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Han T, Khan MA, Wang Y, Tan W, Li C, Ai P, Zhao W, Li Z, Wang Z. Identification of SDG gene family members and exploration of flowering related genes in different cultivars of chrysanthemums and their wild ancestors. BMC PLANT BIOLOGY 2024; 24:813. [PMID: 39210253 PMCID: PMC11360836 DOI: 10.1186/s12870-024-05465-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Accepted: 07/29/2024] [Indexed: 09/04/2024]
Abstract
The SET domain genes (SDGs) are significant contributors to various aspects of plant growth and development, mainly includes flowering, pollen development, root growth, regulation of the biological clock and branching patterns. To clarify the biological functions of the chrysanthemum SDG family, the SDG family members of four chrysanthemum cultivars and three related wild species were identified; their physical and chemical properties, protein domains and conserved motifs were predicted and analyzed. The results showed that 59, 67, 67, 102, 106, 114, and 123 SDGs were identified from Chrysanthemum nankingense, Chrysanthemum lavandulifolium, Chrysanthemum seticuspe, Chrysanthemum × morifolium cv. 'Hechengxinghuo', 'Zhongshanzigui', 'Quanxiangshuichang' and 'Jinbeidahong', respectively. The SDGs were divided into 5-7 subfamilies by cluster analysis; different conserved motifs were observed in particular families. The SDGs of C. lavandulifolium and C. seticuspe were distributed unevenly on 9 chromosomes. SDG promoters of different species include growth and development, photo-response, stress response and hormone responsive elements, among them, the cis-acting elements related to MeJA response had the largest proportion. The expression of chrysanthemum SDG genes was observed for most variable selected genes which has close association with important Arabidopsis thaliana genes related to flowering regulation. The qPCR results showed that the expression trend of SDG genes varied in different tissues at different growth stages with high expression in the flowering period. The ClSDG29 showed higher expression in the flower and bud tissues, which indicate that ClSDG29 might be associated with flowering regulation in chrysanthemum. In summary, the results of this study can provide a basis for subsequent research on chrysanthemum flowering time regulation.
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Affiliation(s)
- Ting Han
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Yiming Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Wenchao Tan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Chenran Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Wenqian Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, Henan, 475004, China.
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2
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Wu D, Wu Y, Gao R, Zhang Y, Zheng R, Fang M, Li Y, Zhang Y, Guan L, Gao Y. Integrated Metabolomics and Transcriptomics Reveal the Key Role of Flavonoids in the Cold Tolerance of Chrysanthemum. Int J Mol Sci 2024; 25:7589. [PMID: 39062834 PMCID: PMC11276724 DOI: 10.3390/ijms25147589] [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: 05/31/2024] [Revised: 06/23/2024] [Accepted: 06/24/2024] [Indexed: 07/28/2024] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium, ground-cover Chrysanthemums), one of the important garden flowers, has a high ornamental and economic value. However, its ornamental value is significantly diminished by the low temperature experienced in northeastern China. Here, metabolomics and transcriptomics were performed on three Chrysanthemum cultivars before and after a low temperature to investigate the dynamic metabolite changes and the molecular regulatory mechanisms. The results showed that 1324 annotated metabolites were detected, among which 327 were identified as flavonoids derived from Chrysanthemum. The accumulation of metabolites and gene expression related to the flavonoid biosynthesis pathway significantly increased in the three cultivars under the low temperature, indicating flavonoid metabolism actively participates in the Chrysanthemum cold response. Specifically, the content of cyanidin and pelargonidin derivatives and the expression of anthocyanin biosynthesis genes significantly increases in XHBF, providing a reasonable explanation for the change in petal color from white to purple under the low temperature. Six candidate UDP-glycosyltransferase genes involved in the glycosylation of flavonoids were identified through correlation networks and phylogenetic analysis. CmNAC1, CmbZIP3, and other transcription factors potentially regulating flavonoid metabolism and responding to low temperatures were discovered by correlation analysis and weighted gene co-expression network analysis (WGCNA). In conclusion, this study elucidated the specific response of flavonoids to low temperatures in Chrysanthemums, providing valuable insights and metabolic data for investigating cold tolerance.
