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Yang Z, Zhu Y, Zhang X, Zhang H, Zhang X, Liu G, Zhao Q, Bao Z, Ma F. Volatile secondary metabolome and transcriptome analysis reveals distinct regulation mechanism of aroma biosynthesis in Syringa oblata and S. vulgaris. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2023; 196:965-973. [PMID: 36889235 DOI: 10.1016/j.plaphy.2023.03.003] [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: 10/26/2022] [Revised: 02/13/2023] [Accepted: 03/01/2023] [Indexed: 06/18/2023]
Abstract
Lilacs have high ornamental value due to their strong aroma. However, the molecular regulatory mechanisms of aroma biosynthesis and metabolism in lilac were largely unclear. In this study, two varieties with distinct aroma, Syringa oblata 'Zi Kui' (faint aroma) and Syringa vulgaris 'Li Fei' (strong aroma), were used for exploring the regulation mechanism of aroma difference. Via GC-MS analysis, a total of 43 volatile components were identified. Terpene volatiles was the most abundant volatiles constituting the aroma of two varieties. Notably, 3 volatile secondary metabolites were unique in 'Zi Kui' and 30 volatile secondary metabolites were unique in 'Li Fei'. Then, a transcriptome analysis was performed to clarify the regulation mechanism of aroma metabolism difference between these two varieties, and identified 6411 differentially expressed genes (DEGs). Interestingly, ubiquinone and other terpenoid-quinone biosynthesis genes were significantly enriched in DEGs. We further conducted a correlation analysis between the volatile metabolome and transcriptome and found that TPS, GGPPS, and HMGS genes might be the key contributors to the differences in floral fragrance composition between the two lilac varieties. Our study improves the understanding in the regulation mechanism of Lilac aroma and would help improve the aroma of ornamental crops by metabolic engineering.
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Affiliation(s)
- Zhiying Yang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Yuanyuan Zhu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Xu Zhang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Hailiang Zhang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Xiaoyu Zhang
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China
| | - Genzhong Liu
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China
| | - Qingzhu Zhao
- Weifang Academy of Agricultural Sciences, Weifang, 261071, Shandong, China.
| | - Zhilong Bao
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
| | - Fangfang Ma
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai-An, 271018, Shandong, China.
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2
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Chen L, Xia B, Li Z, Liu X, Bai Y, Yang Y, Gao W, Meng Q, Xu N, Sun Y, Li Q, Yue L, He M, Zhou Y. Syringa oblata genome provides new insights into molecular mechanism of flower color differences among individuals and biosynthesis of its flower volatiles. FRONTIERS IN PLANT SCIENCE 2022; 13:1078677. [PMID: 36618636 PMCID: PMC9811319 DOI: 10.3389/fpls.2022.1078677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Accepted: 11/24/2022] [Indexed: 06/17/2023]
Abstract
Syringa oblata is a high ornamental value tree owing to its elegant colors, unique aromas and wide adaptability, however, studies on the molecular mechanism underlying the formation of its ornamental traits are still lacking. Here, we presented a chromosome-scale genome assembly of S. oblata and the final genome size was 1.11 Gb with a contig N50 of 4.75 Mb, anchored on 23 chromosomes and was a better reference for S. oblata transcriptome assembly. Further by integrating transcriptomic and metabolic data, it was concluded that F3H, F3'H, 4CL and PAL, especially the F3'H, were important candidates involved in the formation of floral color differences among S. oblata individuals. Genome-wide identification and analysis revealed that the TPS-b subfamily was the most abundant subfamily of TPS family in S. oblata, which together with the CYP76 family genes determined the formation of the major floral volatiles of S. oblata. Overall, our results provide an important reference for mechanistic studies on the main ornamental traits and molecular breeding in S. oblata.
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Affiliation(s)
- Lifei Chen
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Bin Xia
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Ziwei Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Xiaowei Liu
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Yun Bai
- College of Horticulture, Jilin Agricultural University, Changchun, China
| | - Yujia Yang
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Wenjie Gao
- School of Ecological Technology and Engineering, Shanghai Institute of Technology University, Shanghai, China
| | - Qingran Meng
- School of Perfume and Aroma Technology, Shanghai Institute of Technology University, Shanghai, China
| | - Ning Xu
- School of Forestry, Northeast Forestry University, Harbin, China
| | - Ying Sun
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Qiang Li
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Liran Yue
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Miao He
- College of Landscape Architecture, Northeast Forestry University, Harbin, China
| | - Yunwei Zhou
- College of Horticulture, Jilin Agricultural University, Changchun, China
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3
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Huang H, Zhao Y. Effect of clove on improving running ability in aging mice. J Food Biochem 2022; 46:e14339. [DOI: 10.1111/jfbc.14339] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 06/16/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022]
Affiliation(s)
- Haifeng Huang
- Department of Physical Education South China Agricultural University Guangzhou China
| | - Yan Zhao
- Department of Physical Education South China Agricultural University Guangzhou China
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4
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Ma B, Wu J, Shi TL, Yang YY, Wang WB, Zheng Y, Su SC, Yao YC, Xue WB, Porth I, El-Kassaby YA, Leng PS, Hu ZH, Mao JF. Lilac (Syringa oblata) genome provides insights into its evolution and molecular mechanism of petal color change. Commun Biol 2022; 5:686. [PMID: 35810211 PMCID: PMC9271065 DOI: 10.1038/s42003-022-03646-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 06/28/2022] [Indexed: 11/09/2022] Open
Abstract
Color change during flower opening is common; however, little is understood on the biochemical and molecular basis related. Lilac (Syringa oblata), a well-known woody ornamental plant with obvious petal color changes, is an ideal model. Here, we presented chromosome-scale genome assembly for lilac, resolved the flavonoids metabolism, and identified key genes and potential regulatory networks related to petal color change. The genome assembly is 1.05 Gb anchored onto 23 chromosomes, with a BUSCO score of 96.6%. Whole-genome duplication (WGD) event shared within Oleaceae was revealed. Metabolome quantification identified delphinidin-3-O-rutinoside (Dp3Ru) and cyanidin-3-O-rutinoside (Cy3Ru) as the major pigments; gene co-expression networks indicated WRKY an essential regulation factor at the early flowering stage, ERF more important in the color transition period (from violet to light nearly white), while the MBW complex participated in the entire process. Our results provide a foundation for functional study and molecular breeding in lilac.
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Affiliation(s)
- Bo Ma
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Jing Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun-Yao Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Wen-Bo Wang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yi Zheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Shu-Chai Su
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China
| | - Yun-Cong Yao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China
| | - Wen-Bo Xue
- BGI Genomics, BGI-Shenzhen, Shenzhen, 518083, China
| | - Ilga Porth
- Départment des Sciences du Bois et de la Forêt, Faculté de Foresterie, de Géographie et Géomatique, Université Laval, Québec, QC, G1V 0A6, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, Faculty of Forestry, University of British Columbia, Vancouver, BC, V6T 1Z4, Canada
| | - Ping-Sheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.
| | - Zeng-Hui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, College of Landscape Architecture, Beijing Laboratory of Urban and Rural Ecological Environment, Bioinformatics Center, Beijing University of Agriculture, Beijing, 102206, China.
