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Zhou X, Wang X, Wei H, Zhang H, Wu Q, Wang L. Integrative analysis of transcriptome and target metabolites uncovering flavonoid biosynthesis regulation of changing petal colors in Nymphaea 'Feitian 2'. BMC PLANT BIOLOGY 2024; 24:370. [PMID: 38714932 PMCID: PMC11075258 DOI: 10.1186/s12870-024-05078-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 04/28/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Nymphaea (waterlily) is known for its rich colors and role as an important aquatic ornamental plant globally. Nymphaea atrans and some hybrids, including N. 'Feitian 2,' are more appealing due to the gradual color change of their petals at different flower developmental stages. The petals of N. 'Feitian 2' gradually change color from light blue-purple to deep rose-red throughout flowering. The mechanism of the phenomenon remains unclear. RESULTS In this work, flavonoids in the petals of N. 'Feitian 2' at six flowering stages were examined to identify the influence of flavonoid components on flower color changes. Additionally, six cDNA libraries of N. 'Feitian 2' over two blooming stages were developed, and the transcriptome was sequenced to identify the molecular mechanism governing petal color changes. As a result, 18 flavonoid metabolites were identified, including five anthocyanins and 13 flavonols. Anthocyanin accumulation during flower development is the primary driver of petal color change. A total of 12 differentially expressed genes (DEGs) in the flavonoid biosynthesis pathway were uncovered, and these DEGs were significantly positively correlated with anthocyanin accumulation. Six structural genes were ultimately focused on, as their expression levels varied significantly across different flowering stages. Moreover, 104 differentially expressed transcription factors (TFs) were uncovered, and three MYBs associated with flavonoid biosynthesis were screened. The RT-qPCR results were generally aligned with high-throughput sequencing results. CONCLUSIONS This research offers a foundation to clarify the mechanisms underlying changes in the petal color of waterlilies.
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Affiliation(s)
- Xian Zhou
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaohan Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haohui Wei
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
- Hunan Agricultural University, Changsha, 410128, China
| | - Huijin Zhang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
- China National Botanical Garden, Beijing, 100093, China
| | - Qian Wu
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
| | - Liangsheng Wang
- State Key Laboratory of Plant Diversity and Specialty Crops, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China.
- China National Botanical Garden, Beijing, 100093, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
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Ding Y, Wang MY, Yang DH, Hao DC, Li WS, Ling P, Xie SQ. Transcriptome analysis of flower colour reveals the correlation between SNP and differential expression genes in Phalaenopsis. Genes Genomics 2023; 45:1611-1621. [PMID: 37414912 DOI: 10.1007/s13258-023-01422-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 06/27/2023] [Indexed: 07/08/2023]
Abstract
BACKGROUND Phalaenopsis is an important ornamental plant that has great economic value in the world flower market as one of the most popular flower resources. OBJECTIVE To investigate the flower colour formation of Phalaenopsis at the transcription level, the genes involved in flower color formation were identified from RNA-seq in this study. METHODS In this study, white and purple petals of Phalaenopsis were collected and analyzed to obtained (1) differential expression genes (DEGs) between white and purple flower color and (2) the association between single nucleotide polymorphisms (SNP) mutations and DEGs at the transcriptome level. RESULTS The results indicated that a total of 1,175 DEGs were identified, and 718 and 457 of them were up- and down-regulated genes, respectively. Gene Ontology and pathway enrichment showed that the biosynthesis of the secondary metabolites pathway was key to color formation, and the expression of 12 crucial genes (C4H, CCoAOMT, F3'H, UA3'5'GT, PAL, 4CL, CCR, CAD, CALDH, bglx, SGTase, and E1.11.17) that are involved in the regulation of flower color in Phalaenopsis. CONCLUSION This study reported the association between the SNP mutations and DEGs for color formation at RNA level, and provides a new insight to further investigate the gene expression and its relationship with genetic variants from RNA-seq data in other species.
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Affiliation(s)
- Yu Ding
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China
| | - Ma-Yin Wang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China
| | - Ding-Hai Yang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China
| | - Dai-Cheng Hao
- Hainan Boda Orchid Technology Co. Ltd, Haikou, 570311, China
| | - Wei-Shi Li
- Hainan Boda Orchid Technology Co. Ltd, Haikou, 570311, China
| | - Peng Ling
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China.
| | - Shang-Qian Xie
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants, College of Forestry, Hainan University, Haikou, 570228, China.