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Affiliation(s)
- Di Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yingxue Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ruiqi Gao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanhong Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ruiying Zheng
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Minghui Fang
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yuhua Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yang Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Le Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanqiang Gao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.); (R.G.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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Wu D, Zhuang F, Wang J, Gao R, Zhang Q, Wang X, Zhang G, Fang M, Zhang Y, Li Y, Guan L, Gao Y. Metabolomics and Transcriptomics Revealed a Comprehensive Understanding of the Biochemical and Genetic Mechanisms Underlying the Color Variations in Chrysanthemums. Metabolites 2023; 13:742. [PMID: 37367900 PMCID: PMC10301146 DOI: 10.3390/metabo13060742] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 06/07/2023] [Accepted: 06/08/2023] [Indexed: 06/28/2023] Open
Abstract
Flower color is an important characteristic of ornamental plants and is determined by various chemical components, including anthocyanin. In the present study, combined metabolomics and transcriptomics analysis was used to explore color variations in the chrysanthemums of three cultivars, of which the color of JIN is yellow, FEN is pink, and ZSH is red. A total of 29 different metabolites, including nine anthocyanins, were identified in common in the three cultivars. Compared with the light-colored cultivars, all of the nine anthocyanin contents were found to be up-regulated in the dark-colored ones. The different contents of pelargonidin, cyanidin, and their derivates were found to be the main reason for color variations. Transcriptomic analysis showed that the color difference was closely related to anthocyanin biosynthesis. The expression level of anthocyanin structural genes, including DFR, ANS, 3GT, 3MaT1, and 3MaT2, was in accordance with the flower color depth. This finding suggests that anthocyanins may be a key factor in color variations among the studied cultivars. On this basis, two special metabolites were selected as biomarkers to assist in chrysanthemum breeding for color selection.
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Affiliation(s)
- Di Wu
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Fengchao Zhuang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Jiarui Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Ruiqi Gao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Qiunan Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Xiao Wang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Guochao Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Minghui Fang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yang Zhang
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yuhua Li
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Le Guan
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
| | - Yanqiang Gao
- Key Laboratory of Saline-Alkali Vegetation Ecology Restoration, Ministry of Education, Northeast Forestry University, Harbin 150040, China; (D.W.)
- College of Life Science, Northeast Forestry University, Harbin 150040, China
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Song A, Su J, Wang H, Zhang Z, Zhang X, Van de Peer Y, Chen F, Fang W, Guan Z, Zhang F, Wang Z, Wang L, Ding B, Zhao S, Ding L, Liu Y, Zhou L, He J, Jia D, Zhang J, Chen C, Yu Z, Sun D, Jiang J, Chen S, Chen F. Analyses of a chromosome-scale genome assembly reveal the origin and evolution of cultivated chrysanthemum. Nat Commun 2023; 14:2021. [PMID: 37037808 PMCID: PMC10085997 DOI: 10.1038/s41467-023-37730-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 35.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2022] [Accepted: 03/29/2023] [Indexed: 04/12/2023] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium Ramat.) is a globally important ornamental plant with great economic, cultural, and symbolic value. However, research on chrysanthemum is challenging due to its complex genetic background. Here, we report a near-complete assembly and annotation for C. morifolium comprising 27 pseudochromosomes (8.15 Gb; scaffold N50 of 303.69 Mb). Comparative and evolutionary analyses reveal a whole-genome triplication (WGT) event shared by Chrysanthemum species approximately 6 million years ago (Mya) and the possible lineage-specific polyploidization of C. morifolium approximately 3 Mya. Multilevel evidence suggests that C. morifolium is likely a segmental allopolyploid. Furthermore, a combination of genomics and transcriptomics approaches demonstrate the C. morifolium genome can be used to identify genes underlying key ornamental traits. Phylogenetic analysis of CmCCD4a traces the flower colour breeding history of cultivated chrysanthemum. Genomic resources generated from this study could help to accelerate chrysanthemum genetic improvement.