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, The Key Laboratory for Silviculture and Conservation of the Ministry of Education, National Engineering Research Center of Tree Breeding and Ecological Restoration, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, College of Forestry, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, 100083, China.
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5
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Mostafa S, Wang Y, Zeng W, Jin B. Floral Scents and Fruit Aromas: Functions, Compositions, Biosynthesis, and Regulation. FRONTIERS IN PLANT SCIENCE 2022; 13:860157. [PMID: 35360336 PMCID: PMC8961363 DOI: 10.3389/fpls.2022.860157] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/22/2022] [Accepted: 02/09/2022] [Indexed: 05/27/2023]
Abstract
Floral scents and fruit aromas are crucial volatile organic compounds (VOCs) in plants. They are used in defense mechanisms, along with mechanisms to attract pollinators and seed dispersers. In addition, they are economically important for the quality of crops, as well as quality in the perfume, cosmetics, food, drink, and pharmaceutical industries. Floral scents and fruit aromas share many volatile organic compounds in flowers and fruits. Volatile compounds are classified as terpenoids, phenylpropanoids/benzenoids, fatty acid derivatives, and amino acid derivatives. Many genes and transcription factors regulating the synthesis of volatiles have been discovered. In this review, we summarize recent progress in volatile function, composition, biosynthetic pathway, and metabolism regulation. We also discuss unresolved issues and research perspectives, providing insight into improvements and applications of plant VOCs.
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Affiliation(s)
- Salma Mostafa
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
- Department of Floriculture, Faculty of Agriculture, Alexandria University, Alexandria, Egypt
| | - Yun Wang
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Wen Zeng
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
| | - Biao Jin
- College of Horticulture and Plant Protection, Yangzhou University, Yangzhou, China
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6
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Yuan X, Ma K, Zhang M, Wang J, Zhang Q. Integration of Transcriptome and Methylome Analyses Provides Insight Into the Pathway of Floral Scent Biosynthesis in Prunus mume. Front Genet 2022; 12:779557. [PMID: 34976015 PMCID: PMC8714837 DOI: 10.3389/fgene.2021.779557] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2021] [Accepted: 11/19/2021] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is a common epigenetic modification involved in regulating many biological processes. However, the epigenetic mechanisms involved in the formation of floral scent have rarely been reported within a famous traditional ornamental plant Prunus mume emitting pleasant fragrance in China. By combining whole-genome bisulfite sequencing and RNA-seq, we determined the global change in DNA methylation and expression levels of genes involved in the biosynthesis of floral scent in four different flowering stages of P. mume. During flowering, the methylation status in the “CHH” sequence context (with H representing A, T, or C) in the promoter regions of genes showed the most significant change. Enrichment analysis showed that the differentially methylated genes (DMGs) were widely involved in eight pathways known to be related to floral scent biosynthesis. As the key biosynthesis pathway of the dominant volatile fragrance of P. mume, the phenylpropane biosynthesis pathway contained the most differentially expressed genes (DEGs) and DMGs. We detected 97 DMGs participated in the most biosynthetic steps of the phenylpropane biosynthesis pathway. Furthermore, among the previously identified genes encoding key enzymes in the biosynthesis of the floral scent of P. mume, 47 candidate genes showed an expression pattern matching the release of floral fragrances and 22 of them were differentially methylated during flowering. Some of these DMGs may or have already been proven to play an important role in biosynthesis of the key floral scent components of P. mume, such as PmCFAT1a/1c, PmBEAT36/37, PmPAL2, PmPAAS3, PmBAR8/9/10, and PmCNL1/3/5/6/14/17/20. In conclusion, our results for the first time revealed that DNA methylation is widely involved in the biosynthesis of floral scent and may play critical roles in regulating the floral scent biosynthesis of P. mume. This study provided insights into floral scent metabolism for molecular breeding.
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Affiliation(s)
- Xi Yuan
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Kaifeng Ma
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Man Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Jia Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
| | - Qixiang Zhang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation and Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment, Engineering Research Center of Landscape Environment of Ministry of Education, Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants of Ministry of Education, School of Landscape Architecture, Beijing Forestry University, Beijing, China
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7
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Li R, Li Z, Leng P, Hu Z, Wu J, Dou D. Transcriptome sequencing reveals terpene biosynthesis pathway genes accounting for volatile terpene of tree peony. PLANTA 2021; 254:67. [PMID: 34495419 DOI: 10.1007/s00425-021-03715-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 08/29/2021] [Indexed: 06/13/2023]
Abstract
Transcriptomic and volatile component analyses showed that high expression levels of genes from the terpenoid backbone biosynthesis pathway and the monoterpene metabolic pathway can strengthen the floral fragrance of tree peony. Floral fragrance is a crucial ornamental trait whose improvement is one of the primary objectives of tree peony breeding. So far, exploration of the floral fragrance of tree peony has focused on the identification of its volatile components, but the molecular mechanisms responsible for their formation remain unclear. Here, we identified 128 volatile components from the petals of tree peony and found that they consisted primarily of terpenes, alcohols, and esters. Based on the distribution pattern of these major fragrance components, 24 tree peony cultivars were classified into 4 types: grassy scent (ocimene), woody scent (longifolene), lily of the valley scent (linalool), and fruity scent (2-ethyl hexanol). We used RNA-seq to explore the mechanistic basis of terpenoid metabolism in tree peony petals with various scents. The expression levels of AACT, HMGR, PMK, DXS, DXR, HDS, HDR, and GGPS, which encode key enzymes of terpenoid backbone biosynthesis, were upregulated in 'Huangguan' (strong fragrance) compared to 'Fengdan' (faint fragrance). Moreover, the transcript abundance of LIS and MYS, two monoterpene synthase genes, was also enhanced in petals of 'Huangguan' compared to those of 'Fengdan'. Together, these results demonstrate that differences in the expression of genes from the monoterpene synthesis and terpenoid backbone pathways are associated with differences in the fragrance of tree peony. This research provides crucial genetic resources for fragrance improvement and also lays a foundation for further clarification of the mechanisms that underlie tree peony fragrance.
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Affiliation(s)
- Rongchen Li
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ziyao Li
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Pingsheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Zenghui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
| | - Jing Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China.
| | - Dequan Dou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
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8
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Gao J, Liu J, Jiang C, Chen S, Huang L. Identification of suitable reference genes for studies of Syringa pinnatifolia Hemsl. FEBS Open Bio 2021; 11:1041-1053. [PMID: 33484622 PMCID: PMC8016119 DOI: 10.1002/2211-5463.13097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 01/13/2021] [Accepted: 01/21/2021] [Indexed: 11/29/2022] Open
Abstract
Syringa pinnatifolia Hemsl. (Oleaceae) is a species of shrub with a limited distribution in China. Several chemical compounds with pharmacological effects have been isolated from S. pinnatifolia, including new lignans and sesquiterpenes. Studies of gene expression in this species require the identification of suitable reference genes that are stably expressed under different conditions and in different tissues. To identify candidate reference genes, here we used the geNorm, NormFinder, and BestKeeper algorithms to analyze the stability of 12 candidate genes. The geometric mean of the rankings generated with these algorithms was used to obtain a comprehensive ranking. TBP and PP2A were found to be appropriate reference genes for calli treated with different external stimuli, and TIP41 and TBP were found to be appropriate reference genes in differentiated tissues. When calli and differentiated tissues were considered together, TBP and TIP41 were found to be the most reliable reference genes. The selected genes were validated by analysis of HMGR expression in calli and differentiated tissues. This study is the first to screen candidate reference genes in the genus Syringa and could help guide future molecular studies in this genus.
