, and biochemical traits of the three crop species cultivated in the three contrasting planting systems were compared. Results showed that extreme drought conditions induced negative impacts on Z. bungeanum grown in monoculture, due to reduced growth and metabolic impairment. However, limited stomatal conductance, reduced transpiration rate (Tr), and increased water use efficiency, carotenoid content, catalase activity, and accumulation of soluble sugars in Z. bungeanum indicated its adaptive strategies for tolerance of extreme drought stress conditions. Compared with cultivation in monoculture, intercropping with C. annum had positive effects on Z. bungeanum under extreme drought stress conditions, as a result of improved crown diameter, leaf relative water content (LRWC), net photosynthetic rate, and proline content, while intercropping with G. max under extreme drought stress conditions increased net CO2 assimilation rates, LRWC, Tr, and superoxide dismutase (SOD) activity. In conclusion, Z. bungeanum has an effective defense mechanism for extreme drought stress tolerance. Intercropping with G. max enhanced this tolerance potential primarily through its physio-biochemical adjustments, rather than as a result of nitrogen fixation by G. max.
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Affiliation(s)
- Zilong Li
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China.,University of Chinese Academy of Sciences, Beijing, China.,School of Pharmacy, Guizhou University of Traditional Chinese Medicine, Guizhou, China
| | - Akash Tariq
- State Key Laboratory of Desert and Oasis Ecology, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China.,Cele National Station of Observation and Research for Desert-Grassland Ecosystems, Cele, Urumqi, China.,Key Laboratory of Biogeography and Bioresource in Arid Zone, Chinese Academy of Sciences, Urumqi, Xinjiang, China.,Xinjiang Desert Plant Roots Ecology and Vegetation Restoration Laboratory, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, Urumqi, China
| | - Kaiwen Pan
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Corina Graciano
- Instituto de Fisiología Vegetal, Consejo Nacional de Investigaciones Científicas y Técnicas Universidad Nacional de La Plata, Buenos Aires, Argentina
| | - Feng Sun
- CAS Key Laboratory of Mountain Ecological Restoration and Bioresource Utilization & Ecological Restoration Biodiversity Conservation Key Laboratory of Sichuan Province, Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, Sichuan, China
| | - Dagang Song
- Biogas Institute of Ministry of Agriculture and Rural Affairs, Chengdu, China
| | - Olusanya Abiodun Olatunji
- Key Laboratory for Humid Subtropical Eco-Geographical Processes of the Ministry of Education, Fujian Normal University, Fuzhou, China
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21
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Genetic Diversity and Evolutionary Relationships of Chinese Pepper Based on nrDNA Markers. FORESTS 2020. [DOI: 10.3390/f11050543] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Chinese pepper, referring to Zanthoxylum bungeanum Maxim. and Zanthoxylum armatum DC. species, is an important spice crop that has long attracted people’s interest due to its extensive application in Asian cuisine to improve taste. Numerous cultivars have been developed during the long history of domestication and cultivation. However, little to no information is available on the genetic diversity and evolutionary relationships of Chinese pepper cultivars and their historical diversification has not been clarified. Herein, we sequenced two nrDNA non-coding region markers, the external transcribed spacer (ETS) and the internal transcribed spacer 2 (ITS2), to assess genetic diversity and phylogenetic relationships among 39 cultivated and wild populations of Chinese pepper from eight provinces and to address the question of ancient demographic trends which were probably influenced by changing climate during evolutionary history. In total, 31 haplotypes were identified based on 101 polymorphism sites. Our results revealed relatively high level of genetic variation despite long-term cultivation of this crop. AMOVA revealed that genetic variation existed predominantly within provinces rather than among provinces. The genetic structure result based on haplotype network analysis largely reflected historical records, which suggested a Gansu origin for Chinese pepper and an ancient west-to-east spread of Chinese pepper circulating in China. We also provided evidence that changing Pleistocene climates had shaped the demographic trends of Chinese pepper. Taken together, our findings not only suggest that Chinese pepper is a dynamic genetic system that responds to evolutionary forces, but it also provides a fundamental genetic profile for the conservation and responsible exploitation of the extant germplasm of Chinese pepper and for improving the genetic basis for breeding the cultivars.
