1
|
Han X, Zhao J, Zhou H, Zhou X, Deng Z, Liu Z, Yu Y. The biosynthesis of asiaticoside and madecassoside reveals tandem duplication-directed evolution of glycoside glycosyltransferases in the Apiales. PLANT COMMUNICATIONS 2024:101005. [PMID: 38902923 DOI: 10.1016/j.xplc.2024.101005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 06/09/2024] [Accepted: 06/18/2024] [Indexed: 06/22/2024]
Abstract
Certain plant species within the Apiales order accumulate triterpenoid saponins that feature a distinctive glucose-glucose-rhamnose (G-G-R) sugar chain attached at the C-28 position of the pentacyclic triterpene skeleton. Until recently, the genomic basis underlying the biosynthesis and evolution of this sugar chain has remained elusive. In this study, we identified two novel glycoside glycosyltransferases (GGTs) that can sequentially install the sugar chain's second D-glucose and third L-rhamnose during the biosynthesis of asiaticoside and madecassoside, two representative G-G-R sugar chain-containing triterpenoid saponins produced by Centella asiatica. Enzymatic assays revealed the remarkable substrate promiscuity of the two GGTs and the key residues crucial for sugar-donor selectivity of the glucosyltransferase and rhamnosyltransferase. We further identified syntenic tandem gene duplicates of the two GGTs in the Apiaceae and Araliaceae families, suggesting a well-conserved genomic basis underlying sugar chain assembly that likely has evolved in the early ancestors of the Apiales order. Moreover, expression patterns of the two GGTs in pierced leaves of C. asiatica were found to be correlated with the production of asiaticoside and madecassoside, implying their involvement in host defense against herbivores and pathogens. Our work sheds light on the biosynthesis and evolution of complex saponin sugars, paving the way for future engineering of diverse bioactive triterpenoids with unique glycoforms.
Collapse
Affiliation(s)
- Xiaoyang Han
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Jingyi Zhao
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Hong Zhou
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Xuan Zhou
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Zixin Deng
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Zhenhua Liu
- Joint Center for Single Cell Biology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai 200240, China.
| | - Yi Yu
- Department of Gastroenterology, Zhongnan Hospital of Wuhan University, Hubei Clinical Center and Key Laboratory of Intestinal and Colorectal Disease, School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China; State Key Laboratory of Non-Food Biomass and Enzyme Technology, Guangxi Academy of Sciences, Nanning 530007, China.
| |
Collapse
|
2
|
Wan L, Huang Q, Li C, Yu H, Tan G, Wei S, El-Sappah AH, Sooranna S, Zhang K, Pan L, Zhang Z, Lei M. Integrated metabolome and transcriptome analysis identifies candidate genes involved in triterpenoid saponin biosynthesis in leaves of Centella asiatica (L.) Urban. FRONTIERS IN PLANT SCIENCE 2024; 14:1295186. [PMID: 38283979 PMCID: PMC10811118 DOI: 10.3389/fpls.2023.1295186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Accepted: 12/22/2023] [Indexed: 01/30/2024]
Abstract
Centella asiatica (L.) Urban is a well-known medicinal plant which has multiple pharmacological properties. Notably, the leaves of C. asiatica contain large amounts of triterpenoid saponins. However, there have only been a few studies systematically elucidating the metabolic dynamics and transcriptional differences regarding triterpenoid saponin biosynthesis during the leaf development stages of C. asiatica. Here, we performed a comprehensive analysis of the metabolome and transcriptome to reveal the dynamic patterns of triterpenoid saponin accumulation and identified the key candidate genes associated with their biosynthesis in C. asiatica leaves. In this study, we found that the key precursors in the synthesis of terpenoids, including DMAPP, IPP and β-amyrin, as well as 22 triterpenes and eight triterpenoid saponins were considered as differentially accumulated metabolites. The concentrations of DMAPP, IPP and β-amyrin showed significant increases during the entire stage of leaf development. The levels of 12 triterpenes decreased only during the later stages of leaf development, but five triterpenoid saponins rapidly accumulated at the early stages, and later decreased to a constant level. Furthermore, 48 genes involved in the MVA, MEP and 2, 3-oxidosqualene biosynthetic pathways were selected following gene annotation. Then, 17 CYP450s and 26 UGTs, which are respectively responsible for backbone modifications, were used for phylogenetic-tree construction and time-specific expression analysis. From these data, by integrating metabolomics and transcriptomics analyses, we identified CaHDR1 and CaIDI2 as the candidate genes associated with DMAPP and IPP synthesis, respectively, and CaβAS1 as the one regulating β-amyrin synthesis. Two genes from the CYP716 family were confirmed as CaCYP716A83 and CaCYP716C11. We also selected two UGT73 families as candidate genes, associated with glycosylation of the terpenoid backbone at C-3 in C. asiatica. These findings will pave the way for further research on the molecular mechanisms associated with triterpenoid saponin biosynthesis in C. asiatica.