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Affiliation(s)
- Jiaqi Gao
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Pharmacy, Jiangsu University, Zhenjiang, China
| | - Juan Liu
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Chao Jiang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China
| | - Suyile Chen
- Alashan Mongolian Hospital, Alashan East Banner of Alashan, Inner Mongolia, China
| | - Luqi Huang
- National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.,School of Pharmacy, Jiangsu University, Zhenjiang, China
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9
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Shan X, Li Y, Yang S, Yang Z, Qiu M, Gao R, Han T, Meng X, Xu Z, Wang L, Gao X. The spatio-temporal biosynthesis of floral flavonols is controlled by differential phylogenetic MYB regulators in Freesia hybrida. THE NEW PHYTOLOGIST 2020; 228:1864-1879. [PMID: 32696979 DOI: 10.1111/nph.16818] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/06/2020] [Indexed: 05/25/2023]
Abstract
Floral flavonols play specific pivotal roles in pollinator attraction, pollen germination and fertility, in addition to other functions in vegetative organs. For many plants, the process of flavonol biosynthesis in late flower development stages and in mature flower tissues is poorly understood, in contrast to early flower development stages. It is thought that this process may be regulated independently of subgroup 7 R2R3 MYB (SG7 MYB) transcription factors. In this study, two FLS genes were shown to be expressed synchronously with the flower development-specific and tissue-specific biosynthesis of flavonols in Freesia hybrida. FhFLS1 contributed to flavonol biosynthesis in early flower buds, toruses and calyxes, and was regulated by four well-known SG7 MYB proteins, designated as FhMYBFs, with at least partial regulatory redundancy. FhFLS2 accounted for flavonols in late developed flowers and in the petals, stamens and pistils, and was targeted directly by non SG7 MYB protein FhMYB21L2. In parallel, AtMYB21 and AtMYB24 also activated AtFLS1, a gene highly expressed in Arabidopsis anthers and pollen, indicating the conserved regulatory roles of MYB21 against FLS genes in these two evolutionarily divergent angiosperm plants. Our results reveal a novel regulatory and synthetic mechanism underlying flavonol biosynthesis in floral organs and tissues which may be exploited to investigate supplementary roles of flavonols in flowers.
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Affiliation(s)
- Xiaotong Shan
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Song Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Zhongzhou Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Meng Qiu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Ruifang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Taotao Han
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Xiangyu Meng
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Zhengyi Xu
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, 130024, China
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10
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Srinivasan A, Ahn MS, Jo GS, Suh JN, Seo KH, Kim WH, Kang YI, Lee YR, Choi YJ. Analysis of Relative Scent Intensity, Volatile Compounds and Gene Expression in Freesia "Shiny Gold". PLANTS 2020; 9:plants9111597. [PMID: 33213113 PMCID: PMC7698779 DOI: 10.3390/plants9111597] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Revised: 11/11/2020] [Accepted: 11/12/2020] [Indexed: 12/17/2022]
Abstract
Scent is one of the most important economic traits in Freesia hybrida. "Shiny Gold", a popular cultivar in South Korea, is widely cultivated for its scent. The relative scent intensity of "Shiny Gold" was approximately 16% higher in full-bloomed flower when compared to the yellow bud stage, while tissue-specifically, tepals showed higher intensity in electronic-nose (e-nose) analysis. E-nose analysis also showed that the scent intensity of "Shiny Gold" was higher and lower than "10C3-424" and "10C3-894", respectively, and was similar to "Yvonne". These results correlated to those of the olfactory tests. In total, 19 volatile compounds, including linalool, β-ocimene, D-limonene, trans-β-ionone were detected in gas chromatography-mass spectrometry analysis. Among these, linalool was the major volatile compound, accounting for 38.7% in "Shiny Gold". Linalool synthase and TPS gene expression corresponded to the scent intensity of the four cultivars, with the lowest expression in the "10C3-424". TPS 2, TPS 3, TPS 5, TPS 6 and TPS 8 were highly expressed in both bud and flower in "Shiny Gold", while the expression of TPS 4 was lower, relative to other TPS genes in both the flowering stages. These results may aid in enhancing scent composition in Freesia cultivars using marker-assisted selection.
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Affiliation(s)
- Aparna Srinivasan
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
| | - Myung Suk Ahn
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
| | - Gyeong Suk Jo
- Environment-Friendly Agricultural Reasearch Institute, Jeollanamdo Agricultural Research and Extension Service, Najusi, Jeollanamdo 58213, Korea;
| | - Jung Nam Suh
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
| | - Kyung Hye Seo
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
| | - Won Hee Kim
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
| | - Yun Im Kang
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
| | - Young Ran Lee
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
| | - Youn Jung Choi
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, Rural Development Administration, Wanju 55365, Korea; (A.S.); (M.S.A.); (J.N.S.); (K.H.S.); (W.H.K.); (Y.I.K.); (Y.R.L.)
- Correspondence: ; Tel.: +82-63-238-6823
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Foong LC, Chai JY, Ho ASH, Yeo BPH, Lim YM, Tam SM. Comparative transcriptome analysis to identify candidate genes involved in 2-methoxy-1,4-naphthoquinone (MNQ) biosynthesis in Impatiens balsamina L. Sci Rep 2020; 10:16123. [PMID: 32999341 PMCID: PMC7527972 DOI: 10.1038/s41598-020-72997-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 07/10/2020] [Indexed: 11/09/2022] Open
Abstract
Impatiens balsamina L. is a tropical ornamental and traditional medicinal herb rich in natural compounds, especially 2-methoxy-1,4-naphthoquinone (MNQ) which is a bioactive compound with tested anticancer activities. Characterization of key genes involved in the shikimate and 1,4-dihydroxy-2-naphthoate (DHNA) pathways responsible for MNQ biosynthesis and their expression profiles in I. balsamina will facilitate adoption of genetic/metabolic engineering or synthetic biology approaches to further increase production for pre-commercialization. In this study, HPLC analysis showed that MNQ was present in significantly higher quantities in the capsule pericarps throughout three developmental stages (early-, mature- and postbreaker stages) whilst its immediate precursor, 2-hydroxy-1,4-naphthoquinone (lawsone) was mainly detected in mature leaves. Transcriptomes of I. balsamina derived from leaf, flower, and three capsule developmental stages were generated, totalling 59.643 Gb of raw reads that were assembled into 94,659 unigenes (595,828 transcripts). A total of 73.96% of unigenes were functionally annotated against seven public databases and 50,786 differentially expressed genes (DEGs) were identified. Expression profiles of 20 selected genes from four major secondary metabolism pathways were studied and validated using qRT-PCR method. Majority of the DHNA pathway genes were found to be significantly upregulated in early stage capsule compared to flower and leaf, suggesting tissue-specific synthesis of MNQ. Correlation analysis identified 11 candidate unigenes related to three enzymes (NADH-quinone oxidoreductase, UDP-glycosyltransferases and S-adenosylmethionine-dependent O-methyltransferase) important in the final steps of MNQ biosynthesis based on genes expression profiles consistent with MNQ content. This study provides the first molecular insight into the dynamics of MNQ biosynthesis and accumulation across different tissues of I. balsamina and serves as a valuable resource to facilitate further manipulation to increase production of MNQ.