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22
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Chai M, Ye H, Wang Z, Zhou Y, Wu J, Gao Y, Han W, Zang E, Zhang H, Ru W, Sun G, Wang Y. Genetic Divergence and Relationship Among Opisthopappus Species Identified by Development of EST-SSR Markers. Front Genet 2020; 11:177. [PMID: 32194635 PMCID: PMC7065708 DOI: 10.3389/fgene.2020.00177] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2019] [Accepted: 02/13/2020] [Indexed: 12/16/2022] Open
Abstract
Opisthopappus Shih is an endemic and endangered genus restricted to the Taihang Mountains that has important ornamental and economic value. According to the Flora Reipublicae Popularis Sinicae (FRPS, Chinese version), this genus contains two species (Opisthopappus longilobus and Opisthopappus taihangensis), whereas in the Flora of China (English version) only one species O. taihangensis is present. The interspecific phylogenetic relationship remains unclear and undefined, which might primarily be due to the lack of specific molecular markers for phylogenetic analysis. For this study, 2644 expressed sequence tag-simple sequence repeats (EST-SSRs) from 33,974 unigenes using a de novo transcript assembly of Opisthopappus were identified with a distribution frequency of 7.78% total unigenes. Thereinto, mononucleotides (1200, 45.39%) were the dominant repeat motif, followed by trinucleotides (992, 37.52%), and dinucleotides (410, 15.51%). The most dominant trinucleotide repeat motif was ACC/GGT (207, 20.87%). Based on the identified EST-SSRs, 245 among 1444 designed EST-SSR primers were selected for the development of potential molecular markers. Among these markers, 63 pairs of primers (25.71%) generated clear and reproducible bands with expected sizes. Eventually, 11 primer pairs successfully amplified all individuals from the studied populations. Through the EST-SSR markers, a high level of genetic diversity was detected between Opisthopappus populations. A significant genetic differentiation between the O. longilobus and O. taihangensis populations was found. All studied populations were divided into two clusters by UPGMA, NJ, STRUCTURE, and PCoA. These results fully supported the view of the FRPS, namely, that O. longilobus and O. taihangensis should be regarded as two distinct species. Our study demonstrated that transcriptome sequences, as a valuable tool for the quick and cost-effective development of molecular markers, was helpful toward obtaining comprehensive EST-SSR markers that could contribute to an in-depth assessment of the genetic and phylogenetic relationships between Opisthopappus species.
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Affiliation(s)
- Min Chai
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hang Ye
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Zhi Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Yuancheng Zhou
- Triticeae Research Institute, Shanxi Academy of Agricultural Science, Linfen, China
| | - Jiahui Wu
- School of Life Sciences, Shanxi Normal University, Linfen, China.,Changzhi University, Changzhi, China
| | - Yue Gao
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Wei Han
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - En Zang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | - Hao Zhang
- School of Life Sciences, Shanxi Normal University, Linfen, China
| | | | - Genlou Sun
- Department of Biology, Saint Mary's University, Halifax, NS, Canada
| | - Yling Wang
- School of Life Sciences, Shanxi Normal University, Linfen, China
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23
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Hui WK, Zhao FY, Wang JY, Chen XY, Li JW, Zhong Y, Li HY, Zheng JX, Zhang LZ, Que QM, Wu AM, Gong W. De novo transcriptome assembly for the five major organs of Zanthoxylum armatum and the identification of genes involved in terpenoid compound and fatty acid metabolism. BMC Genomics 2020; 21:81. [PMID: 31992199 PMCID: PMC6986037 DOI: 10.1186/s12864-020-6521-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 01/20/2020] [Indexed: 12/12/2022] Open
Abstract