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Affiliation(s)
- Aiping Song
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jiangshuo Su
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Haibin Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhongren Zhang
- Novogene Bioinformatics Institute, Beijing, 100083, China
| | - Xingtan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, Guangdong, 518120, China
| | - Yves Van de Peer
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB Center for Plant Systems Biology, 9052, Ghent, Belgium
- Center for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, 0028, South Africa
| | - Fei Chen
- College of tropical crops, Sanya Nanfan Research Institute, Hainan University & Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
| | - Weimin Fang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhiyong Guan
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Fei Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhenxing Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Likai Wang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Baoqing Ding
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Shuang Zhao
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Lian Ding
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Ye Liu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Lijie Zhou
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jun He
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Diwen Jia
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jiali Zhang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Chuwen Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Zhongyu Yu
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Daojin Sun
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China
| | - Jiafu Jiang
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Sumei Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
| | - Fadi Chen
- State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, Key Laboratory of Landscaping, Key Laboratory of Flower Biology and Germplasm Innovation (South), Ministry of Agriculture and Rural Affairs, Key Laboratory of Biology of Ornamental Plants in East China, National Forestry and Grassland Administration, College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, 210095, China.
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5
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Kang D, Khan MA, Song P, Liu Y, Wu Y, Ai P, Li Z, Wang Z. Comparative analysis of the chrysanthemum transcriptome with DNA methylation inhibitors treatment and silencing MET1 lines. BMC PLANT BIOLOGY 2023; 23:47. [PMID: 36670371 PMCID: PMC9862865 DOI: 10.1186/s12870-023-04036-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 01/02/2023] [Indexed: 06/17/2023]
Abstract
BACKGROUND As one of the ten most famous flowers in China, the chrysanthemum has rich germplasm with a variety of flowering induction pathways, most of which are photoperiod-induced. After treatment with DNA methylation inhibitors, it was found that DNA methylation plays an important role in flowering regulation, but the mechanism of action remains unclear. Therefore, in this study, curcumin, 5-azaC, their mixed treatment, and MET1-RNAi lines were used for transcriptome sequencing to find out how different treatments affected gene expression in chrysanthemums at different stages of flowering. RESULTS Genomic DNA methylation levels were measured using HPLC technology. The methylation level of the whole genome in the vegetative growth stage was higher than that in the flowering stage. The methylation level of DNA in the vegetative growth stage was the lowest in the curcumin and mixed treatment, and the methylation level of DNA in the transgenic line, mixed treatment, and curcumin treatment was the lowest in the flowering stage. The flowering rate of mixed treatment and curcumin treatment was the lowest. Analysis of differentially expressed genes in transcriptomes showed that 5-azaC treatment had the most differentially expressed genes, followed by curcumin and transgenic lines, and mixed treatment had the fewest. In addition, 5-azaC treatment resulted in the differential expression of multiple DNA methylation transferases, which led to the differential expression of many genes. Analysis of differentially expressed genes in different treatments revealed that different treatments had gene specificity. However, the down-regulated GO pathway in all 4 treatments was involved in the negative regulation of the reproductive process, and post-embryonic development, and regulation of flower development. Several genes associated with DNA methylation and flowering regulation showed differential expression in response to various treatments. CONCLUSIONS Both DNA methylase reagent treatment and targeted silencing of the MET1 gene can cause differential expression of the genes. The operation of the exogenous application is simple, but the affected genes are exceedingly diverse and untargeted. Therefore, it is possible to construct populations with DNA methylation phenotypic diversity and to screen genes for DNA methylation regulation.
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Affiliation(s)
- Dongru Kang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Pan Song
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Yvru Liu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Yifei Wu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
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6
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Kishi-Kaboshi M, Tanaka T, Sasaki K, Noda N, Aida R. Combination of long-read and short-read sequencing provides comprehensive transcriptome and new insight for Chrysanthemum morifolium ray-floret colorization. Sci Rep 2022; 12:17874. [PMID: 36284128 PMCID: PMC9596691 DOI: 10.1038/s41598-022-22589-z] [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: 06/19/2022] [Accepted: 10/17/2022] [Indexed: 01/20/2023] Open
Abstract
Chrysanthemum morifolium is one of the most popular ornamental plants globally. Owing to its large and complex genome (around 10 Gb, segmental hexaploid), it has been difficult to obtain comprehensive transcriptome, which will promote to perform new breeding technique, such as genome editing, in C. morifolium. In this study, we used single-molecule real-time (SMRT) sequencing and RNA-seq technologies, combined them with an error-correcting process, and obtained high-coverage ray-floret transcriptome. The SMRT-seq data increased the ratio of long mRNAs containing complete open-reading frames, and the combined dataset provided a more complete transcriptomic data than those produced from either SMRT-seq or RNA-seq-derived transcripts. We finally obtained 'Sei Arabella' transcripts containing 928,645 non-redundant mRNA, which showed 96.6% Benchmarking Universal Single-Copy Orthologs (BUSCO) score. We also validated the reliability of the dataset by analyzing a mapping rate, annotation and transcript expression. Using the dataset, we searched anthocyanin biosynthesis gene orthologs and performed a qRT-PCR experiment to assess the usability of the dataset. The assessment of the dataset and the following analysis indicated that our dataset is reliable and useful for molecular biology. The combination of sequencing methods provided genetic information and a way to analyze the complicated C. morifolium transcriptome.
