Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent
Rose (<i>Rosa</i> sp.) is a widely used raw material for essential oil extraction and fragrance production. The carotenoid cleavage dioxygenases pathway is one of the main metabolic pathways for the degradation of carotenoids, which is located downstream of the terpenoids biosynthesis pa...
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| Format: | Article |
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MDPI AG
2023-01-01
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| Series: | Horticulturae |
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| Online Access: | https://www.mdpi.com/2311-7524/9/1/115 |
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| author | Fangfang Ji Jie Wu Zhao Zhang |
| author_facet | Fangfang Ji Jie Wu Zhao Zhang |
| author_sort | Fangfang Ji |
| collection | DOAJ |
| description | Rose (<i>Rosa</i> sp.) is a widely used raw material for essential oil extraction and fragrance production. The carotenoid cleavage dioxygenases pathway is one of the main metabolic pathways for the degradation of carotenoids, which is located downstream of the terpenoids biosynthesis pathway and is closely related to the biosynthesis of volatile compounds. We performed a comprehensive genome-wide analysis of the rose <i>CCD</i> family genes (<i>RcCCDs</i>) in terms of phylogeny, sequence characterization, gene structure, gene duplication events, and transcriptome. Finally, 15 <i>CCD</i> family members were identified from the rose genome, and they were classified into three clades: nine for the CCD clade, four for the NCED clade, and two for the CCD-LIKE clade. The <i>RcCCDs</i> were distributed on chromosomes 1, 4, 5, 6, and 7, and were concentrated on both ends of the chromosomes. RcCCDs did not have paralogous genes or whole genome duplication events (WGD), eleven of them were single-copy genes, and their repetitive sequences were mainly dispersed and tandem. Ten <i>RcCCDs</i> were differentially expressed in the transcriptomes of different flowering stages. The expression of four of them increased and then decreased, which was the same process as the accumulation of volatile compounds, and it was speculated that these genes might be involved in the biosynthesis of volatile compounds. A total of fifteen modules were obtained by weighted gene co-expression network analysis of eighteen volatile compounds-related genes, of which six modules were a highly significant positive correlation with volatile compounds, and 20 hub genes in the modules were predicted. These hub genes all exercised their functions in the early flowering stage with strict temporal specificity. This study provided a theoretical basis for further exploring the biological functions of <i>RcCCDs</i> and hub genes regulating the synthesis and metabolism of volatile compounds in rose. |
| first_indexed | 2024-03-09T12:28:56Z |
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| institution | Directory Open Access Journal |
| issn | 2311-7524 |
| language | English |
| last_indexed | 2024-03-09T12:28:56Z |
| publishDate | 2023-01-01 |
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| series | Horticulturae |
| spelling | doaj.art-ab2000d823bd49e4b42b9e819036df842023-11-30T22:31:10ZengMDPI AGHorticulturae2311-75242023-01-019111510.3390/horticulturae9010115Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower ScentFangfang Ji0Jie Wu1Zhao Zhang2Beijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, ChinaBeijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, ChinaBeijing Key Laboratory of Development and Quality Control of Ornamental Crops, Department of Ornamental Horticulture, China Agricultural University, Beijing 100193, ChinaRose (<i>Rosa</i> sp.) is a widely used raw material for essential oil extraction and fragrance production. The carotenoid cleavage dioxygenases pathway is one of the main metabolic pathways for the degradation of carotenoids, which is located downstream of the terpenoids biosynthesis pathway and is closely related to the biosynthesis of volatile compounds. We performed a comprehensive genome-wide analysis of the rose <i>CCD</i> family genes (<i>RcCCDs</i>) in terms of phylogeny, sequence characterization, gene structure, gene duplication events, and transcriptome. Finally, 15 <i>CCD</i> family members were identified from the rose genome, and they were classified into three clades: nine for the CCD clade, four for the NCED clade, and two for the CCD-LIKE clade. The <i>RcCCDs</i> were distributed on chromosomes 1, 4, 5, 6, and 7, and were concentrated on both ends of the chromosomes. RcCCDs did not have paralogous genes or whole genome duplication events (WGD), eleven of them were single-copy genes, and their repetitive sequences were mainly dispersed and tandem. Ten <i>RcCCDs</i> were differentially expressed in the transcriptomes of different flowering stages. The expression of four of them increased and then decreased, which was the same process as the accumulation of volatile compounds, and it was speculated that these genes might be involved in the biosynthesis of volatile compounds. A total of fifteen modules were obtained by weighted gene co-expression network analysis of eighteen volatile compounds-related genes, of which six modules were a highly significant positive correlation with volatile compounds, and 20 hub genes in the modules were predicted. These hub genes all exercised their functions in the early flowering stage with strict temporal specificity. This study provided a theoretical basis for further exploring the biological functions of <i>RcCCDs</i> and hub genes regulating the synthesis and metabolism of volatile compounds in rose.https://www.mdpi.com/2311-7524/9/1/115rose<i>CCD</i> familyvolatile compoundsWGCNAhub gene |
| spellingShingle | Fangfang Ji Jie Wu Zhao Zhang Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent Horticulturae rose <i>CCD</i> family volatile compounds WGCNA hub gene |
| title | Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent |
| title_full | Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent |
| title_fullStr | Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent |
| title_full_unstemmed | Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent |
| title_short | Identification and Characterization of <i>CCD</i> Gene Family in Rose (<i>Rosa chinensis</i> Jacq. ‘Old Blush’) and Gene Co-Expression Network in Biosynthesis of Flower Scent |
| title_sort | identification and characterization of i ccd i gene family in rose i rosa chinensis i jacq old blush and gene co expression network in biosynthesis of flower scent |
| topic | rose <i>CCD</i> family volatile compounds WGCNA hub gene |
| url | https://www.mdpi.com/2311-7524/9/1/115 |
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