Background Zanthoxylum armatum (Z. armatum) is a highly economically important tree that presents a special numbing taste. However, the underlying regulatory mechanism of the numbing taste remains poorly understood. Thus, the elucidation of the key genes associated with numbing taste biosynthesis pathways is critical for providing genetic information on Z. armatumand the breeding of high-quality germplasms of this species. Results Here, de novo transcriptome assembly was performed for the five major organs of Z. armatum, including the roots, stems, leaf buds, mature leaves and fruits. A total of 111,318 unigenes were generated with an average length of 1014 bp. Additionally, a large number of SSRs were obtained to improve our understanding of the phylogeny and genetics of Z. armatum. The organ-specific unigenes of the five major samples were screened and annotated via GO and KEGG enrichment analysis. A total of 53 and 34 unigenes that were exclusively upregulated in fruit samples were identified as candidate unigenes for terpenoid biosynthesis or fatty acid biosynthesis, elongation and degradation pathways, respectively. Moreover, 40 days after fertilization (Fr4 stage) could be an important period for the accumulation of terpenoid compounds during the fruit development and maturation of Z. armatum. The Fr4 stage could be a key point at which the first few steps of the fatty acid biosynthesis process are promoted, and the catalysis of subsequent reactions could be significantly induced at 62 days after fertilization (Fr6 stage). Conclusions The present study realized de novo transcriptome assembly for the five major organs of Z. armatum. To the best of our knowledge, this study provides the first comprehensive analysis revealing the genes underlying the special numbing taste of Z. armatum. The assembled transcriptome profiles expand the available genetic information on this species and will contribute to gene functional studies, which will aid in the engineering of high-quality cultivars of Z. armatum.
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Affiliation(s)
- Wen-Kai Hui
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Fei-Yan Zhao
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Jing-Yan Wang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Xiao-Yang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Jue-Wei Li
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Yu Zhong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Hong-Yun Li
- Agricultural Technology Extension Center in Yantan District, Zigong, 643030, China
| | - Jun-Xing Zheng
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Liang-Zhen Zhang
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China
| | - Qing-Min Que
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China
| | - Ai-Min Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou, 510642, China.
| | - Wei Gong
- Key Laboratory of Ecological Forestry Engineering of Sichuan Province, College of Forestry, Sichuan Agricultural University, Chengdu, 611130, China.
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24
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Zhao K, Li L, Quan H, Yang J, Zhang Z, Liao Z, Lan X. Comparative Analyses of Chloroplast Genomes From 14 Zanthoxylum Species: Identification of Variable DNA Markers and Phylogenetic Relationships Within the Genus. FRONTIERS IN PLANT SCIENCE 2020; 11:605793. [PMID: 33519856 PMCID: PMC7838127 DOI: 10.3389/fpls.2020.605793] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Accepted: 12/18/2020] [Indexed: 05/21/2023]
Abstract
Zanthoxylum L. is an economic crop with a long history of cultivation and domestication and has important economic, ecological, and medicinal value. To solve the classification problems caused by the similar morphological characteristics of Zanthoxylum and establish a credible phylogenetic relationship, we sequenced and annotated six Zanthoxylum chloroplast (cp) genomes (Z. piasezkii, Z. armatum, Z. motuoense, Z. oxyphyllum, Z. multijugum, and Z. calcicola) and combined them with previously published genomes for the Zanthoxylum species. We used bioinformatics methods to analyze the genomic characteristics, contraction, and expansion of inverted repeat (IR) regions; differences in simple sequence repeats (SSRs) and long repeat sequences; species pairwise Ka/Ks ratios; divergence hotspots; and phylogenetic relationships of the 14 Zanthoxylum species. The results revealed that cp genomes of Zanthoxylum range in size from 158,071 to 158,963 bp and contain 87 protein-coding, 37 tRNA, and 8 rRNA genes. Seven mutational hotspots were identified as candidate DNA barcode sequences to distinguish Zanthoxylum species. The phylogenetic analysis strongly supported the genus Fagara as a subgenus of Zanthoxylum and proposed the possibility of a new subgenus in Zanthoxylum. The availability of these genomes will provide valuable information for identifying species, molecular breeding, and evolutionary analysis of Zanthoxylum.