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Affiliation(s)
- Mitsuko Kishi-Kaboshi
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan ,grid.416835.d0000 0001 2222 0432Present Address: Institute of Crop Science, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Tsuyoshi Tanaka
- grid.416835.d0000 0001 2222 0432Research Center for Advanced Analysis, National Agriculture and Food Research Organization (NARO), Kannondai 2-1-2, Tsukuba, Ibaraki 305-8518 Japan
| | - Katsutomo Sasaki
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
| | - Naonobu Noda
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
| | - Ryutaro Aida
- grid.416835.d0000 0001 2222 0432Institute of Vegetable and Floriculture Science, National Agriculture and Food Research Organization (NARO), Fujimoto 2-1, Tsukuba, Ibaraki 305-0852 Japan
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Mekapogu M, Kwon OK, Song HY, Jung JA. Towards the Improvement of Ornamental Attributes in Chrysanthemum: Recent Progress in Biotechnological Advances. Int J Mol Sci 2022; 23:ijms232012284. [PMID: 36293140 PMCID: PMC9603847 DOI: 10.3390/ijms232012284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Revised: 10/07/2022] [Accepted: 10/10/2022] [Indexed: 11/15/2022] Open
Abstract
Incessant development and introduction of novel cultivars with improved floral attributes are vital in the dynamic ornamental industry. Chrysanthemum (Chrysanthemum morifolium) is a highly favored ornamental plant, ranking second globally in the cut flower trade, after rose. Development of new chrysanthemum cultivars with improved and innovative modifications in ornamental attributes, including floral color, shape, plant architecture, flowering time, enhanced shelf life, and biotic and abiotic stress tolerance, is a major goal in chrysanthemum breeding. Despite being an economically important ornamental plant, the application of conventional and molecular breeding approaches to various key traits of chrysanthemum is hindered owing to its genomic complexity, heterozygosity, and limited gene pool availability. Although classical breeding of chrysanthemum has resulted in the development of several hundreds of cultivars with various morphological variations, the genetic and transcriptional control of various important ornamental traits remains unclear. The coveted blue colored flowers of chrysanthemums cannot be achieved through conventional breeding and mutation breeding due to technical limitations. However, blue-hued flower has been developed by genetic engineering, and transgenic molecular breeding has been successfully employed, leading to substantial progress in improving various traits. The recent availability of whole-genome sequences of chrysanthemum offers a platform to extensively employ MAS to identify a large number of markers for QTL mapping, and GWAS to dissect the genetic control of complex traits. The combination of NGS, multi-omic platforms, and genome editing technologies has provided a tremendous scope to decipher the molecular and regulatory mechanisms. However, the application and integration of these technologies remain inadequate for chrysanthemum. This review, therefore, details the significance of floral attributes, describes the efforts of recent advancements, and highlights the possibilities for future application towards the improvement of crucial ornamental traits in the globally popular chrysanthemum plant.