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Du Y, Lin Y, Zhang K, Rothenberg DO, Zhang H, Zhou H, Su H, Zhang L. The Chemical Composition and Transcriptome Analysis Reveal the Mechanism of Color Formation in Tea ( Camellia sinensis) Pericarp. Int J Mol Sci 2023; 24:13198. [PMID: 37686006 PMCID: PMC10487661 DOI: 10.3390/ijms241713198] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 08/21/2023] [Accepted: 08/22/2023] [Indexed: 09/10/2023] Open
Abstract
To elucidate the molecular mechanisms underlying the differential metabolism of albino (white), green, and purple pericarp coloration, biochemical profiling and transcriptome sequencing analyses were performed on three different tea pericarps, Zhongbaiyihao (Camellia sinensis L. var. Zhongbai), Jinxuan (Camellia sinensis L. var. Jinxuan), and Baitangziya (Camellia sinensis L. var. Baitang). Results of biochemical analysis revealed that low chlorophyll content and low chlorophyll/carotene ratio may be the biochemical basis for albino characteristics in the 'Zhongbaiyihao' pericarp. The differentially expressed genes (DEGs) involved in anthocyanin biosynthesis, including DFR, F3'5'H, CCoAOMT, and 4-coumaroyl-CoA, were highly expressed in the purple 'Baitangziya' pericarp. In the chlorophyll synthesis of white pericarp, GUN5 (Genome Uncoupled 5) and 8-vinyl-reductase both showed high expression levels compared to the green one, which indicated that albino 'Zhongbaiyihao' pericarp had a higher chlorophyll synthesis capacity than 'Jinxuan'. Meanwhile, chlorophyllase (CLH, CSS0004684) was lower in 'Baitang' than in 'Jinxuan' and 'Zhongbaiyihao' pericarp. Among the differentially expressed transcription factors, MYB59, WRKY41-like2 (CS ng17509), bHLH62 like1 (CS ng6804), and bHLH62-like3 (CSS0039948) were downregulated in Jinxuan pericarp, suggesting that transcription factors played a role in regulating tea pericarp coloration. These findings provide a better understanding of the molecular mechanisms and theoretical basis for utilizing functional components of tea pericarp.
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Affiliation(s)
| | | | | | | | | | | | | | - Lingyun Zhang
- College of Horticulture, South China Agricultural University, Guangzhou 510640, China; (Y.D.); (Y.L.); (K.Z.); (D.O.R.); (H.Z.); (H.Z.); (H.S.)
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Scutt CP. Model Species to Investigate the Origin of Flowers. Methods Mol Biol 2023; 2686:83-109. [PMID: 37540355 DOI: 10.1007/978-1-0716-3299-4_4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/05/2023]
Abstract
The angiosperms, or flowering plants, arose at least 135 million years ago (Ma) and rapidly diversified to form over 300,000 species alive today. This group appears, however, to have separated from its closest living relatives, the extant gymnosperms, much earlier: over 300 Ma. Representatives of basally-diverging angiosperm lineages are of key importance to studies aimed at reconstructing the most recent common ancestor of living angiosperms, including its morphological, anatomical, eco-physiological and molecular aspects. Furthermore, evo-devo comparisons of angiosperms with living gymnosperms may help to determine how the many novel aspects of angiosperms, including those of the flower, first came about. This chapter reviews literature on the origin of angiosperms and focusses on basally-diverging angiosperms and gymnosperms that show advantages as potential experimental models, reviewing information and protocols for the use of these species in an evo-devo context. The final section suggests a means by which data from living and fossil groups could be integrated to better elucidate evolutionary events that took place on the long stem-lineage that apparently preceded the radiation of living angiosperms.
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Affiliation(s)
- Charles P Scutt
- Laboratoire Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCB Lyon-1, CNRS, INRA, Lyon, France.
