1
|
Pei Y, Leng L, Sun W, Liu B, Feng X, Li X, Chen S. Whole-genome sequencing in medicinal plants: current progress and prospect. SCIENCE CHINA. LIFE SCIENCES 2024; 67:258-273. [PMID: 37837531 DOI: 10.1007/s11427-022-2375-y] [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: 02/12/2023] [Accepted: 05/23/2023] [Indexed: 10/16/2023]
Abstract
Advancements in genomics have dramatically accelerated the research on medicinal plants, and the development of herbgenomics has promoted the "Project of 1K Medicinal Plant Genome" to decipher their genetic code. However, it is difficult to obtain their high-quality whole genomes because of the prevalence of polyploidy and/or high genomic heterozygosity. Whole genomes of 123 medicinal plants were published until September 2022. These published genome sequences were investigated in this review, covering their classification, research teams, ploidy, medicinal functions, and sequencing strategies. More than 1,000 institutes or universities around the world and 50 countries are conducting research on medicinal plant genomes. Diploid species account for a majority of sequenced medicinal plants. The whole genomes of plants in the Poaceae family are the most studied. Almost 40% of the published papers studied species with tonifying, replenishing, and heat-cleaning medicinal effects. Medicinal plants are still in the process of domestication as compared with crops, thereby resulting in unclear genetic backgrounds and the lack of pure lines, thus making their genomes more difficult to complete. In addition, there is still no clear routine framework for a medicinal plant to obtain a high-quality whole genome. Herein, a clear and complete strategy has been originally proposed for creating a high-quality whole genome of medicinal plants. Moreover, whole genome-based biological studies of medicinal plants, including breeding and biosynthesis, were reviewed. We also advocate that a research platform of model medicinal plants should be established to promote the genomics research of medicinal plants.
Collapse
Affiliation(s)
- Yifei Pei
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Liang Leng
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China
| | - Wei Sun
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Baocai Liu
- Institute of Agricultural Bioresource, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Xue Feng
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Xiwen Li
- Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China.
| | - Shilin Chen
- Institute of Herbgenomics, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
- Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, 611137, China.
| |
Collapse
|
2
|
Cai G, Cao Y, Tian M, Mo H, Chen X, Li Z, Ji Q, He K, Du G, Yang H. Characterization of the transcriptional responses of Armillaria gallica 012m to GA3. Arch Microbiol 2023; 205:308. [PMID: 37594611 DOI: 10.1007/s00203-023-03621-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 06/28/2023] [Accepted: 06/29/2023] [Indexed: 08/19/2023]
Abstract
Gastrodia elata needs to establish a symbiotic relationship with Armillaria strains to obtain nutrients and energy. However, the signaling cross talk between G. elata and Armillaria strains is still unclear. During our experiment, we found that the vegetative mycelium of Armillaria gallica 012m grew significantly better in the media containing gibberellic acid (GA3) than the blank control group (BK). To explore the response mechanism, we performed an RNA-sequencing experiment to profile the transcriptome changes of A. gallica 012m cultured in the medium with exogenous GA3. The transcriptome-guided differential expression genes (DEGs) analysis of GA3 and BK showed that a total of 1309 genes were differentially expressed, including 361 upregulated genes and 948 downregulated genes. Some of those DEGs correlated with the biological process, including positive regulation of chromosome segregation, mitotic metaphase/anaphase transition, attachment of mitotic spindle microtubules to kinetochore, mitotic cytokinesis, and nuclear division. These analyses explained that GA3 actively promoted the growth of A. gallica to some extent. Further analysis of protein domain features showed that the deduced polypeptide contained 41 candidate genes of GA receptor, and 27 of them were expressed in our samples. We speculate that GA receptors exist in A. gallica 012m. Comparative studies of proteins showed that the postulated GA receptor domains of A. gallica 012m have a higher homologous correlation with fungi than others based on cluster analysis.
Collapse
Affiliation(s)
- Guolei Cai
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Yapu Cao
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Menghua Tian
- Zhaotong Tianma Research Institute, Zhaotong, Yunnan, China
| | - Haiying Mo
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Xin Chen
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Zhihao Li
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Qiaolin Ji
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China
| | - Kaixiang He
- School of Chemistry and Environment, Yunnan Minzu University, Kunming, China
| | - Gang Du
- Key Laboratory of Chemistry in Ethnic Medicinal Resources, State Ethnic Affairs Commission and Ministry of Education, Yunnan Minzu University, 2929 Yuehua Street, Chenggong District, Kunming, Yunnan, China.
| | - Haiying Yang
- School of Chemistry and Environment, Yunnan Minzu University, Kunming, China.