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Huang H, Gao X, Gao X, Zhang S, Zheng Y, Zhang N, Hong B, Zhao X, Gu Z. Flower color mutation, pink to orange, through CmGATA4 - CCD4a-5 module regulates carotenoids degradation in chrysanthemum. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2022; 322:111290. [PMID: 35753140 DOI: 10.1016/j.plantsci.2022.111290] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Revised: 04/11/2022] [Accepted: 04/14/2022] [Indexed: 06/15/2023]
Abstract
The carotenoids biosynthesis pathway in plants has been studied extensively, yet little is known about the regulatory mechanisms underlying this process, especially for ornamental horticulture plants. In this study, a natural variation of chrysanthemum with orange coloration was identified and compared with the wild type with pink coloration; the content and component of carotenoids were largely enriched in the mutant with orange coloration. CmCCD4a-5, the DNA sequence in both 'Pink yan' and the mutant, was identified and shown to function as a carotenoid degradation enzyme. Compared with 'Pink yan', the mutant shows lower expression level of CmCCD4a-5. Furthermore, CmGATA4 was found to have an opposite expression trend to CmCCD4a-5, and it could directly bind with the CmCCD4a-5 promoter. Taken together, this study demonstrates that CmGATA4 acts as a negative regulator of CmCCD4a-5 and, furthermore, low expression of CmCCD4a-5 resulted in carotenoid accumulation in the mutant.
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Affiliation(s)
- Hongfeng Huang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
| | - Xuekai Gao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun 130024, China.
| | - Shiqi Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
| | - Ying Zheng
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
| | - Ning Zhang
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
| | - Bo Hong
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
| | - Xin Zhao
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China; State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China.
| | - Zhaoyu Gu
- Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, China.
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9
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Comparative transcriptome analyses identify genes involved into the biosynthesis of forsythin and forsythoside A in Forsythia suspensa. Funct Integr Genomics 2022; 22:731-741. [DOI: 10.1007/s10142-022-00887-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/12/2022] [Accepted: 07/12/2022] [Indexed: 11/04/2022]
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10
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Ai P, Liu X, Li Z, Kang D, Khan MA, Li H, Shi M, Wang Z. Comparison of chrysanthemum flowers grown under hydroponic and soil-based systems: yield and transcriptome analysis. BMC PLANT BIOLOGY 2021; 21:517. [PMID: 34749661 PMCID: PMC8574001 DOI: 10.1186/s12870-021-03255-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 10/06/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Flowers of Chrysanthemum × morifolium Ramat. are used as tea in traditional Chinese cuisine. However, with increasing population and urbanization, water and land availability have become limiting for chrysanthemum tea production. Hydroponic culture enables effective, rapid nutrient exchange, while requiring no soil and less water than soil cultivation. Hydroponic culture can reduce pesticide residues in food and improve the quantity or size of fruits, flowers, and leaves, and the levels of active compounds important for nutrition and health. To date, studies to improve the yield and active compounds of chrysanthemum have focused on soil culture. Moreover, the molecular effects of hydroponic and soil culture on chrysanthemum tea development remain understudied. RESULTS Here, we studied the effects of soil and hydroponic culture on yield and total flavonoid and chlorogenic acid contents in chrysanthemum flowers (C. morifolium 'wuyuanhuang'). Yield and the total flavonoids and chlorogenic acid contents of chrysanthemum flowers were higher in the hydroponic culture system than in the soil system. Transcriptome profiling using RNA-seq revealed 3858 differentially expressed genes (DEGs) between chrysanthemum flowers grown in soil and hydroponic conditions. Gene Ontology (GO) enrichment annotation revealed that these differentially transcribed genes are mainly involved in "cytoplasmic part", "biosynthetic process", "organic substance biosynthetic process", "cell wall organization or biogenesis" and other processes. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis revealed enrichment in "metabolic pathways", "biosynthesis of secondary metabolites", "ribosome", "carbon metabolism", "plant hormone signal transduction" and other metabolic processes. In functional annotations, pathways related to yield and formation of the main active compounds included phytohormone signaling, secondary metabolism, and cell wall metabolism. Enrichment analysis of transcription factors also showed that under the hydroponic system, bHLH, MYB, NAC, and ERF protein families were involved in metabolic pathways, biosynthesis of secondary metabolites, and plant hormone signal transduction. CONCLUSIONS Hydroponic culture is a simple and effective way to cultivate chrysanthemum for tea production. A transcriptome analysis of chrysanthemum flowers grown in soil and hydroponic conditions. The large number of DEGs identified confirmed the difference of the regulatory machinery under two culture system.
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Affiliation(s)
- Penghui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Xiaoqi Liu
- Zhengzhou A Boluo Fertilizer Company, Zhiji Road, Zhengzhou, 450121, Henan, China
| | - Zhongai Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Dongru Kang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Han Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Mengkang Shi
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China
| | - Zicheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University, Jinming Road, Kaifeng, 475004, Henan, China.