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Affiliation(s)
- Lian Chee Foong
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia.,Faculty of Applied Sciences, UCSI University, Jalan Puncak Menara Gading, UCSI Heights, 56000, Cheras, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Jian Yi Chai
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia
| | - Anthony Siong Hock Ho
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia
| | - Brandon Pei Hui Yeo
- Fairview International School, Lot 4178, Jalan 1/27d, Seksyen 6 Wangsa Maju, 53300, Kuala Lumpur, Wilayah Persekutuan Kuala Lumpur, Malaysia
| | - Yang Mooi Lim
- Department of Pre-Clinical Sciences, Faculty of Medicine and Health Sciences, Universiti Tunku Abdul Rahman, Lot PT 21144, Jalan Sungai Long, Bandar Sungai Long, 43000, Kajang, Selangor, Malaysia
| | - Sheh May Tam
- School of Biosciences, Faculty of Health and Medical Sciences, Taylor's University, Jalan Taylors, 47500, Subang Jaya, Selangor, Malaysia.
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Yang Y, He R, Zheng J, Hu Z, Wu J, Leng P. Development of EST-SSR markers and association mapping with floral traits in Syringa oblata. BMC PLANT BIOLOGY 2020; 20:436. [PMID: 32957917 PMCID: PMC7507607 DOI: 10.1186/s12870-020-02652-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 09/15/2020] [Indexed: 05/10/2023]
Abstract
BACKGROUND Lilac (Syringa oblata) is an important woody plant with high ornamental value. However, very limited genetic marker resources are currently available, and little is known about the genetic architecture of important ornamental traits for S. oblata, which is hindering its genetic studies. Therefore, it is of great significance to develop effective molecular markers and understand the genetic architecture of complex floral traits for the genetic research of S. oblata. RESULTS In this study, a total of 10,988 SSRs were obtained from 9864 unigene sequences with an average of one SSR per 8.13 kb, of which di-nucleotide repeats were the dominant type (32.86%, 3611). A set of 2042 primer pairs were validated, out of which 932 (45.7%) exhibited successful amplifications, and 248 (12.1%) were polymorphic in eight S. oblata individuals. In addition, 30 polymorphic EST-SSR markers were further used to assess the genetic diversity and the population structure of 192 cultivated S. oblata individuals. Two hundred thirty-four alleles were detected, and the PIC values ranged from 0.23 to 0.88 with an average of 0.51, indicating a high level of genetic diversity within this cultivated population. The analysis of population structure showed two major subgroups in the association population. Finally, 20 significant associations were identified involving 17 markers with nine floral traits using the mixed linear model. Moreover, marker SO104, SO695 and SO790 had significant relationship with more than one trait. CONCLUSION The results showed newly developed markers were valuable resource and provided powerful tools for genetic breeding of lilac. Beyond that, our study could serve an efficient foundation for further facilitate genetic improvement of floral traits for lilac.
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Affiliation(s)
- Yunyao Yang
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Ruiqing He
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
| | - Zenghui Hu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
| | - Jing Wu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China.
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China.
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China.
| | - Pingsheng Leng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, Beijing University of Agriculture, Beijing, 102206, China
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, 102206, China
- Beijing Laboratory of Urban and Rural Ecological Environment, Beijing, 102206, China
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Yang Z, Li Y, Gao F, Jin W, Li S, Kimani S, Yang S, Bao T, Gao X, Wang L. MYB21 interacts with MYC2 to control the expression of terpene synthase genes in flowers of Freesia hybrida and Arabidopsis thaliana. JOURNAL OF EXPERIMENTAL BOTANY 2020; 71:4140-4158. [PMID: 32275056 DOI: 10.1093/jxb/eraa184] [Citation(s) in RCA: 80] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 04/09/2020] [Indexed: 05/09/2023]
Abstract
Previously, linalool was found to be the most abundant component among the cocktail of volatiles released from flowers of Freesia hybrida. Linalool formation is catalysed by monoterpene synthase TPS1. However, the regulatory network developmentally modulating the expression of the TPS1 gene in Freesia hybrida remains unexplored. In this study, three regulatory genes, FhMYB21L1, FhMYB21L2, and FhMYC2, were screened from 52 candidates. Two MYB transcription factor genes were synchronously expressed with FhTPS1 and could activate its expression significantly when overexpressed, and the binding of FhMYB21L2 to the MYBCORE sites in the FhTPS1 promoter was further confirmed, indicating a direct role in activation. FhMYC2 showed an inverse expression pattern compared with FhTPS1; its expression led to a decreased binding of FhMYB21 to the FhTPS1 promoter to reduce its activation capacity when co-expressed, suggesting a role for an MYB-bHLH complex in the regulation of the FhTPS1 gene. In Arabidopsis, both MYB21 and MYC2 regulators were shown to activate the expression of sesquiterpene synthase genes, and the regulatory roles of AtMYB21 and AtMYC2 in the expression of the linalool synthase gene were also confirmed, implying conserved functions of the MYB-bHLH complex in these two evolutionarily divergent plants. Moreover, the expression ratio between MYB21 and MYC2 orthologues might be a determinant factor in floral linalool emission.
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Affiliation(s)
- Zhongzhou Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Yueqing Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Fengzhan Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Wei Jin
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Shuying Li
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Shadrack Kimani
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
- Department of Biological and Physical Sciences, Karatina University, Karatina, Kenya
| | - Song Yang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Tingting Bao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
| | - Xiang Gao
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
- National Demonstration Center for Experimental Biology Education, Northeast Normal University, Changchun, China
| | - Li Wang
- Key Laboratory of Molecular Epigenetics of MOE and Institute of Genetics & Cytology, Northeast Normal University, Changchun, China
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Ramya M, Jang S, An HR, Lee SY, Park PM, Park PH. Volatile Organic Compounds from Orchids: From Synthesis and Function to Gene Regulation. Int J Mol Sci 2020; 21:ijms21031160. [PMID: 32050562 PMCID: PMC7037033 DOI: 10.3390/ijms21031160] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 02/04/2020] [Accepted: 02/07/2020] [Indexed: 01/26/2023] Open
Abstract
Orchids are one of the most significant plants that have ecologically adapted to every habitat on earth. Orchids show a high level of variation in their floral morphologies, which makes them popular as ornamental plants in the global market. Floral scent and color are key traits for many floricultural crops. Volatile organic compounds (VOCs) play vital roles in pollinator attraction, defense, and interaction with the environment. Recent progress in omics technology has led to the isolation of genes encoding candidate enzymes responsible for the biosynthesis and regulatory circuits of plant VOCs. Uncovering the biosynthetic pathways and regulatory mechanisms underlying the production of floral scents is necessary not only for a better understanding of the function of relevant genes but also for the generation of new cultivars with desirable traits through molecular breeding approaches. However, little is known about the pathways responsible for floral scents in orchids because of their long life cycle as well as the complex and large genome; only partial terpenoid pathways have been reported in orchids. Here, we review the biosynthesis and regulation of floral volatile compounds in orchids. In particular, we focused on the genes responsible for volatile compounds in various tissues and developmental stages in Cymbidium orchids. We also described the emission of orchid floral volatiles and their function in pollination ecology. Taken together, this review will provide a broad scope for the study of orchid floral scents.