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Li Y, Li H, Wang S, Li J, Bacha SAS, Xu G, Li J. Metabolomic and transcriptomic analyses of the flavonoid biosynthetic pathway in blueberry ( Vaccinium spp.). FRONTIERS IN PLANT SCIENCE 2023; 14:1082245. [PMID: 37152168 PMCID: PMC10157174 DOI: 10.3389/fpls.2023.1082245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 03/29/2023] [Indexed: 05/09/2023]
Abstract
As a highly economic small fruit crop, blueberry is enjoyed by most people in terms of color, taste, and rich nutrition. To better understand its coloring mechanism on the process of ripening, an integrative analysis of the metabolome and transcriptome profiles was performed in three blueberry varieties at three developmental stages. In this study, 41 flavonoid metabolites closely related to the coloring in blueberry samples were analyzed. It turned out that the most differential metabolites in the ripening processes were delphinidin-3-O-arabinoside (dpara), peonidin-3-O-glucoside (pnglu), and delphinidin-3-O-galactoside (dpgal), while the most differential metabolites among different varieties were flavonols. Furthermore, to obtain more accurate and comprehensive transcripts of blueberry during the developmental stages, PacBio and Illumina sequencing technology were combined to obtain the transcriptome of the blueberry variety Misty, for the very first time. Finally, by applying the gene coexpression network analysis, the darkviolet and bisque4 modules related to flavonoid synthesis were determined, and the key genes related to two flavonoid 3', 5'-hydroxylase (F3'5'H) genes in the darkviolet module and one bHLH transcription factor in the bisque4 module were predicted. It is believed that our findings could provide valuable information for the future study on the molecular mechanism of flavonoid metabolites and flavonoid synthesis pathways in blueberries.
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Affiliation(s)
- Yinping Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Haifei Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Shiyao Wang
- Department of Applied Biosciences, Toyo University, Ora-gun, Japan
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Syed Asim Shah Bacha
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
| | - Guofeng Xu
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
| | - Jing Li
- Laboratory of Quality and Safety Risk Assessment for Fruit, Research Institute of Pomology, Chinese Academy of Agricultural Sciences, Xingcheng, Liaoning, China
- *Correspondence: Guofeng Xu, ; Jing Li,
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Xia X, Gong R, Zhang C. Integrative analysis of transcriptome and metabolome reveals flavonoid biosynthesis regulation in Rhododendron pulchrum petals. BMC PLANT BIOLOGY 2022; 22:401. [PMID: 35974307 PMCID: PMC9380304 DOI: 10.1186/s12870-022-03762-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Accepted: 07/15/2022] [Indexed: 06/02/2023]
Abstract
BACKGROUND Color is the major ornamental feature of the Rhododendron genus, and it is related to the contents of flavonoid in petals. However, the regulatory mechanism of flavonoid biosynthesis in Rhododendron pulchrum remains unknown. The transcriptome and metabolome analysis of Rhododendron pulchrum with white, pink and purple color in this study aimed to reveal the mechanism of flavonoid biosynthesis and to provide insight for improving the petal color. RESULTS Flavonoids and flavonols are the major components of flavonoid metabolites in R.pulchrum, such as laricitrin, apigenin, tricin, luteolin, isoorientin, isoscutellarein, diosmetin and their glycosides derivatives. With transcriptome and metabolome analysis, we found CHS, FLS, F3'H, F3'5'H, DFR, ANS, GT, FNS, IFR and FAOMT genes showed significantly differential expression in cultivar 'Zihe'. FNS and IFR were discovered to be associated with coloration in R.pulchrum for the first time. The FNS gene existed in the form of FNSI. The IFR gene and its related metabolites of medicarpin derivatives were highly expressed in purple petal. In cultivar 'Fenhe', up-regulation of F3'H and F3'5'H and down-regulation of 4CL, DFR, ANS, and GT were associated with pink coloration. With the transcription factor analysis, a subfamily of DREBs was found to be specifically enriched in pink petals. This suggested that the DREB family play an important role in pink coloration. In cultivars 'Baihe', flavonoid biosynthesis was inhibited by low expression of CHS, while pigment accumulation was inhibited by low expression of F3'5'H, DFR, and GT, which led to a white coloration. CONCLUSIONS By analyzing the transcriptome and metabolome of R.pulchrum, principal differential expression genes and metabolites of flavonoid biosynthesis pathway were identified. Many novel metabolites, genes, and transcription factors associated with coloration have been discovered. To reveal the mechanism of the coloration of different petals, a model of the flavonoid biosynthesis pathway of R.pulchrum was constructed. These results provide in depth information regarding the coloration of the petals and the flavonoid metabolism of R.pulcherum. The study of transcriptome and metabolome profiling gains insight for further genetic improvement in Rhododendron.