Collapse
Affiliation(s)
- Lingyun Wan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Qiulan Huang
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
| | - Cui Li
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Haixia Yu
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Guiyu Tan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Shugen Wei
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ahmed H. El-Sappah
- Faculty of Agriculture, Forestry and Food Engineering, Yibin University, Yibin, China
- Genetics Department, Faculty of Agriculture, Zagazig University, Zagazig, Egypt
| | - Suren Sooranna
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, United Kingdom
| | - Kun Zhang
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Limei Pan
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Zhanjiang Zhang
- Guangxi Key Laboratory for High-Quality Formation and Utilization of Dao-Di Herbs, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| | - Ming Lei
- National Center for Traditional Chinese Medicine (TCM) Inheritance and Innovation, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
- National Engineering Research Center for the Development of Southwestern Endangered Medicinal Materials, Guangxi Botanical Garden of Medicinal Plants, Nanning, China
| |
Collapse
|
3
|
Shelake RM, Jadhav AM, Bhosale PB, Kim JY. Unlocking secrets of nature's chemists: Potential of CRISPR/Cas-based tools in plant metabolic engineering for customized nutraceutical and medicinal profiles. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 203:108070. [PMID: 37816270 DOI: 10.1016/j.plaphy.2023.108070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/12/2023]
Abstract
Plant species have evolved diverse metabolic pathways to effectively respond to internal and external signals throughout their life cycle, allowing adaptation to their sessile and phototropic nature. These pathways selectively activate specific metabolic processes, producing plant secondary metabolites (PSMs) governed by genetic and environmental factors. Humans have utilized PSM-enriched plant sources for millennia in medicine and nutraceuticals. Recent technological advances have significantly contributed to discovering metabolic pathways and related genes involved in the biosynthesis of specific PSM in different food crops and medicinal plants. Consequently, there is a growing demand for plant materials rich in nutrients and bioactive compounds, marketed as "superfoods". To meet the industrial demand for superfoods and therapeutic PSMs, modern methods such as system biology, omics, synthetic biology, and genome editing (GE) play a crucial role in identifying the molecular players, limiting steps, and regulatory circuitry involved in PSM production. Among these methods, clustered regularly interspaced short palindromic repeats-CRISPR associated protein (CRISPR/Cas) is the most widely used system for plant GE due to its simple design, flexibility, precision, and multiplexing capabilities. Utilizing the CRISPR-based toolbox for metabolic engineering (ME) offers an ideal solution for developing plants with tailored preventive (nutraceuticals) and curative (therapeutic) metabolic profiles in an ecofriendly way. This review discusses recent advances in understanding the multifactorial regulation of metabolic pathways, the application of CRISPR-based tools for plant ME, and the potential research areas for enhancing plant metabolic profiles.
Collapse
Affiliation(s)
- Rahul Mahadev Shelake
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea.
| | - Amol Maruti Jadhav
- Research Institute of Green Energy Convergence Technology (RIGET), Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Pritam Bhagwan Bhosale
- Department of Veterinary Medicine, Research Institute of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea
| | - Jae-Yean Kim
- Division of Applied Life Science (BK21 Four Program), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea; Division of Life Science, Gyeongsang National University, 501 Jinju-daero, Jinju, 52828, Republic of Korea; Nulla Bio Inc, 501 Jinju-daero, Jinju, 52828, Republic of Korea.