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Affiliation(s)
- Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Seonghoe Jang
- World Vegetable Center Korea Office (WKO), Wanju-gun, Jellabuk-do 55365, Korea;
| | - Hye-Ryun An
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Su-Young Lee
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Pil-Man Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
| | - Pue Hee Park
- Floriculture Research Division, National Institute of Horticultural and Herbal Science, RDA, Wanju-gun, Jellabuk-do 55365, Korea; (M.R.); (H.-R.A.); (S.-Y.L.); (P.-M.P.)
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul 08826, Korea
- Correspondence: or ; Tel.: +82-10-4507-8321 or +82-63-238-6842; Fax: +82-63-238-6805
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15
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He D, Zhang J, Zhang X, He S, Xie D, Liu Y, Li C, Wang Z, Liu Y. Development of SSR markers in Paeonia based on De Novo transcriptomic assemblies. PLoS One 2020; 15:e0227794. [PMID: 31999761 PMCID: PMC6991952 DOI: 10.1371/journal.pone.0227794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 12/30/2019] [Indexed: 12/31/2022] Open
Abstract
Peony is a famous ornamental and medicinal plant in China, and peony hybrid breeding is an important means of germplasm innovation. However, research on the genome of this species is limited, thereby hindering the genetic and breeding research on peony. In the present study, simple sequence repeat (SSR) locus analysis was performed on expressed sequence tags obtained by the transcriptome sequencing of Paeonia using Microsatellite software. Primers with polymorphism were obtained via polymerase chain reaction amplification and electrophoresis. As a result, a total of 86,195 unigenes were obtained by assembling the transcriptome data of Paeonia. Functional annotations were obtained in seven functional databases including 49,172 (Non-Redundant Protein Sequence Database: 57.05%), 38,352 (Nucleotide Sequence Database: 44.49%), 36,477 (Swiss Prot: 42.32%), 38,905 (Clusters of Orthologous Groups for Eukaryotic Complete Genomes: 45.14%), 37,993 (Kyoto Encyclopedia of Genes and Genomes: 44.08%), 26,832 (Gene Ontology: 31.13%) and 37,758 (Pfam: 43.81%) unigenes. Meanwhile, 21,998 SSR loci were distributed in 17,567 unigenes containing SSR sequences, and the SSR distribution frequency was 25.52%, with an average of one SSR sequence per 4.66 kb. Mononucleotide, dinucleotide, and trinucleotide were the main repeat types, accounting for 55.74%, 25.58%, and 13.21% of the total repeat times, respectively. Forty-five pairs of the 100 pairs of primers selected randomly could amplify clear polymorphic bands. The polymorphic primers of these 45 pairs were used to cluster and analyze 16 species of peony. The new SSR molecular markers can be useful for the study of genetic diversity and marker-assisted breeding of peony.
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Affiliation(s)
- Dan He
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Institute of Science and Technology, Postdoctor Research Base, Xinxiang, Henan, China
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jiaorui Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuefeng Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Songlin He
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
- Henan Institute of Science and Technology, Xinxiang, Henan, China
- * E-mail:
| | - Dongbo Xie
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yang Liu
- Department of Genetics, Cell Biology, and Development, University of Minnesota, St Paul, Minnesota, United States of America
| | - Chaomei Li
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Zheng Wang
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yiping Liu
- College of Forestry, Henan Agricultural University, Zhengzhou, Henan, China
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Liu YY, Chen XR, Wang JP, Cui WQ, Xing XX, Chen XY, Ding WY, God'spower BO, Eliphaz N, Sun MQ, Li YH. Transcriptomic analysis reveals flavonoid biosynthesis of Syringa oblata Lindl. in response to different light intensity. BMC PLANT BIOLOGY 2019; 19:487. [PMID: 31711412 PMCID: PMC6849326 DOI: 10.1186/s12870-019-2100-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 10/25/2019] [Indexed: 05/04/2023]
Abstract
BACKGROUND Hazy weather significantly increase air pollution and affect light intensity which may also affect medicinal plants growth. Syringa oblata Lindl. (S. oblata), an effective anti-biofilm medicinal plants, is also vulnerable to changes in plant photoperiods and other abiotic stress responses. Rutin, one of the flavonoids, is the main bioactive ingredient in S. oblata that inhibits Streptococcus suis biofilm formation. Thus, the present study aims to explore the biosynthesis and molecular basis of flavonoids in S. oblata in response to different light intensity. RESULTS In this study, it was shown that compared with natural (Z0) and 25% ~ 35% (Z2) light intensities, the rutin content of S. oblata under 50% ~ 60% (Z1) light intensity increased significantly. In addition, an integrated analysis of metabolome and transcriptome was performed using light intensity stress conditions from two kinds of light intensities which S. oblata was subjected to: Z0 and Z1. The results revealed that differential metabolites and genes were mainly related to the flavonoid biosynthetic pathway. We found out that 13 putative structural genes and a transcription factor bHLH were significantly up-regulated in Z1. Among them, integration analysis showed that 3 putative structural genes including 4CL1, CYP73A and CYP75B1 significantly up-regulated the rutin biosynthesis, suggesting that these putative genes may be involved in regulating the flavonoid biosynthetic pathway, thereby making them key target genes in the whole metabolic process. CONCLUSIONS The present study provided helpful information to search for the novel putative genes that are potential targets for S. oblata in response to light intensity.
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Affiliation(s)
- Yan-Yan Liu
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xing-Ru Chen
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Jin-Peng Wang
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wen-Qiang Cui
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xiao-Xu Xing
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Xue-Ying Chen
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Wen-Ya Ding
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Bello-Onaghise God'spower
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Nsabimana Eliphaz
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Meng-Qing Sun
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China
| | - Yan-Hua Li
- College of Veterinary Medicine, Northeast Agricultural University, 600 Changjiang Road, Xiangfang, Harbin, Heilongjiang, 150030, People's Republic of China.
- Heilongjiang Key Laboratory for Animal Disease Control and Pharmaceutical Development, Harbin, China.