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Affiliation(s)
- Xi Xia
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China
| | - Rui Gong
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China
| | - Chunying Zhang
- Shanghai Urban Plant Resources Development and Application Engineering Research Center, Shanghai Botanical Garden, Shanghai, China.
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Wang D, Wang J, Wang Y, Yao D, Niu Y. Metabolomic and Transcriptomic Profiling Uncover the Underlying Mechanism of Color Differentiation in Scutellaria baicalensis Georgi. Flowers. FRONTIERS IN PLANT SCIENCE 2022; 13:884957. [PMID: 35755689 PMCID: PMC9218823 DOI: 10.3389/fpls.2022.884957] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 05/10/2022] [Indexed: 06/15/2023]
Abstract
Scutellaria baicalensis Georgi. (Chinese skullcap or Huang-qin) is an extremely crucial medicinal plant in the Labiate family, and the color of its flowers naturally appears purple. However, during the long-term cultivation of S. baicalensis, very few plants of S. baicalensis also present white and purple-red flower colors under the same ecological conditions. However, the complex metabolic and transcriptional networks underlying color formation in white, purple-red, and purple flowers of S. baicalensis remain largely unclarified. To gain an insight into this issue, we conducted transcriptome and metabolomic profiling to elucidate the anthocyanin synthesis metabolic pathway in the flowers of S. baicalensis, and to identify the differentially expressed candidate genes potentially involved in the biosynthesis of anthocyanins. The results showed that 15 anthocyanins were identified, among which cyanidin 3-rutinoside and delphin chloride were the primary anthocyanins, and accumulation was significantly related to the flower color changes of S. baicalensis. Furthermore, the down-regulation of SbDFR (Sb02g31040) reduced the anthocyanin levels in the flowers of S. baicalensis. The differential expression of the Sb3GT (Sb07g04780 and Sb01g72290) gene in purple and purple-red flowers affected anthocyanin accumulation, suggesting that anthocyanin levels were closely associated with the expression of SbDFR and Sb3GT, which play important roles in regulating the anthocyanin biosynthesis process of S. baicalensis flowers. Transcriptomic analysis revealed that transcription factors WRKY, bHLH, and NAC were also highly correlated with anthocyanin accumulation, especially for NAC35, which positively regulated SbDFR (Sb02g31040) gene expression and modulated anthocyanin biosynthesis in flower color variation of S. baicalensis. Overall, this study presents the first experimental evidence for the metabolomic and transcriptomic profiles of S. baicalensis in response to flower coloration, which provides a foundation for dynamic metabolic engineering and plant breeding, and to understand floral evolution in S. baicalensis plants.
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Affiliation(s)
| | | | | | | | - Yanbing Niu
- College of Life Sciences, Shanxi Agricultural University, Jinzhong, China
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Qiu L, Zheng T, Liu W, Zhuo X, Li P, Wang J, Cheng T, Zhang Q. Integration of Transcriptome and Metabolome Reveals the Formation Mechanism of Red Stem in Prunus mume. FRONTIERS IN PLANT SCIENCE 2022; 13:884883. [PMID: 35599903 PMCID: PMC9120947 DOI: 10.3389/fpls.2022.884883] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/25/2022] [Indexed: 06/15/2023]
Abstract
Prunus mume var. purpurea, commonly known as "Red Bone", is a special variety with pink or purple-red xylem. It is famous due to gorgeous petals and delightful aromas, playing important roles in urban landscaping. The regulation mechanism of color formation in P. mume var. purpurea stem development is unclear. Here, we conducted a comprehensive analysis of transcriptome and metabolome in WYY ('Wuyuyu' accession, red stem) and FLE ('Fei Lve' accession, green stem), and found a total of 256 differential metabolites. At least 14 anthocyanins were detected in WYY, wherein cyanidin 3,5-O-diglucoside and peonidin3-O-glucoside were significantly accumulated through LC-MS/MS analysis. Transcriptome data showed that the genes related to flavonoid-anthocyanin biosynthesis pathways were significantly enriched in WYY. The ratio of dihydroflavonol 4-reductase (DFR) and flavonol synthase (FLS) expression levels may affect metabolic balance in WYY, suggesting a vital role in xylem color formation. In addition, several transcription factors were up-regulated, which may be the key factors contributing to transcriptional changes in anthocyanin synthesis. Overall, the results provide a reference for further research on the molecular mechanism of xylem color regulation in P. mume and lay a theoretical foundation for cultivating new varieties.