| |
Collapse
|
4
|
Pucker B, Iorizzo M. Apiaceae FNS I originated from F3H through tandem gene duplication. PLoS One 2023; 18:e0280155. [PMID: 36656808 PMCID: PMC9851555 DOI: 10.1371/journal.pone.0280155] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Accepted: 12/21/2022] [Indexed: 01/20/2023] Open
Abstract
BACKGROUND Flavonoids are specialized metabolites with numerous biological functions in stress response and reproduction of plants. Flavones are one subgroup that is produced by the flavone synthase (FNS). Two distinct enzyme families evolved that can catalyze the biosynthesis of flavones. While the membrane-bound FNS II is widely distributed in seed plants, one lineage of soluble FNS I appeared to be unique to Apiaceae species. RESULTS We show through phylogenetic and comparative genomic analyses that Apiaceae FNS I evolved through tandem gene duplication of flavanone 3-hydroxylase (F3H) followed by neofunctionalization. Currently available datasets suggest that this event happened within the Apiaceae in a common ancestor of Daucus carota and Apium graveolens. The results also support previous findings that FNS I in the Apiaceae evolved independent of FNS I in other plant species. CONCLUSION We validated a long standing hypothesis about the evolution of Apiaceae FNS I and predicted the phylogenetic position of this event. Our results explain how an Apiaceae-specific FNS I lineage evolved and confirm independence from other FNS I lineages reported in non-Apiaceae species.
Collapse
Affiliation(s)
- Boas Pucker
- Institute of Plant Biology, TU Braunschweig, Braunschweig, Germany
- BRICS, TU Braunschweig, Braunschweig, Germany
- * E-mail: (BP); (MI)
| | - Massimo Iorizzo
- Plants for Human Health Institute, NC State University, Kannapolis, North Carolina, United States of America
- Department of Horticultural Science, NC State University, Raleigh, North Carolina, United States of America
- * E-mail: (BP); (MI)
| |
Collapse
|
5
|
Han X, Li C, Sun S, Ji J, Nie B, Maker G, Ren Y, Wang L. The chromosome-level genome of female ginseng (Angelica sinensis) provides insights into molecular mechanisms and evolution of coumarin biosynthesis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 112:1224-1237. [PMID: 36259135 DOI: 10.1111/tpj.16007] [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: 07/12/2022] [Revised: 10/06/2022] [Accepted: 10/14/2022] [Indexed: 06/16/2023]
Abstract
Coumarins are natural products with important medicinal values, and include simple coumarins, furanocoumarins and pyranocoumarins. Female ginseng (Angelica sinensis) is a renowned herb with abundant coumarins, originated in China and known for the treatment of female ailments for thousands of years. The molecular basis of simple coumarin biosynthesis in A. sinensis and the evolutionary history of the genes involved in furanocoumarin biosynthesis are largely unknown. Here, we generated the first chromosome-scale genome of A. sinensis. It has a genome size of 2.37 Gb, which was generated by combining PacBio and Hi-C sequencing technologies. The genome was predicted to contain 43 202 protein-coding genes dispersed mainly on 11 pseudochromosomes. We not only provided evidence for whole-genome duplication (WGD) specifically occurring in the Apioideae subfamily, but also demonstrated the vital role of tandem duplication for phenylpropanoid biosynthesis in A. sinensis. Combined analyses of transcriptomic and metabolomic data revealed key genes and candidate transcription factors regulating simple coumarin biosynthesis. Furthermore, phylogenomic synteny network analyses suggested prenyltransferase genes involved in furanocoumarin biosynthesis evolved independently in the Moraceae, Fabaceae, Rutaceae and Apiaceae after ζ and ε WGD. Our work sheds light on coumarin biosynthesis, and provides a benchmark for accelerating genetic research and molecular breeding in A. sinensis.
