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Yang X, Yue Y, Li H, Ding W, Chen G, Shi T, Chen J, Park MS, Chen F, Wang L. The chromosome-level quality genome provides insights into the evolution of the biosynthesis genes for aroma compounds of Osmanthus fragrans. HORTICULTURE RESEARCH 2018; 5:72. [PMID: 30479779 PMCID: PMC6246602 DOI: 10.1038/s41438-018-0108-0] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Revised: 11/12/2018] [Accepted: 11/13/2018] [Indexed: 05/21/2023]
Abstract
Sweet osmanthus (Osmanthus fragrans) is a very popular ornamental tree species throughout Southeast Asia and USA particularly for its extremely fragrant aroma. We constructed a chromosome-level reference genome of O. fragrans to assist in studies of the evolution, genetic diversity, and molecular mechanism of aroma development. A total of over 118 Gb of polished reads was produced from HiSeq (45.1 Gb) and PacBio Sequel (73.35 Gb), giving 100× depth coverage for long reads. The combination of Illumina-short reads, PacBio-long reads, and Hi-C data produced the final chromosome quality genome of O. fragrans with a genome size of 727 Mb and a heterozygosity of 1.45 %. The genome was annotated using de novo and homology comparison and further refined with transcriptome data. The genome of O. fragrans was predicted to have 45,542 genes, of which 95.68 % were functionally annotated. Genome annotation found 49.35 % as the repetitive sequences, with long terminal repeats (LTR) being the richest (28.94 %). Genome evolution analysis indicated the evidence of whole-genome duplication 15 million years ago, which contributed to the current content of 45,242 genes. Metabolic analysis revealed that linalool, a monoterpene is the main aroma compound. Based on the genome and transcriptome, we further demonstrated the direct connection between terpene synthases (TPSs) and the rich aromatic molecules in O. fragrans. We identified three new flower-specific TPS genes, of which the expression coincided with the production of linalool. Our results suggest that the high number of TPS genes and the flower tissue- and stage-specific TPS genes expressions might drive the strong unique aroma production of O. fragrans.
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Affiliation(s)
- Xiulian Yang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
| | - Yuanzheng Yue
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
| | - Haiyan Li
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
| | - Wenjie Ding
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
| | - Gongwei Chen
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
| | - Tingting Shi
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
| | - Junhao Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Min S. Park
- Nextomics Bioscience Institute, Wuhan, China
| | - Fei Chen
- State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Lianggui Wang
- Co-Innovation Center for Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing, China
- College of Landscape Architecture, Nanjing Forestry University, Nanjing, China
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Xu C, Li H, Yang X, Gu C, Mu H, Yue Y, Wang L. Cloning and Expression Analysis of MEP Pathway Enzyme-encoding Genes in Osmanthus fragrans. Genes (Basel) 2016; 7:genes7100078. [PMID: 27690108 PMCID: PMC5083917 DOI: 10.3390/genes7100078] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Revised: 09/15/2016] [Accepted: 09/22/2016] [Indexed: 12/15/2022] Open
Abstract
The 2-C-methyl-d-erythritol 4-phosphate (MEP) pathway is responsible for the biosynthesis of many crucial secondary metabolites, such as carotenoids, monoterpenes, plastoquinone, and tocopherols. In this study, we isolated and identified 10 MEP pathway genes in the important aromatic plant sweet osmanthus (Osmanthus fragrans). Multiple sequence alignments revealed that 10 MEP pathway genes shared high identities with other reported proteins. The genes showed distinctive expression profiles in various tissues, or at different flower stages and diel time points. The qRT-PCR results demonstrated that these genes were highly expressed in inflorescences, which suggested a tissue-specific transcript pattern. Our results also showed that OfDXS1, OfDXS2, and OfHDR1 had a clear diurnal oscillation pattern. The isolation and expression analysis provides a strong foundation for further research on the MEP pathway involved in gene function and molecular evolution, and improves our understanding of the molecular mechanism underlying this pathway in plants.
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Affiliation(s)
- Chen Xu
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China.
| | - Huogeng Li
- Key Laboratory of Forest Genetics & Gene Engineering of the Ministry of Education, Nanjing Forestry University, Nanjing 210037, China.
| | - Xiulian Yang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China.
| | - Chunsun Gu
- Institute of Botany, Jiangsu Province and Chinese Academy of Sciences, Nanjing 210014, China.
| | - Hongna Mu
- College of Horticulture and Gardening, Yangtze University, Jingzhou 434025, China.
| | - Yuanzheng Yue
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China.
| | - Lianggui Wang
- College of Landscape Architecture, Nanjing Forestry University, Nanjing 210037, China.
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