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Wang XJ, Peng XQ, Shu XC, Li YH, Wang Z, Zhuang WB. Genome-wide identification and characterization of PdbHLH transcription factors related to anthocyanin biosynthesis in colored-leaf poplar (Populus deltoids). BMC Genomics 2022; 23:244. [PMID: 35350981 PMCID: PMC8962177 DOI: 10.1186/s12864-022-08460-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/07/2022] [Indexed: 11/26/2022] Open
Abstract
Basic helix-loop-helix (bHLH) proteins are transcription factors (TFs) that have been shown to regulate anthocyanin biosynthesis in many plant species. However, the bHLH gene family in Populus deltoids has not yet been reported. In this study, 185 PdbHLH genes were identified in the Populus deltoids genome and were classified into 15 groups based on their sequence similarity and phylogenetic relationships. Analysis of the gene structure, chromosome location and conserved motif of the PdbHLH genes were performed by bioinformatic methods. Gene duplication analyses revealed that 114 PdbHLH were expanded and retained after WGD/segmental and proximal duplication. Investigation of cis-regulatory elements of PdbHLH genes indicated that many PdbHLH genes are involved in the regulation of anthocyanin biosynthesis. The expression patterns of PdbHLHs were obtained from previous data in two colored-leaf poplar (QHP and JHP) and green leaf poplar (L2025). Further analysis revealed that 12 candidate genes, including 3 genes (PdbHLH57, PdbHLH143, and PdbHLH173) from the subgroup III(f) and 9 gene from other groups, were positively associated with anthocyanin biosynthesis. In addition, 4 genes (PdbHLH4, PdbHLH1, PdbHLH18, and PdbHLH164) may be involved in negatively regulating the anthocyanin biosynthesis. These results provide a basis for the functional characterization of bHLH genes and investigations on the molecular mechanisms of anthocyanin biosynthesis in colored-leaf poplar.
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Yu Y, Yang Z, Jiang Y, Wang L, Wu Y, Liao J, Yang R, Zhang L. Inheritance and QTL Mapping for Flower Color in Salvia miltiorrhiza Bunge. J Hered 2022; 113:248-256. [PMID: 35259262 DOI: 10.1093/jhered/esac012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/04/2022] [Indexed: 11/12/2022] Open
Abstract
Salvia miltiorrhiza Bunge is an outcross-pollinated plant with diverse flower colors, ranging from white to purple. To clarify the genetic basis of S. miltiorrhiza flower color, we crossed white-flowered S. miltiorrhiza f. alba with dark violet-flowered S. miltiorrhiza, and selfed F1 to obtain an F2 population. The RGB color system was used to describe the flower color of the parents, F1 progeny, and F2 individuals. Afterward, we used genotyping-by-sequencing (GBS) technology to construct a high-density linkage map of S. miltiorrhiza based on the F2 population. Finally, the linkage map was used to locate the QTLs of the genes that control flower color in S. miltiorrhiza. Through measurement and cluster analysis of the R, G, and B values of flowers from the parents, F1, and F2 individuals, it was found that the purple flower color of S. miltiorrhiza is a quantitative trait controlled by two loci of major genes. The genetic map contained 605 SNPs with a total length of 738.3 cM in eight linkage groups (LGs), and the average distance between two markers was 1.22 cM. Based on the constructed genetic map and the flower R, G, B, and R+G+B values, two QTLs were detected for flower color, located on LG4 and LG5. The results of this study lay the foundation for cloning genes that control flower color and studying the molecular mechanism of flower color regulation in S. miltiorrhiza.