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11
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Wang P. Statistical Identification of Important Nodes in Biological Systems. JOURNAL OF SYSTEMS SCIENCE AND COMPLEXITY 2021; 34:1454-1470. [PMID: 34393461 PMCID: PMC8353063 DOI: 10.1007/s11424-020-0013-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/23/2020] [Indexed: 06/13/2023]
Abstract
Biological systems can be modeled and described by biological networks. Biological networks are typical complex networks with widely real-world applications. Many problems arising in biological systems can be boiled down to the identification of important nodes. For example, biomedical researchers frequently need to identify important genes that potentially leaded to disease phenotypes in animal and explore crucial genes that were responsible for stress responsiveness in plants. To facilitate the identification of important nodes in biological systems, one needs to know network structures or behavioral data of nodes (such as gene expression data). If network topology was known, various centrality measures can be developed to solve the problem; while if only behavioral data of nodes were given, some sophisticated statistical methods can be employed. This paper reviewed some of the recent works on statistical identification of important nodes in biological systems from three aspects, that is, 1) in general complex networks based on complex networks theory and epidemic dynamic models; 2) in biological networks based on network motifs; and 3) in plants based on RNA-seq data. The identification of important nodes in a complex system can be seen as a mapping from the system to the ranking score vector of nodes, such mapping is not necessarily with explicit form. The three aspects reflected three typical approaches on ranking nodes in biological systems and can be integrated into one general framework. This paper also proposed some challenges and future works on the related topics. The associated investigations have potential real-world applications in the control of biological systems, network medicine and new variety cultivation of crops.
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Affiliation(s)
- Pei Wang
- School of Mathematics and Statistics, Institute of Applied Mathematics, Laboratory of Data Analysis Technology, Henan University, Kaifeng, 475004 China
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12
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Kang DR, Zhu Y, Li SL, Ai PH, Khan MA, Ding HX, Wang Y, Wang ZC. Transcriptome analysis of differentially expressed genes in chrysanthemum MET1 RNA interference lines. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:1455-1468. [PMID: 34366589 PMCID: PMC8295425 DOI: 10.1007/s12298-021-01022-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2020] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 05/14/2023]
Abstract
UNLABELLED DNA methylation is the most important epigenetic modification involved in many essential biological processes. MET1 is one of DNA methyltransferases that affect the level of methylation in the entire genome. To explore the effect of MET1 gene silencing on gene expression profile of Chrysanthemum × morifolium 'Zijingling'. The stem section and leaves at the young stage were taken for transcriptome sequencing. MET1-RNAi leaves had 8 differentially expressed genes while 156 differentially expressed genes were observed in MET1-RNAi stem compared with control leaves and stem. These genes encode many key proteins in plant biological processes, such as transcription factors, signal transduction mechanisms, secondary metabolite synthesis, transport and catabolism and interaction. In general, 34.58% of the differentially expressed genes in leaves and stems were affected by the reduction of the MET1 gene. The differentially expressed genes in stem and leaves of transgenic plants went through significant changes. We found adequate amount of candidate genes associated with flowering, however, the number of genes with significant differences between transgenic and control lines was not too high. Several flowering related genes were screened out for gene expression verification and all of them were obseved as consistent with transcriptome data. These candidate genes may play important role in flowering variation of chrysanthemum. This study reveals the mechanism of CmMET1 interference on the growth and development of chrysanthemum at the transcriptional level, which provides the basis for further research on the epigenetic regulation mechanism in flower induction and development. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s12298-021-01022-1.