| |
Collapse
|
3
|
Song C, Wang Y, Manzoor MA, Mao D, Wei P, Cao Y, Zhu F. In-depth analysis of genomes and functional genomics of orchid using cutting-edge high-throughput sequencing. FRONTIERS IN PLANT SCIENCE 2022; 13:1018029. [PMID: 36212315 PMCID: PMC9539832 DOI: 10.3389/fpls.2022.1018029] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Accepted: 09/05/2022] [Indexed: 06/01/2023]
Abstract
High-throughput sequencing technology has been facilitated the development of new methodologies and approaches for studying the origin and evolution of plant genomes and subgenomes, population domestication, and functional genomics. Orchids have tens of thousands of members in nature. Many of them have promising application potential in the extension and conservation of the ecological chain, the horticultural use of ornamental blossoms, and the utilization of botanical medicines. However, a large-scale gene knockout mutant library and a sophisticated genetic transformation system are still lacking in the improvement of orchid germplasm resources. New gene editing tools, such as the favored CRISPR-Cas9 or some base editors, have not yet been widely applied in orchids. In addition to a large variety of orchid cultivars, the high-precision, high-throughput genome sequencing technology is also required for the mining of trait-related functional genes. Nowadays, the focus of orchid genomics research has been directed to the origin and classification of species, genome evolution and deletion, gene duplication and chromosomal polyploidy, and flower morphogenesis-related regulation. Here, the progressing achieved in orchid molecular biology and genomics over the past few decades have been discussed, including the evolution of genome size and polyploidization. The frequent incorporation of LTR retrotransposons play important role in the expansion and structural variation of the orchid genome. The large-scale gene duplication event of the nuclear genome generated plenty of recently tandem duplicated genes, which drove the evolution and functional divergency of new genes. The evolution and loss of the plastid genome, which mostly affected genes related to photosynthesis and autotrophy, demonstrated that orchids have experienced more separate transitions to heterotrophy than any other terrestrial plant. Moreover, large-scale resequencing provide useful SNP markers for constructing genetic maps, which will facilitate the breeding of novel orchid varieties. The significance of high-throughput sequencing and gene editing technologies in the identification and molecular breeding of the trait-related genes in orchids provides us with a representative trait-improving gene as well as some mechanisms worthy of further investigation. In addition, gene editing has promise for the improvement of orchid genetic transformation and the investigation of gene function. This knowledge may provide a scientific reference and theoretical basis for orchid genome studies.
Collapse
Affiliation(s)
- Cheng Song
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yan Wang
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | | | - Di Mao
- Albrecht Daniel Thaer Institute for Agricultural and Horticultural Sciences, Humboldt University of Berlin, Berlin, Germany
| | - Peipei Wei
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| | - Yunpeng Cao
- Chinese Academy of Sciences (CAS) Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, China
| | - Fucheng Zhu
- College of Biological and Pharmaceutical Engineering, West Anhui University, Lu’an, China
| |
Collapse
|
5
|
Li MH, Liu KW, Li Z, Lu HC, Ye QL, Zhang D, Wang JY, Li YF, Zhong ZM, Liu X, Yu X, Liu DK, Tu XD, Liu B, Hao Y, Liao XY, Jiang YT, Sun WH, Chen J, Chen YQ, Ai Y, Zhai JW, Wu SS, Zhou Z, Hsiao YY, Wu WL, Chen YY, Lin YF, Hsu JL, Li CY, Wang ZW, Zhao X, Zhong WY, Ma XK, Ma L, Huang J, Chen GZ, Huang MZ, Huang L, Peng DH, Luo YB, Zou SQ, Chen SP, Lan S, Tsai WC, Van de Peer Y, Liu ZJ. Genomes of leafy and leafless Platanthera orchids illuminate the evolution of mycoheterotrophy. NATURE PLANTS 2022; 8:373-388. [PMID: 35449401 PMCID: PMC9023349 DOI: 10.1038/s41477-022-01127-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2021] [Accepted: 03/09/2022] [Indexed: 05/12/2023]
Abstract
To improve our understanding of the origin and evolution of mycoheterotrophic plants, we here present the chromosome-scale genome assemblies of two sibling orchid species: partially mycoheterotrophic Platanthera zijinensis and holomycoheterotrophic Platanthera guangdongensis. Comparative analysis shows that mycoheterotrophy is associated with increased substitution rates and gene loss, and the deletion of most photoreceptor genes and auxin transporter genes might be linked to the unique phenotypes of fully mycoheterotrophic orchids. Conversely, trehalase genes that catalyse the conversion of trehalose into glucose have expanded in most sequenced orchids, in line with the fact that the germination of orchid non-endosperm seeds needs carbohydrates from fungi during the protocorm stage. We further show that the mature plant of P. guangdongensis, different from photosynthetic orchids, keeps expressing trehalase genes to hijack trehalose from fungi. Therefore, we propose that mycoheterotrophy in mature orchids is a continuation of the protocorm stage by sustaining the expression of trehalase genes. Our results shed light on the molecular mechanism underlying initial, partial and full mycoheterotrophy.