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Affiliation(s)
- Kaihui Zhao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Lianqiang Li
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
| | - Hong Quan
- Key Laboratory of Forest Ecology in Tibet Plateau, Tibet Agricultural and Animal Husbandry University, Ministry of Education, Nyingchi, China
| | - Junbo Yang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhirong Zhang
- Germplasm Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Zhihua Liao
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
- Key Laboratory of Eco-Environments in the Three Gorges Reservoir Region, Ministry of Education, Chongqing Engineering and Technology Research Center for Sweetpotato, School of Life Sciences, Southwest University, Chongqing, China
| | - Xiaozhong Lan
- TAAHC-SWU Medicinal Plant Joint R&D Center, Tibetan Collaborative Innovation Center of Agricultural and Animal Husbandry Resources, Food Science College, Tibet Agriculture and Animal Husbandry University, Nyingchi, China
- *Correspondence: Xiaozhong Lan,
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25
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Molecular basis of neurophysiological and antioxidant roles of Szechuan pepper. Biomed Pharmacother 2019; 112:108696. [DOI: 10.1016/j.biopha.2019.108696] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 02/14/2019] [Accepted: 02/14/2019] [Indexed: 01/18/2023] Open
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26
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Taheri S, Abdullah TL, Rafii MY, Harikrishna JA, Werbrouck SPO, Teo CH, Sahebi M, Azizi P. De novo assembly of transcriptomes, mining, and development of novel EST-SSR markers in Curcuma alismatifolia (Zingiberaceae family) through Illumina sequencing. Sci Rep 2019; 9:3047. [PMID: 30816255 PMCID: PMC6395698 DOI: 10.1038/s41598-019-39944-2] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2018] [Accepted: 02/06/2019] [Indexed: 11/24/2022] Open
Abstract
Curcuma alismatifolia widely used as an ornamental plant in Thailand and Cambodia. This species of herbaceous perennial from the Zingiberaceae family, includes cultivars with a wide range of colours and long postharvest life, and is used as an ornamental cut flower, as a potted plant, and in exterior landscapes. For further genetic improvement, however, little genomic information and no specific molecular markers are available. The present study used Illumina sequencing and de novo transcriptome assembly of two C. alismatifolia cvs, 'Chiang Mai Pink' and 'UB Snow 701', to develop simple sequence repeat markers for genetic diversity studies. After de novo assembly, 62,105 unigenes were generated and 48,813 (78.60%) showed significant similarities versus six functional protein databases. In addition, 9,351 expressed sequence tag-simple sequence repeats (EST-SSRs) were identified with a distribution frequency of 12.5% total unigenes. Out of 8,955 designed EST-SSR primers, 150 primers were selected for the development of potential molecular markers. Among these markers, 17 EST-SSR markers presented a moderate level of genetic diversity among three C. alismatifolia cultivars, one hybrid, three Curcuma, and two Zingiber species. Three different genetic groups within these species were revealed using EST-SSR markers, indicating that the markers developed in this study can be effectively applied to the population genetic analysis of Curcuma and Zingiber species. This report describes the first analysis of transcriptome data of an important ornamental ginger cultivars, also provides a valuable resource for gene discovery and marker development in the genus Curcuma.
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Affiliation(s)
- Sima Taheri
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia.
| | - Thohirah Lee Abdullah
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia.
| | - M Y Rafii
- Department of Crop Science, Faculty of Agriculture, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Jennifer Ann Harikrishna
- Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Stefaan P O Werbrouck
- Laboratory of Applied Science In Vitro Plant Biotechnology, Department of Plants and Crops, Faculty of Bioscience Engineering, University Ghent, Valentin Vaerwyckweg 1, BE-9000, Gent, Belgium
| | - Chee How Teo
- Centre of Research in Biotechnology for Agriculture (CEBAR), University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Mahbod Sahebi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
| | - Parisa Azizi
- Laboratory of Climate-Smart Food Crop Production, Institute of Tropical Agriculture and Food Security, Universiti Putra Malaysia, 43400, Serdang, Selangor, Malaysia
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