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Affiliation(s)
- Yan Yu
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Zaijun Yang
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Yuanyuan Jiang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Long Wang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Yichao Wu
- College of Life Science, China West Normal University, Nanchong, 637009, Sichuan, China
| | - Jinqiu Liao
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Ruiwu Yang
- Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
| | - Li Zhang
- College of Sciences, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China.,Featured Medicinal Plants Sharing and Service Platform of Sichuan Province, Sichuan Agricultural University, Ya'an, 625014, Sichuan, China
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Zhu J, Guo X, Li X, Tang D. Composition of Flavonoids in the Petals of Freesia and Prediction of Four Novel Transcription Factors Involving in Freesia Flavonoid Pathway. FRONTIERS IN PLANT SCIENCE 2021; 12:756300. [PMID: 34868147 PMCID: PMC8634401 DOI: 10.3389/fpls.2021.756300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
Freesia hybrida is rich in flower colors with beautiful flower shapes and pleasant aroma. Flavonoids are vital to the color formation of its flowers. In this study, five Freesia cultivars with different flower colors were used to study on the level of accumulation of their flavonoids and expression of flavonoid-related genes and further explore new novel transcription factor (TF). Ultra-high-performance liquid chromatography and VION ion mobility quadrupole time-of-flight mass spectrometer (UPLC-Q-TOF-MS) were used to determine the flavonoids. Combined with transcriptome sequencing technology, the molecular mechanism of the flavonoid metabolism difference in Freesia was revealed. A total of 10 anthoxanthin components and 12 anthocyanin components were detected using UPLC-Q-TOF-MS. All six common anthocyanin aglycones in high plants, including cyanidin, delphinidin, petunidin, peonidin, malvidin, and pelargonidin, were detected in Freesia at first time in this study. In orange, yellow, and white cultivars, anthoxanthins gradually decreased with the opening of the petals, while in red and purple cultivars, anthoxanthins first increased and then decreased. No anthocyanin was detected in yellow and white cultivars, while anthocyanins increased with the opening of the petals and reached their maximum at the flowering stage (S3) in other three cultivars. The correlation analysis revealed that the color of Freesia petals was closely related to the composition and content of anthoxanthins and anthocyanins. Petals of five cultivars at S3 were then selected for transcriptome sequencing by using the Illumina Hiseq 4000 platform, and a total of 100,539 unigenes were obtained. There were totally 5,162 differentially expressed genes (DEGs) when the four colored cultivars were compared with the white cultivar at S3. Comparing all DEGs with gene ontology (GO), KEGG, and Pfam databases, it was found that the genes involved in the flavonoid biosynthesis pathway were significantly different. In addition, AP2, WRKY, and bHLH TF families ranked the top three among all differently expressed TFs in all DEGs. Quantitative real-time PCR (qRT-PCR) technology was used to analyze the expression patterns of the structural genes of flavonoid biosynthesis pathway in Freesia. The results showed that metabolic process was affected significantly by structural genes in this pathway, such as CHS1, CHI2, DFR1, ANS1, 3GT1, and FLS1. Cluster analysis was performed by using all annotated WRKY and AP2 TFs and the above structural genes based on their relatively expression. Four novel candidate TFs of WRKY and AP2 family were screened. Their spatiotemporal expression patterns revealed that these four novel TFs may participate in the regulation of the flavonoid biosynthesis, thus controlling its color formation in Freesia petals.
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Affiliation(s)
- Jiayi Zhu
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Xueying Guo
- School of Design, Shanghai Jiao Tong University, Shanghai, China
| | - Xin Li
- Instrumental Analysis Center, Shanghai Jiao Tong University, Shanghai, China
| | - Dongqin Tang
- School of Design, Shanghai Jiao Tong University, Shanghai, China
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Zhao Y, Zhou W, Chen Y, Li Z, Song X, Wang J, Tian D, Niu J. Metabolite analysis in Nymphaea 'Blue Bird' petals reveal the roles of flavonoids in color formation, stress amelioration, and bee orientation. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 312:111025. [PMID: 34620430 DOI: 10.1016/j.plantsci.2021.111025] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 07/04/2021] [Accepted: 08/12/2021] [Indexed: 06/13/2023]
Abstract
In this study, metabolome of open petals (OP) and closed petals (CP) from Nymphaea 'Blue Bird' was firstly investigated. A total of 455 metabolites was identified in Nymphaea 'Blue Bird' petals, which was mainly composed of 100 flavonoids, 83 phenolic acids, 64 amino acids and derivatives, 60 lipids, 32 alkaloids, 32 organic acids, 24 nucleotides and derivatives, and 12 lignans and coumarins. By differential analysis, 192 metabolites were identified with variable importance in project ≥ 1, among which 83 and 109 metabolites were up- and down-regulated in OP group, respectively. Further analysis (Log2 fold change ≥ 1) identified 26 and 7 metabolites exhibited significantly lower and higher contents in CP group, relative to OP group. Importantly, KEGG analysis indicated that flavonoid biosynthesis exhibited the most significant enrichment. qRT-PCR analysis indicated that the PAL, CHS, and HCDBR genes showed a significantly higher expression in OP group than in CP group. These data explain the increase of naringenin chalcone and phloretin in OP. However, there was no significant difference of total flavonoids between OP and CP groups. Considering the increase of H2O2 content and ultraviolet (UV) absorption peak in OP, our results implied that diurnal stressful conditions induced the degradation of flavonoids, which contributed to environmental stress amelioration. Moreover, a higher absorption peak of 360-380 nm UV was observed in the extract liquor of OP. The sensitivity maximum of the UV-photoreceptor of bees is situated around 340-380 nm UV. This suggested, as noted for the maximum absorption of dihydrokaempferol in 340-370 nm, rhythmic accumulation and loss of these differential flavonoids in Nymphaea 'Blue Bird' petals might enhance UV pattern to some degree, influencing pollinator attraction.