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Affiliation(s)
- Dong-ru Kang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Yi Zhu
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Shuai-lei Li
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Peng-hui Ai
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Muhammad Ayoub Khan
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Hong-xu Ding
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Ying Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
| | - Zi-cheng Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, Plant Germplasm Resources and Genetic Laboratory, Kaifeng Key Laboratory of Chrysanthemum Biology, School of Life Sciences, Henan University. Jinming Road, Kaifeng, 475004 Henan China
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CmNAC73 Mediates the Formation of Green Color in Chrysanthemum Flowers by Directly Activating the Expression of Chlorophyll Biosynthesis Genes HEMA1 and CRD1. Genes (Basel) 2021; 12:genes12050704. [PMID: 34066887 PMCID: PMC8151904 DOI: 10.3390/genes12050704] [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: 04/18/2021] [Revised: 05/03/2021] [Accepted: 05/04/2021] [Indexed: 02/07/2023] Open
Abstract
Chrysanthemum is one of the most beautiful and popular flowers in the world, and the flower color is an important ornamental trait of chrysanthemum. Compared with other flower colors, green flowers are relatively rare. The formation of green flower color is attributed to the accumulation of chlorophyll; however, the regulatory mechanism of chlorophyll metabolism in chrysanthemum with green flowers remains largely unknown. In this study, we performed Illumina RNA sequencing on three chrysanthemum materials, Chrysanthemum vestitum and Chrysanthemum morifolium cultivars ‘Chunxiao’ and ‘Green anna’, which produce white, light green and dark green flowers, respectively. Based on the results of comparative transcriptome analysis, a gene encoding a novel NAC family transcription factor, CmNAC73, was found to be highly correlated to chlorophyll accumulation in the outer whorl of ray florets in chrysanthemum. The results of transient overexpression in chrysanthemum leaves showed that CmNAC73 acts as a positive regulator of chlorophyll biosynthesis. Furthermore, transactivation and yeast one-hybrid assays indicated that CmNAC73 directly binds to the promoters of chlorophyll synthesis-related genes HEMA1 and CRD1. Thus, this study uncovers the transcriptional regulation of chlorophyll synthesis-related genes HEMA1 and CRD1 by CmNAC73 and provides new insights into the development of green flower color in chrysanthemum and chlorophyll metabolism in plants.
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14
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Wang P. Statistical Identification of Important Nodes in Biological Systems. JOURNAL OF SYSTEMS SCIENCE AND COMPLEXITY 2021:1-17. [PMID: 33456274 PMCID: PMC7801784 DOI: 10.1007/s11424-021-0001-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 05/23/2020] [Indexed: 05/08/2023]
Abstract
Biological systems can be modeled and described by biological networks. Biological networks are typical complex networks with widely real-world applications. Many problems arising in biological systems can be boiled down to the identification of important nodes. For example, biomedical researchers frequently need to identify important genes that potentially leaded to disease phenotypes in animal and explore crucial genes that were responsible for stress responsiveness in plants. To facilitate the identification of important nodes in biological systems, one needs to know network structures or behavioral data of nodes (such as gene expression data). If network topology was known, various centrality measures can be developed to solve the problem; while if only behavioral data of nodes were given, some sophisticated statistical methods can be employed. This paper reviewed some of the recent works on statistical identification of important nodes in biological systems from three aspects, that is, 1) in general complex networks based on complex networks theory and epidemic dynamic models; 2) in biological networks based on network motifs; and 3) in plants based on RNA-seq data. The identification of important nodes in a complex system can be seen as a mapping from the system to the ranking score vector of nodes, such mapping is not necessarily with explicit form. The three aspects reflected three typical approaches on ranking nodes in biological systems and can be integrated into one general framework. This paper also proposed some challenges and future works on the related topics. The associated investigations have potential real-world applications in the control of biological systems, network medicine and new variety cultivation of crops.