Collapse
Affiliation(s)
- Xiaoxu Han
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
- College of Science, Health, Engineering and Education, Murdoch University, 6150, Western Australia, Murdoch, 90 South Street, Australia
| | - Cheng Li
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Shichao Sun
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Jiaojiao Ji
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Bao Nie
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
| | - Garth Maker
- College of Science, Health, Engineering and Education, Murdoch University, 6150, Western Australia, Murdoch, 90 South Street, Australia
| | - Yonglin Ren
- College of Science, Health, Engineering and Education, Murdoch University, 6150, Western Australia, Murdoch, 90 South Street, Australia
| | - Li Wang
- Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, 518120, Shenzhen, China
- Kunpeng Institute of Modern Agriculture at Foshan, Chinese Academy of Agricultural Sciences, 528200, Foshan, China
| |
Collapse
|
6
|
Pootakham W, Sonthirod C, Naktang C, Kongkachana W, U-Thoomporn S, Phetchawang P, Maknual C, Jiumjamrassil D, Pravinvongvuthi T, Tangphatsornruang S. A de novo reference assembly of the yellow mangrove Ceriops zippeliana genome. G3 (BETHESDA, MD.) 2022; 12:6519851. [PMID: 35106563 PMCID: PMC8982413 DOI: 10.1093/g3journal/jkac025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 01/25/2022] [Indexed: 11/13/2022]
Abstract
Mangroves are of great ecological and economical importance, providing shelters for a wide range of species and nursery habitats for commercially important marine species. Ceriops zippeliana (yellow mangrove) belongs to Rhizophoraceae family and is commonly distributed in the tropical and subtropical coastal communities. In this study, we present a high-quality assembly of the C. zippeliana genome. We constructed an initial draft assembly of 240,139,412 bases with an N50 contig length of 564,761 bases using the 10x Genomics linked-read technology. This assembly was further scaffolded with RagTag using a chromosome-scale assembly of a closely related Ceriops species as a reference. The final assembly contained 243,228,612 bases with an N50 scaffold length of 10,559,178 Mb. The size of the final assembly was close to those estimated using DNA flow cytometry (248 Mb) and the k-mer distribution analysis (246 Mb). We predicted a total of 23,474 gene models and 21,724 protein-coding genes in the C. zippeliana genome, of which 16,002 were assigned gene ontology terms. We recovered 97.1% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs analysis. The phylogenetic analysis based on single-copy orthologous genes illustrated that C. zippeliana and Ceriops tagal diverged approximately 10.2 million years ago (MYA), and their last common ancestor and Kandelia obovata diverged approximately 29.9 MYA. The high-quality assembly of C. zippeliana presented in this work provides a useful genomic resource for studying mangroves' unique adaptations to stressful intertidal habitats and for developing sustainable mangrove forest restoration and conservation programs.
Collapse
Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Sonicha U-Thoomporn
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Phakamas Phetchawang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani 12120, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, Bangkok 10210, Thailand
| | | | | | | |
Collapse
|
7
|
Pootakham W, Naktang C, Sonthirod C, Kongkachana W, Yoocha T, Jomchai N, Maknual C, Chumriang P, Pravinvongvuthi T, Tangphatsornruang S. De novo reference assembly of the upriver orange mangrove (Bruguiera sexangula) genome. Genome Biol Evol 2022; 14:6527208. [PMID: 35148390 PMCID: PMC8872974 DOI: 10.1093/gbe/evac025] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/01/2022] [Indexed: 11/21/2022] Open
Abstract
Upriver orange mangrove (Bruguiera sexangula) is a member of the most mangrove-rich taxon (Rhizophoraceae family) and is commonly distributed in the intertidal zones in tropical and subtropical latitudes. In this study, we employed the 10× Genomics linked-read technology to obtain a preliminary de novo assembly of the B. sexangula genome, which was further scaffolded to a pseudomolecule level using the Bruguiera parviflora genome as a reference. The final assembly of the B. sexangula genome contained 260 Mb with an N50 scaffold length of 11,020,310 bases. The assembly comprised 18 pseudomolecules (corresponding to the haploid chromosome number in B. sexangula), covering 204,645,832 bases or 78.6% of the 260-Mb assembly. We predicted a total of 23,978 protein-coding sequences, 17,598 of which were associated with gene ontology terms. Our gene prediction recovered 96.6% of the highly conserved orthologs based on the Benchmarking Universal Single-Copy Orthologs (BUSCO) analysis. The chromosome-level assembly presented in this work provides a valuable genetic resource to help strengthen our understanding of mangroves’ physiological and morphological adaptations to the intertidal zones.