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Affiliation(s)
- Ying Zhao
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Weijuan Zhou
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Yan Chen
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Zhaoji Li
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Xiqiang Song
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Jian Wang
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China
| | - Daike Tian
- Shanghai Key Laboratory of Plant Functional Genomics and Resources, Shanghai Chenshan Plant Science Research Center, Shanghai Chenshan Botanical Garden, Chinese Academy of Sciences, Shanghai, 201602, China
| | - Jun Niu
- Key Laboratory of Ministry of Education for Genetics and Germplasm Innovation of Tropical Special Trees and Ornamental Plants / Hainan Biological Key Laboratory for Germplasm Resources of Tropical Special Ornamental Plants, School of Forestry, Hainan University, Haikou, 570228, China.
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Feng X, Gao G, Yu C, Zhu A, Chen J, Chen K, Wang X, Abubakar AS, Chen P. Transcriptome and metabolome analysis reveals anthocyanin biosynthesis pathway associated with ramie (Boehmeria nivea (L.) Gaud.) leaf color formation. BMC Genomics 2021; 22:684. [PMID: 34548018 PMCID: PMC8456610 DOI: 10.1186/s12864-021-08007-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Accepted: 09/13/2021] [Indexed: 11/10/2022] Open
Abstract
Background The bast fiber crop ramie can be used as high-quality forage resources, especially in tropical or subtropical region where there is lack of high-quality protein feed. Hongxuan No.1 (HX_1) is a unique ramie variety with a light reddish brown leaf color, which is obviously different from elite cultivar, Zhongzhu No.1 (ZZ_1, green leaf). While, the regulatory mechanism of color difference or secondary metaboliates synthesis between these two varieties have not been studied. Results In this study, phenotypic, transcriptomic and metabolomic analysis of HX_1 and ZZ_1 were conducted to elucidate the mechanism of leaf color formation. Chromaticity value and pigment content measuring showed that anthocyanin was the main metabolites imparting the different leaf color phenotype between the two varieties. Based on LC/MS, at least 14 anthocyanins were identified in leaves of HX_1 and ZZ_1, and the HX_1 showed the higher relative content of malvidin-, pelargonidin-,and cyanidin-based anthocyanins. Transcriptome and metabolome co-analysis revealed that the up-regulated expression of flavonoids synthesis gene was positively correlated with total anthocyanins accumulation in ramie leaf, and the differentfially expression of “blue gene” (F3’5’H) and the “red gene” (F3’H) in leaves bring out HX_1 metabolic flow more input into the cyanidin branch. Furthermore, the enrichment of glycosylated modification pathway (UGT and AT) and the expression of flavonoid 3-O-glucosyl transferase (UFGT), anthocyanidin reductase (ANR), in leaves were significantly influenced the diversity of anthocyanins between HX_1 and ZZ_1. Conclusions Phenotypic, transcriptomic and metabolomic analysis of HX_1 and ZZ_1 indicated that the expression levels of genes related to anthocyanin metabolism contribute to the color formation of ramie variety. Anthocyanins are important plant secandary metabilates with many physiological functions, the results of this study will deepened our understanding of ramie leaf color formation, and provided basis for molecular breeding of functional forage ramie. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08007-0.
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Affiliation(s)
- Xinkang Feng
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Gang Gao
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Chunming Yu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Aiguo Zhu
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Jikang Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Kunmei Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Xiaofei Wang
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Aminu Shehu Abubakar
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China
| | - Ping Chen
- Institute of Bast Fiber Crops, Chinese Academy of Agricultural Sciences, Changsha, 410205, China.