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Ramya M, Park PH, Chuang YC, Kwon OK, An HR, Park PM, Baek YS, Kang BC, Tsai WC, Chen HH. RNA sequencing analysis of Cymbidium goeringii identifies floral scent biosynthesis related genes. BMC PLANT BIOLOGY 2019; 19:337. [PMID: 31375064 PMCID: PMC6679452 DOI: 10.1186/s12870-019-1940-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 07/17/2019] [Indexed: 05/21/2023]
Abstract
BACKGROUND Cymbidium goeringii belongs to the Orchidaceae, which is one of the most abundant angiosperm families. Cymbidium goeringii consist with high economic value and characteristics include fragrance and multiple flower colors. Floral scent is one of the important strategies for ensuring fertilization. However, limited genetic data is available in this non-model plant, and little known about the molecular mechanism responsible for floral scent in this orchid. Transcriptome and expression profiling data are needed to identify genes and better understand the biological mechanisms of floral scents in this species. Present transcriptomic data provides basic information on the genes and enzymes related to and pathways involved in flower secondary metabolism in this plant. RESULTS In this study, RNA sequencing analyses were performed to identify changes in gene expression and biological pathways related scent metabolism. Three cDNA libraries were obtained from three developmental floral stages: closed bud, half flowering stage and full flowering stage. Using Illumina technique 159,616,374 clean reads were obtained and were assembled into 85,868 final unigenes (average length 1194 nt), 33.85% of which were annotated in the NCBI non redundant protein database. Among this unigenes 36,082 were assigned to gene ontology and 23,164 were combined with COG groups. Total 33,417 unigenes were assigned in 127 pathways according to the Kyoto Encyclopedia of Genes and Genomes pathway database. According these transcriptomic data we identified number of candidates genes which differentially expressed in different developmental stages of flower related to fragrance biosynthesis. In q-RT-PCR most of the fragrance related genes highly expressed in half flowering stage. CONCLUSIONS RNA-seq and DEG data provided comprehensive gene expression information at the transcriptional level that could be facilitate the molecular mechanisms of floral biosynthesis pathways in three developmental phase's flowers in Cymbidium goeringii, moreover providing useful information for further analysis on C. goeringii, and other plants of genus Cymbidium.
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Affiliation(s)
- Mummadireddy Ramya
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Pue Hee Park
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul, 08826 South Korea
| | - Yu-Chen Chuang
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
| | - Oh Keun Kwon
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Hye Ryun An
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Pil Man Park
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Yun Su Baek
- Floriculture Research Division, National Institute of Horticultural & Herbal Science (NIHHS), Rural Development Administration (RDA), Wanju, 55365 South Korea
| | - Byoung-Chorl Kang
- Department of Horticultural Science and Biotechnology, Seoul National University (SNU), Seoul, 08826 South Korea
| | - Wen-Chieh Tsai
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
- Orchid Research and Development Center, National Cheng Kung University, Tainan, 701 Taiwan
| | - Hong-Hwa Chen
- Department of Life Sciences, National Cheng Kung University (NCKU), Tainan, 701 Taiwan
- Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701 Taiwan
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Dhandapani S, Jin J, Sridhar V, Chua NH, Jang IC. CYP79D73 Participates in Biosynthesis of Floral Scent Compound 2-Phenylethanol in Plumeria rubra. PLANT PHYSIOLOGY 2019; 180:171-184. [PMID: 30804010 PMCID: PMC6501094 DOI: 10.1104/pp.19.00098] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Accepted: 02/12/2019] [Indexed: 05/19/2023]
Abstract
Plumeria (Plumeria rubra), well known for its brightly colored and fragrant flowers, emits a number of floral volatile organic compounds (VOCs). Plumeria flowers emit a total of 43 VOCs including nine phenylpropanoids/benzenoids, such as 2-phenylethanol (2PE), benzaldehyde, 2-phenylacetaldehyde (PAld), (E/Z)-phenylacetaldoxime (PAOx), benzyl nitrile (BN), and 2-phenylnitroethane (PN). To identify genes and pathways involved in the production of the major compound 2PE, we analyzed the plumeria floral transcriptome and found a highly expressed, flower-specific gene encoding a cytochrome P450 family 79D protein (PrCYP79D73), which catalyzed the formation of (E/Z)-PAOx. Feeding experiments with deuterated phenylalanine or deuterated (E/Z)-PAOx showed that (E/Z)-PAOx is an intermediate in the biosynthesis of 2PE, as are two nitrogen-containing volatiles, BN and PN, in plumeria flowers. Crude enzyme extracts from plumeria flowers converted l-phenylalanine to (E/Z)-PAOx, PAld, 2PE, BN, and PN. The biosynthesis of these compounds increased with addition of PrCYP79D73-enriched microsomes but was blocked by pretreatment with 4-phenylimidazole, an inhibitor of cytochrome P450 enzymes. Moreover, overexpression of PrCYP79D73 in Nicotiana benthamiana resulted in the emission of (E/Z)-PAOx as well as PAld, 2PE, BN, and PN, all of which were also found among plumeria floral VOCs. Taken together, our results demonstrate that PrCYP79D73 is a crucial player in the biosynthesis of the major floral VOC 2PE and other nitrogen-containing volatiles. These volatiles may be required for plant defense as well as to attract pollinators for the successful reproduction of plumeria.
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Affiliation(s)
- Savitha Dhandapani
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Jingjing Jin
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - Vishweshwaran Sridhar
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - Nam-Hai Chua
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
| | - In-Cheol Jang
- Temasek Life Sciences Laboratory, National University of Singapore, Singapore 117604
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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Hou DY, Shi LC, Yang MM, Li J, Zhou S, Zhang HX, Xu HW. De novo transcriptomic analysis of leaf and fruit tissue of Cornus officinalis using Illumina platform. PLoS One 2018; 13:e0192610. [PMID: 29451882 PMCID: PMC5815590 DOI: 10.1371/journal.pone.0192610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 01/27/2018] [Indexed: 01/06/2023] Open
Abstract
Cornus officinalis is one of the most widely used medicinal plants in China and other East Asian countries to cure diseases such as liver, kidney, cardiovascular diseases and frequent urination for thousands of years. It is a Level 3 protected species, and is one of the 42 national key protected wild species of animals and plants in China. However, the genetics and molecular biology of C. officinalis are poorly understood, which has hindered research on the molecular mechanism of its metabolism and utilization. Hence, enriching its genomic data and information is very important. In recent years, the fast-growing technology of next generation sequencing has provided an effective path to gain genomic information from nonmodel species. This study is the first to explore the leaf and fruit tissue transcriptome of C. officinalis using the Illumina HiSeq 4000 platform. A total of 57,954,134 and 60,971,652 clean reads from leaf and fruit were acquired, respectively (GenBank number SRP115440). The pooled reads from all two libraries were assembled into 56,392 unigenes with an average length 856 bp. Among these, 41,146 unigenes matched with sequences in the NCBI nonredundant protein database. The Gene Ontology database assigned 24,336 unigenes with biological process (83.26%), cellular components (53.58%), and molecular function (83.93%). In addition, 10,808 unigenes were assigned a KOG functional classification by the KOG database. Searching against the KEGG pathway database indicated that 18,435 unigenes were mapped to 371 KEGG pathways. Moreover, the edgeR database identified 4,585 significant differentially expressed genes (DEGs), of which 1,392 were up-regulated and 3,193 were down-regulated in fruit tissue compared with leaf tissue. Finally, we explored 581 transcription factors with 50 transcription factor gene families. Most DEGs and transcription factors were related to terpene biosynthesis and secondary metabolic regulation. This study not only represented the first de novo transcriptomic analysis of C. officinalis but also provided fundamental information on its genes and biosynthetic pathway. These findings will help us explore the molecular metabolism mechanism of terpene biosynthesis in C. officinalis.