Collapse
Affiliation(s)
- Wirulda Pootakham
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chaiwat Naktang
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chutima Sonthirod
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Wasitthee Kongkachana
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Thippawan Yoocha
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Nukoon Jomchai
- National Omics Center, National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
| | - Pranom Chumriang
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
| | - Tamanai Pravinvongvuthi
- Department of Marine and Coastal Resources, 120 The Government Complex, Chaengwatthana Rd., Thung Song Hong, Bangkok, 10210, Thailand
| | | |
Collapse
|
8
|
Pootakham W, Sonthirod C, Naktang C, Kongkachana W, Sangsrakru D, U‐thoomporn S, Maknual C, Meepol W, Promchoo W, Maprasop P, Phormsin N, Tangphatsornruang S. A chromosome‐scale reference genome assembly of yellow mangrove (
Bruguiera parviflora
) reveals a whole genome duplication event associated with the Rhizophoraceae lineage. Mol Ecol Resour 2022; 22:1939-1953. [DOI: 10.1111/1755-0998.13587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 01/06/2022] [Accepted: 01/12/2022] [Indexed: 11/27/2022]
Affiliation(s)
- Wirulda Pootakham
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chutima Sonthirod
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chaiwat Naktang
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Wasitthee Kongkachana
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Duangjai Sangsrakru
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Sonicha U‐thoomporn
- National Omics Center National Science and Technology Development Agency (NSTDA) Pathum Thani Thailand
| | - Chatree Maknual
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Wijarn Meepol
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Waratthaya Promchoo
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Pasin Maprasop
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | - Nawin Phormsin
- Department of Marine and Coastal Resources 120 The Government Complex, Chaengwatthana Rd. Thung Song Hong, Bangkok 10210 Thailand
| | | |
Collapse
|
9
|
Transcriptome sequencing revealed the influence of blue light on the expression levels of light-stress response genes in Centella asiatica. PLoS One 2021; 16:e0260468. [PMID: 34843573 PMCID: PMC8629183 DOI: 10.1371/journal.pone.0260468] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Accepted: 11/11/2021] [Indexed: 11/21/2022] Open
Abstract
Centella asiatica is rich in medical and cosmetic properties. While physiological responses of C. asiatica to light have been widely reported, the knowledge of the effects of light on its gene expression is sparse. In this study, we used RNA sequencing (RNA-seq) to investigate the expression of the C. asiatica genes in response to monochromatic red and blue light. Most of the differentially expressed genes (DEGs) under blue light were up-regulated but those under red light were down-regulated. The DEGs encoded for CRY-DASH and UVR3 were among up-regulated genes that play significant roles in responses under blue light. The DEGs involved in the response to photosystem II photodamages and in the biosynthesis of photoprotective xanthophylls were also up-regulated. The expression of flavonoid biosynthetic DEGs under blue light was up-regulated but that under red light was down-regulated. Correspondingly, total flavonoid content under blue light was higher than that under red light. The ABI5, MYB4, and HYH transcription factors appeared as hub nodes in the protein-protein interaction network of the DEGs under blue light while ERF38 was a hub node among the DEGs under red light. In summary, stress-responsive genes were predominantly up-regulated under blue light to respond to stresses that could be induced under high energy light. The information obtained from this study can be useful to better understand the responses of C. asiatica to different light qualities.
Collapse
|
10
|
Mathavaraj S, Sabu KK. Genetic diversity and structure revealed by genomic microsatellite markers in Centella asiatica (L.) Urb., a plant with medicinal potential. Mol Biol Rep 2021; 48:7387-7396. [PMID: 34716865 DOI: 10.1007/s11033-021-06748-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 09/15/2021] [Indexed: 10/19/2022]
Abstract
BACKGROUND Around the world, medicinal plants are utilised for various purposes. Centella asiatica is one of the important medicinal plants widely used in many medicinal systems. Nevertheless, analysis of the genetic diversity would pave the way for its most suitable utilisation. METHODS AND RESULTS The present study analyses the genetic diversity and structure of eighty C. asiatica accessions collected from the southern states of India, using ten genomic microsatellite markers. The mean Nei's gene diversity (0.46) indicates considerable genetic diversity. Analysis of molecular variance (82.48%) exhibited significant genetic variance between samples within the population. The cluster analysis brought out the structure of the analysed populations as three subpopulations based on the genetic differentiation. CONCLUSIONS The study showed significant intra-population variation, predominant inbreeding and population differentiation in C. asiatica. The findings will help better understanding of the genetic structure and gene pool of the plant.