Collapse
Affiliation(s)
- Ming-He Li
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ke-Wei Liu
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Zhen Li
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Hsiang-Chia Lu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Qin-Liang Ye
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Diyang Zhang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie-Yu Wang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Yu-Feng Li
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Zhi-Ming Zhong
- Zijin Baixi Provincial Nature Reserve of Guangdong, Heyuan, China
| | - Xuedie Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xia Yu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ding-Kun Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xiong-De Tu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Bin Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yang Hao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xing-Yu Liao
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Ting Jiang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Wei-Hong Sun
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jinliao Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yan-Qiong Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ye Ai
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jun-Wen Zhai
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Sha-Sha Wu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhuang Zhou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yu-Yun Hsiao
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
| | - Wan-Lin Wu
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - You-Yi Chen
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Yu-Fu Lin
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Jui-Ling Hsu
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan
| | - Chia-Ying Li
- Department of Applied Chemistry, National Pingtung University, Pingtung, Taiwan
| | | | | | | | - Xiao-Kai Ma
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Liang Ma
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Jie Huang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Gui-Zhen Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Ming-Zhong Huang
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Laiqiang Huang
- Tsinghua-Berkeley Shenzhen Institute (TBSI), Center for Biotechnology and Biomedicine, Shenzhen Key Laboratory of Gene and Antibody Therapy, State Key Laboratory of Chemical Oncogenomics, State Key Laboratory of Health Sciences and Technology, Institute of Biopharmaceutical and Health Engineering (iBHE), Shenzhen International Graduate School, Tsinghua University, Shenzhen, China
| | - Dong-Hui Peng
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yi-Bo Luo
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Shuang-Quan Zou
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shi-Pin Chen
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Siren Lan
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
| | - Wen-Chieh Tsai
- Orchid Research and Development Center, National Cheng Kung University, Tainan, Taiwan.
- Department of Life Sciences, National Cheng Kung University, Tainan, Taiwan.
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium.
- VIB Center for Plant Systems Biology, Ghent, Belgium.
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa.
- College of Horticulture, Academy for Advanced Interdisciplinary Studies, Nanjing Agricultural University, Nanjing, China.
| | - Zhong-Jian Liu
- Key Laboratory of Orchid Conservation and Utilization of National Forestry and Grassland Administration at College of Landscape Architecture, Fujian Agriculture and Forestry University, Fuzhou, China.
- Fujian Colleges and Universities Engineering Research Institute of Conservation and Utilization of Natural Bioresources, College of Forestry, Fujian Agriculture and Forestry University, Fuzhou, China.
- Henry Fok College of Biology and Agriculture, Shaoguan University, Shaoguan, China.
| |
Collapse
|
6
|
Xu Y, Lei Y, Su Z, Zhao M, Zhang J, Shen G, Wang L, Li J, Qi J, Wu J. A chromosome-scale Gastrodia elata genome and large-scale comparative genomic analysis indicate convergent evolution by gene loss in mycoheterotrophic and parasitic plants. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2021; 108:1609-1623. [PMID: 34647389 DOI: 10.1111/tpj.15528] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 09/27/2021] [Accepted: 09/29/2021] [Indexed: 05/27/2023]
Abstract
Mycoheterotrophic and parasitic plants are heterotrophic and parasitize on fungi and plants, respectively, to obtain nutrients. Large-scale comparative genomics analysis has not been conducted in mycoheterotrophic or parasitic plants or between these two groups of parasites. We assembled a chromosome-level genome of the fully mycoheterotrophic plant Gastrodia elata (Orchidaceae) and performed comparative genomic analyses on the genomes of G. elata and four orchids (initial mycoheterotrophs), three parasitic plants (Cuscuta australis, Striga asiatica, and Sapria himalayana), and 36 autotrophs from various angiosperm lineages. It was found that while in the hemiparasite S. asiatica and initial mycoheterotrophic orchids, approximately 4-5% of the conserved orthogroups were lost, the fully heterotrophic G. elata and C. australis both lost approximately 10% of the conserved orthogroups, indicating that increased heterotrophy is positively associated with gene loss. Importantly, many genes that are essential for autotrophs, including those involved in photosynthesis, the circadian clock, flowering time regulation, immunity, nutrient uptake, and root and leaf development, were convergently lost in both G. elata and C. australis. The high-quality genome of G. elata will facilitate future studies on the physiology, ecology, and evolution of mycoheterotrophic plants, and our findings highlight the critical role of gene loss in the evolution of plants with heterotrophic lifestyles.
Collapse
Affiliation(s)
- Yuxing Xu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Yunting Lei
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Zhongxiang Su
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Man Zhao
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jingxiong Zhang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Guojing Shen
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Lei Wang
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jing Li
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jinfeng Qi
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
| | - Jianqiang Wu
- Yunnan Key Laboratory for Wild Plant Resources, Department of Economic Plants and Biotechnology, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
7
|
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
|