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Affiliation(s)
- Dian-Yun Hou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
- * E-mail:
| | - Lin-Chun Shi
- Institute of Medicinal Plant Development (IMPLAD), Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Meng-Meng Yang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Jiong Li
- Chinese Medicinal Materials Production Technology Service Center, Department of Agriculture of Henan Province, Zhengzhou, Henan Province, China
| | - Shuang Zhou
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hong-Xiao Zhang
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
| | - Hua-Wei Xu
- Agricultural College, Henan University of Science and Technology, Luoyang, Henan Province, China
- The Luoyang Engineering Research Center of Breeding and Utilization of Dao-di Herbs, Luoyang, Henan Province, China
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20
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Wang Y, Dou Y, Wang R, Guan X, Hu Z, Zheng J. Molecular characterization and functional analysis of chalcone synthase from Syringa oblata Lindl. in the flavonoid biosynthetic pathway. Gene 2017; 635:16-23. [PMID: 28890377 DOI: 10.1016/j.gene.2017.09.002] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 08/09/2017] [Accepted: 09/01/2017] [Indexed: 01/07/2023]
Abstract
The flower color of Syringa oblata Lindl., which is often modulated by the flavonoid content, varies and is an important ornamental feature. Chalcone synthase (CHS) catalyzes the first key step in the flavonoid biosynthetic pathway. However, little is known about the role of S. oblata CHS (SoCHS) in flavonoid biosynthesis in this species. Here, we isolate and analyze the cDNA (SoCHS1) that encodes CHS in S. oblata. We also sought to analyzed the molecular characteristics and function of flavonoid metabolism by SoCHS1. We successfully isolated the CHS-encoding genomic DNA (gDNA) in S. oblata (SoCHS1), and the gene structural analysis indicated it had no intron. The opening reading frame (ORF) sequence of SoCHS1 was 1170bp long and encoded a 389-amino acid polypeptide. Multiple sequence alignment revealed that both the conserved CHS active site residues and CHS signature sequence were in the deduced amino acid sequence of SoCHS1. Crystallographic analysis revealed that the protein structure of SoCHS1 is highly similar to that of FnCHS1 in Freesia hybrida. The quantitative real-time polymerase chain reaction (PCR) performed to detect the SoCHS1 transcript expression levels in flowers, and other tissues revealed the expression was significantly correlated with anthocyanin accumulation during flower development. The ectopic expression results of Nicotiana tabacum showed that SoCHS1 overexpression in transgenic tobacco changed the flower color from pale pink to pink. In conclusion, these results suggest that SoCHS1 plays an essential role in flavonoid biosynthesis in S. oblata, and could be used to modify flavonoid components in other plant species.
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Affiliation(s)
- Yu Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Ying Dou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Rui Wang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Xuelian Guan
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China
| | - Zenghui Hu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing 102206, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing 102206, China; Beijing Collaborative Innovation Center for Eco-Environmental Improvement with Forestry and Fruit Trees, Beijing 102206, China.
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21
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Liu C, Dou Y, Guan X, Fu Q, Zhang Z, Hu Z, Zheng J, Lu Y, Li W. De novo transcriptomic analysis and development of EST-SSRs for Sorbus pohuashanensis (Hance) Hedl. PLoS One 2017; 12:e0179219. [PMID: 28614366 PMCID: PMC5470691 DOI: 10.1371/journal.pone.0179219] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2016] [Accepted: 05/25/2017] [Indexed: 11/18/2022] Open
Abstract
Sorbus pohuashanensis is a native tree species of northern China that is used for a variety of ecological purposes. The species is often grown as an ornamental landscape tree because of its beautiful form, silver flowers in early summer, attractive pinnate leaves in summer, and red leaves and fruits in autumn. However, development and further utilization of the species are hindered by the lack of comprehensive genetic information, which impedes research into its genetics and molecular biology. Recent advances in de novo transcriptome sequencing (RNA-seq) technology have provided an effective means to obtain genomic information from non-model species. Here, we applied RNA-seq for sequencing S. pohuashanensis leaves and obtained a total of 137,506 clean reads. After assembly, 96,213 unigenes with an average length of 770 bp were obtained. We found that 64.5% of the unigenes could be annotated using bioinformatics tools to analyze gene function and alignment with the NCBI database. Overall, 59,089 unigenes were annotated using the Nr database(non-redundant protein database), 35,225 unigenes were annotated using the GO (Gene Ontology categories) database, and 33,168 unigenes were annotated using COG (Cluster of Orthologous Groups). Analysis of the unigenes using the KEGG (Kyoto Encyclopedia of Genes and Genomes) database indicated that 13,953 unigenes were involved in 322 metabolic pathways. Finally, simple sequence repeat (SSR) site detection identified 6,604 unigenes that included EST-SSRs and a total of 7,473 EST-SSRs in the unigene sequences. Fifteen polymorphic SSRs were screened and found to be of use for future genetic research. These unigene sequences will provide important genetic resources for genetic improvement and investigation of biochemical processes in S. pohuashanensis.
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Affiliation(s)
- Congcong Liu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Ying Dou
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Xuelian Guan
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Qiang Fu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Ze Zhang
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Zenghui Hu
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of Agriculture, Beijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit Trees, Beijing, China
- Beijing Engineering Research Center of rural landscape planning and design, Beijing, China
- * E-mail:
| | - Yizeng Lu
- Shandong Provincial Center of Forest Tree Germplasm Resources, Jinan, Shandong Province, China
| | - Wei Li
- College of Landscape Architecture and Forestry, Qingdao Agricultural University, Qingdao, China
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Filiz E, Vatansever R, Ozyigit II. Dissecting a co-expression network of basic helix-loop-helix ( bHLH ) genes from phosphate (Pi)-starved soybean ( Glycine max ). ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Hu Z, Tang B, Wu Q, Zheng J, Leng P, Zhang K. Transcriptome Sequencing Analysis Reveals a Difference in Monoterpene Biosynthesis between Scented Lilium 'Siberia' and Unscented Lilium 'Novano'. FRONTIERS IN PLANT SCIENCE 2017; 8:1351. [PMID: 28824685 PMCID: PMC5543080 DOI: 10.3389/fpls.2017.01351] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/19/2017] [Indexed: 05/08/2023]
Abstract
Lilium is a world famous fragrant bulb flower with high ornamental and economic values, and significant differences in fragrance are found among different Lilium genotypes. In order to explore the mechanism underlying the different fragrances, the floral scents of Lilium 'Sibeia', with a strong fragrance, and Lilium 'Novano', with a very faint fragrance, were collected in vivo using a dynamic headspace technique. These scents were identified using automated thermal desorption-gas chromatography/mass spectrometry (ATD-GC/MS) at different flowering stages. We used RNA-Seq technique to determine the petal transcriptome at the full-bloom stage and analyzed differentially expressed genes (DEGs) to investigate the molecular mechanism of floral scent biosynthesis. The results showed that a significantly higher amount of Lilium 'Siberia' floral scent was released compared with Lilium 'Novano'. Moreover, monoterpenes played a dominant role in the floral scent of Lilium 'Siberia'; therefore, it is believed that the different emissions of monoterpenes mainly contributed to the difference in the floral scent between the two Lilium genotypes. Transcriptome sequencing analysis indicated that ~29.24 Gb of raw data were generated and assembled into 124,233 unigenes, of which 35,749 unigenes were annotated. Through a comparison of gene expression between these two Lilium genotypes, 6,496 DEGs were identified. The genes in the terpenoid backbone biosynthesis pathway showed significantly different expression levels. The gene expressions of 1-deoxy-D-xylulose 5-phosphate synthase (DXS), 1-deoxy-D-xylulose-5-phosphate reductoisomerase (DXR), 4-hydroxy-3-methylbut-2-enyl diphosphate synthase (HDS), 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HDR), isopentenyl diphosphate isomerase (IDI), and geranyl diphosphate synthase (GPS/GGPS), were upregulated in Lilium 'Siberia' compared to Lilium 'Novano', and two monoterpene synthase genes, ocimene synthase gene (OCS) and myrcene synthase gene (MYS), were also expressed at higher levels in the tepals of Lilium 'Siberia', which was consistent with the monoterpene release amounts. We demonstrated that the high activation levels of the pathways contributed to monoterpene biosynthesis in Lilium 'Siberia' resulting in high accumulations and emissions of monoterpenes, which led to the difference in fragrance between these two Lilium genotypes.