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Affiliation(s)
- Pei Wang
- School of Mathematics and Statistics, Institute of Applied Mathematics, Laboratory of Data Analysis Technology, Henan University, Kaifeng, 475004 China
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15
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Wang M, Zhu X, Li Y, Xia Z. Transcriptome analysis of a new maize albino mutant reveals that zeta-carotene desaturase is involved in chloroplast development and retrograde signaling. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2020; 156:407-419. [PMID: 33010551 DOI: 10.1016/j.plaphy.2020.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Accepted: 09/21/2020] [Indexed: 05/24/2023]
Abstract
Carotenoids are a group of natural tetraterpenoid pigments with essential roles in a variety of physiological processes of plants. Although carotenoid biosynthesis has been well characterized, the genetic basis of the pathway, especially in crop plants, is largely unknown. In this study, we characterized a new albino maize mutant called albino1 (alb1), which was obtained from a Mutator mutagenized population. The alb1 mutant showed defective chloroplast development and declined photosynthetic pigments, leading to a seedling-lethal phenotype. Genetic and molecular analyses indicated that ALB1 encoded a putative ζ-carotene desaturase (ZDS) involved in carotenoid biosynthesis. Measurement of carotenoids revealed that several major carotenoid compounds downstream of the ZDS were significantly reduced in alb1 mutant, indicating that ALB1 is a functional ZDS. Further transcriptome analysis revealed that several groups of nuclear genes involved in photosynthesis, such as light-harvesting complex, pigment metabolism, and chloroplast function, were significantly down-regulated in alb1 compared with wide type. Interestingly, expression of some maize plastid-localized nuclear genes, including POR, CAO, Lhcb, and RbcS, was substantially reduced in alb1 plants. Furthermore, treatment of the inhibitor fluridone significantly rescued gene transcripts of these nucleus-encoded genes in alb1 mutant, which supported the retrograde signaling of ζ-carotene/phytofluene derived molecules. These results suggested that ALB1/ZDS might function as a regulator to coordinate nuclear photosynthetic gene expression in plastid-to-nucleus retrograde signaling during development of maize plants. Together, these results have demonstrated that ALB1/ZDS is essential for carotenoids biosynthesis and plays crucial roles in chloroplast biogenesis and development in maize.
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Affiliation(s)
- Meiping Wang
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, PR China; Department of Information, Library of Henan Agricultural University, Zhengzhou, 450002, PR China
| | - Xianfeng Zhu
- School of Life Sciences, Henan University, Kaifeng, 475004, PR China
| | - Yu Li
- College of Food Science and Technology, Henan Agricultural University, Zhengzhou, 450002, PR China.
| | - Zongliang Xia
- College of Life Science, Henan Agricultural University, Zhengzhou, 450002, PR China; Synergetic Innovation Center of Henan Grain Crops and State Key Laboratory of Wheat & Maize Crop Science, Zhengzhou, 450002, PR China.
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16
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Mekapogu M, Vasamsetti BMK, Kwon OK, Ahn MS, Lim SH, Jung JA. Anthocyanins in Floral Colors: Biosynthesis and Regulation in Chrysanthemum Flowers. Int J Mol Sci 2020; 21:ijms21186537. [PMID: 32906764 PMCID: PMC7554973 DOI: 10.3390/ijms21186537] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Revised: 09/04/2020] [Accepted: 09/04/2020] [Indexed: 12/21/2022] Open
Abstract
Chrysanthemum (Chrysanthemum morifolium) is an economically important ornamental crop across the globe. As floral color is the major factor determining customer selection, manipulation of floral color has been a major objective for breeders. Anthocyanins are one of the main pigments contributing to a broad variety of colors in the ray florets of chrysanthemum. Manipulating petal pigments has resulted in the development of a vast range of floral colors. Although the candidate genes involved in anthocyanin biosynthesis have been well studied, the genetic and transcriptional control of floral color remains unclear. Despite advances in multi-omics technology, these methods remain in their infancy in chrysanthemum, owing to its large complex genome and hexaploidy. Hence, there is a need to further elucidate and better understand the genetic and molecular regulatory mechanisms in chrysanthemum, which can provide a basis for future advances in breeding for novel and diverse floral colors in this commercially beneficial crop. Therefore, this review describes the significance of anthocyanins in chrysanthemum flowers, and the mechanism of anthocyanin biosynthesis under genetic and environmental factors, providing insight into the development of novel colored ray florets. Genetic and molecular regulatory mechanisms that control anthocyanin biosynthesis and the various breeding efforts to modify floral color in chrysanthemum are detailed.
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Affiliation(s)
- Manjulatha Mekapogu
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
| | - Bala Murali Krishna Vasamsetti
- Chemical Safety Division, National Institute of Agricultural Sciences, Rural Development Administration, Wanju 55365, Korea;
| | - Oh-Keun Kwon
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
| | - Myung-Suk Ahn
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
| | - Sun-Hyung Lim
- Division of Horticultural Biotechnology, School of Biotechnology, Hankyoung National University, Anseong 17579, Korea;
| | - Jae-A Jung
- Floriculture Research Division, National Institute of Horticultural & Herbal Science, Rural Development Administration, Wanju 55365, Korea; (M.M.); (O.-K.K.); (M.-S.A.)
- Correspondence:
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