Collapse
Affiliation(s)
- Sakthipriya Mathavaraj
- Jawaharlal Nehru Tropical Botanic Garden and Research Institute (JNTBGRI), Palode, Thiruvananthapuram, 695562, India
| | | |
Collapse
|
11
|
Palumbo F, Vannozzi A, Barcaccia G. Impact of Genomic and Transcriptomic Resources on Apiaceae Crop Breeding Strategies. Int J Mol Sci 2021; 22:ijms22189713. [PMID: 34575872 PMCID: PMC8465131 DOI: 10.3390/ijms22189713] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 09/03/2021] [Accepted: 09/04/2021] [Indexed: 01/18/2023] Open
Abstract
The Apiaceae taxon is one of the most important families of flowering plants and includes thousands of species used for food, flavoring, fragrance, medical and industrial purposes. This study had the specific intent of reviewing the main genomics and transcriptomic data available for this family and their use for the constitution of new varieties. This was achieved starting from the description of the main reproductive systems and barriers, with particular reference to cytoplasmic (CMS) and nuclear (NMS) male sterility. We found that CMS and NMS systems have been discovered and successfully exploited for the development of varieties only in Foeniculum vulgare, Daucus carota, Apium graveolens and Pastinaca sativa; whereas, strategies to limit self-pollination have been poorly considered. Since the constitution of new varieties benefits from the synergistic use of marker-assisted breeding in combination with conventional breeding schemes, we also analyzed and discussed the available SNP and SSR marker datasets (20 species) and genomes (8 species). Furthermore, the RNA-seq studies aimed at elucidating key pathways in stress tolerance or biosynthesis of the metabolites of interest were limited and proportional to the economic weight of each species. Finally, by aligning 53 plastid genomes from as many species as possible, we demonstrated the precision offered by the super barcoding approach to reconstruct the phylogenetic relationships of Apiaceae species. Overall, despite the impressive size of this family, we documented an evident lack of molecular data, especially because genomic and transcriptomic resources are circumscribed to a small number of species. We believe that our contribution can help future studies aimed at developing molecular tools for boosting breeding programs in crop plants of the Apiaceae family.
Collapse
|
12
|
Cheng QQ, Ouyang Y, Tang ZY, Lao CC, Zhang YY, Cheng CS, Zhou H. Review on the Development and Applications of Medicinal Plant Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:791219. [PMID: 35003182 PMCID: PMC8732986 DOI: 10.3389/fpls.2021.791219] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/23/2021] [Indexed: 05/04/2023]
Abstract
With the development of sequencing technology, the research on medicinal plants is no longer limited to the aspects of chemistry, pharmacology, and pharmacodynamics, but reveals them from the genetic level. As the price of next-generation sequencing technology becomes affordable, and the long-read sequencing technology is established, the medicinal plant genomes with large sizes have been sequenced and assembled more easily. Although the review of plant genomes has been reported several times, there is no review giving a systematic and comprehensive introduction about the development and application of medicinal plant genomes that have been reported until now. Here, we provide a historical perspective on the current situation of genomes in medicinal plant biology, highlight the use of the rapidly developing sequencing technologies, and conduct a comprehensive summary on how the genomes apply to solve the practical problems in medicinal plants, like genomics-assisted herb breeding, evolution history revelation, herbal synthetic biology study, and geoherbal research, which are important for effective utilization, rational use and sustainable protection of medicinal plants.
Collapse
Affiliation(s)
- Qi-Qing Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yue Ouyang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Zi-Yu Tang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chi-Chou Lao
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Yan-Yu Zhang
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
| | - Chun-Song Cheng
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Lushan Botanical Garden, Chinese Academy of Sciences, Jiujiang, China
| | - Hua Zhou
- State Key Laboratory of Quality Research in Chinese Medicine, Faculty of Chinese Medicine, Macau University of Science and Technology, Taipa, Macao SAR, China
- Joint Laboratory for Translational Cancer Research of Chinese Medicine, The Ministry of Education of the People’s Republic of China, Macau University of Science and Technology, Taipa, Macao SAR, China
- *Correspondence: Hua Zhou,
| |
Collapse
|