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Affiliation(s)
- Zenghui Hu
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
| | - Biao Tang
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
| | - Qi Wu
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
| | - Jian Zheng
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
| | - Pingsheng Leng
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
- *Correspondence: Pingsheng Leng
| | - Kezhong Zhang
- College of Landscape Architecture, Beijing University of AgricultureBeijing, China
- Beijing Collaborative Innovation Center for Eco-environmental Improvement with Forestry and Fruit TreesBeijing, China
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Lu Z, Xu J, Li W, Zhang L, Cui J, He Q, Wang L, Jin B. Transcriptomic Analysis Reveals Mechanisms of Sterile and Fertile Flower Differentiation and Development in Viburnum macrocephalum f. keteleeri. FRONTIERS IN PLANT SCIENCE 2017; 8:261. [PMID: 28298915 PMCID: PMC5331048 DOI: 10.3389/fpls.2017.00261] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 02/13/2017] [Indexed: 05/19/2023]
Abstract
Sterile and fertile flowers are an important evolutionary developmental (evo-devo) phenotype in angiosperm flowers, playing important roles in pollinator attraction and sexual reproductive success. However, the gene regulatory mechanisms underlying fertile and sterile flower differentiation and development remain largely unknown. Viburnum macrocephalum f. keteleeri, which possesses fertile and sterile flowers in a single inflorescence, is a useful candidate species for investigating the regulatory networks in differentiation and development. We developed a de novo-assembled flower reference transcriptome. Using RNA sequencing (RNA-seq), we compared the expression patterns of fertile and sterile flowers isolated from the same inflorescence over its rapid developmental stages. The flower reference transcriptome consisted of 105,683 non-redundant transcripts, of which 5,675 transcripts showed significant differential expression between fertile and sterile flowers. Combined with morphological and cytological changes between fertile and sterile flowers, we identified expression changes of many genes potentially involved in reproductive processes, phytohormone signaling, and cell proliferation and expansion using RNA-seq and qRT-PCR. In particular, many transcription factors (TFs), including MADS-box family members and ABCDE-class genes, were identified, and expression changes in TFs involved in multiple functions were analyzed and highlighted to determine their roles in regulating fertile and sterile flower differentiation and development. Our large-scale transcriptional analysis of fertile and sterile flowers revealed the dynamics of transcriptional networks and potentially key components in regulating differentiation and development of fertile and sterile flowers in Viburnum macrocephalum f. keteleeri. Our data provide a useful resource for Viburnum transcriptional research and offer insights into gene regulation of differentiation of diverse evo-devo processes in flowers.
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Zhao K, Yang W, Zhou Y, Zhang J, Li Y, Ahmad S, Zhang Q. Comparative Transcriptome Reveals Benzenoid Biosynthesis Regulation as Inducer of Floral Scent in the Woody Plant Prunus mume. FRONTIERS IN PLANT SCIENCE 2017; 8:319. [PMID: 28344586 PMCID: PMC5345196 DOI: 10.3389/fpls.2017.00319] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 02/22/2017] [Indexed: 05/08/2023]
Abstract
Mei (Prunus mume) is a peculiar woody ornamental plant famous for its inviting fragrance in winter. However, in this valuable plant, the mechanism behind floral volatile development remains poorly defined. Therefore, to explore the floral scent formation, a comparative transcriptome was conducted in order to identify the global transcripts specifying flower buds and blooming flowers of P. mume. Differentially expressed genes were identified between the two different stages showing great discrepancy in floral volatile production. Moreover, according to the expression specificity among the organs (stem, root, fruit, leaf), we summarized one gene cluster regulating the benzenoid floral scent. Significant gene changes were observed in accordance with the formation of benzenoid, thus pointing the pivotal roles of genes as well as cytochrome-P450s and short chain dehydrogenases in the benzenoid biosynthetic process. Further, transcription factors like EMISSION OF BENZENOID I and ODORANT I performed the same expression pattern suggesting key roles in the management of the downstream genes. Taken together, these data provide potential novel anchors for the benzenoid pathway, and the insight for the floral scent induction and regulation mechanism in woody plants.
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Qiu L, Jiang B, Fang J, Shen Y, Fang Z, Rm SK, Yi K, Shen C, Yan D, Zheng B. Analysis of transcriptome in hickory (Carya cathayensis), and uncover the dynamics in the hormonal signaling pathway during graft process. BMC Genomics 2016; 17:935. [PMID: 27855649 PMCID: PMC5114764 DOI: 10.1186/s12864-016-3182-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Accepted: 10/21/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Hickory (Carya cathayensis), a woody plant with high nutritional and economic value, is widely planted in China. Due to its long juvenile phase, grafting is a useful technique for large-scale cultivation of hickory. To reveal the molecular mechanism during the graft process, we sequenced the transcriptomes of graft union in hickory. RESULTS In our study, six RNA-seq libraries yielded a total of 83,676,860 clean short reads comprising 4.19 Gb of sequence data. A large number of differentially expressed genes (DEGs) at three time points during the graft process were identified. In detail, 777 DEGs in the 7 d vs 0 d (day after grafting) comparison were classified into 11 enriched Gene Ontology (GO) categories, and 262 DEGs in the 14 d vs 0 d comparison were classified into 15 enriched GO categories. Furthermore, an overview of the PPI network was constructed by these DEGs. In addition, 20 genes related to the auxin-and cytokinin-signaling pathways were identified, and some were validated by qRT-PCR analysis. CONCLUSIONS Our comprehensive analysis provides basic information on the candidate genes and hormone signaling pathways involved in the graft process in hickory and other woody plants.
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Affiliation(s)
- Lingling Qiu
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Bo Jiang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Jia Fang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Yike Shen
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Zhongxiang Fang
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Saravana Kumar Rm
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China
| | - Keke Yi
- Key Laboratory of Plant Nutrition and Fertilizer, Ministry of Agriculture, Institute of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Chenjia Shen
- College of Life and Environmental Sciences, Hangzhou Normal University, Hangzhou, 310036, China
| | - Daoliang Yan
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China. .,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.
| | - Bingsong Zheng
- Nurturing Station for the State Key Laboratory of Subtropical Silviculture, Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China. .,Center for Cultivation of Subtropical Forest Resources (CCSFR), Zhejiang A & F University, Linan, Hangzhou, 311300, People's Republic of China.
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