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Gao YF, Zhao DH, Zhang JQ, Chen JS, Li JL, Weng Z, Rong LP. De novo transcriptome sequencing and anthocyanin metabolite analysis reveals leaf color of Acer pseudosieboldianum in autumn. BMC Genomics 2021; 22:383. [PMID: 34034673 PMCID: PMC8145822 DOI: 10.1186/s12864-021-07715-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Accepted: 05/14/2021] [Indexed: 11/10/2022] Open
Abstract
Background Leaf color is an important ornamental trait of colored-leaf plants. The change of leaf color is closely related to the synthesis and accumulation of anthocyanins in leaves. Acer pseudosieboldianum is a colored-leaf tree native to Northeastern China, however, there was less knowledge in Acer about anthocyanins biosynthesis and many steps of the pathway remain unknown to date. Results Anthocyanins metabolite and transcript profiling were conducted using HPLC and ESI-MS/MS system and high-throughput RNA sequencing respectively. The results demonstrated that five anthocyanins were detected in this experiment. It is worth mentioning that Peonidin O-hexoside and Cyanidin 3, 5-O-diglucoside were abundant, especially Cyanidin 3, 5-O-diglucoside displayed significant differences in content change at two periods, meaning it may be play an important role for the final color. Transcriptome identification showed that a total of 67.47 Gb of clean data were obtained from our sequencing results. Functional annotation of unigenes, including comparison with COG and GO databases, yielded 35,316 unigene annotations. 16,521 differentially expressed genes were identified from a statistical analysis of differentially gene expression. The genes related to leaf color formation including PAL, ANS, DFR, F3H were selected. Also, we screened out the regulatory genes such as MYB, bHLH and WD40. Combined with the detection of metabolites, the gene pathways related to anthocyanin synthesis were analyzed. Conclusions Cyanidin 3, 5-O-diglucoside played an important role for the final color. The genes related to leaf color formation including PAL, ANS, DFR, F3H and regulatory genes such as MYB, bHLH and WD40 were selected. This study enriched the available transcriptome information for A. pseudosieboldianum and identified a series of differentially expressed genes related to leaf color, which provides valuable information for further study on the genetic mechanism of leaf color expression in A. pseudosieboldianum. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07715-x.
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Affiliation(s)
- Yu-Fu Gao
- Agriculture College, Yanbian University, 977 Gongyuan Road, 133002, Yanji, China
| | - Dong-Hui Zhao
- Agriculture College, Yanbian University, 977 Gongyuan Road, 133002, Yanji, China
| | - Jia-Qi Zhang
- Agriculture College, Yanbian University, 977 Gongyuan Road, 133002, Yanji, China
| | - Jia-Shuo Chen
- Agriculture College, Yanbian University, 977 Gongyuan Road, 133002, Yanji, China
| | - Jia-Lin Li
- Agriculture College, Yanbian University, 977 Gongyuan Road, 133002, Yanji, China
| | - Zhuo Weng
- Agriculture College, Yanbian University, 977 Gongyuan Road, 133002, Yanji, China
| | - Li-Ping Rong
- Agriculture College, Yanbian University, 977 Gongyuan Road, 133002, Yanji, China.
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15
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Dudeja SS, Suneja-Madan P, Paul M, Maheswari R, Kothe E. Bacterial endophytes: Molecular interactions with their hosts. J Basic Microbiol 2021; 61:475-505. [PMID: 33834549 DOI: 10.1002/jobm.202000657] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 03/07/2021] [Accepted: 03/16/2021] [Indexed: 01/19/2023]
Abstract
Plant growth promotion has been found associated with plants on the surface (epiphytic), inside (endophytic), or close to the plant roots (rhizospheric). Endophytic bacteria mainly have been researched for their beneficial activities in terms of nutrient availability, plant growth hormones, and control of soil-borne and systemic pathogens. Molecular communications leading to these interactions between plants and endophytic bacteria are now being unrevealed using multidisciplinary approaches with advanced techniques such as metagenomics, metaproteomics, metatranscriptomics, metaproteogenomic, microRNAs, microarray, chips as well as the comparison of complete genome sequences. More than 400 genes in both the genomes of host plant and bacterial endophyte are up- or downregulated for the establishment of endophytism and plant growth-promoting activity. The involvement of more than 20 genes for endophytism, about 50 genes for direct plant growth promotion, about 25 genes for biocontrol activity, and about 10 genes for mitigation of different stresses has been identified in various bacterial endophytes. This review summarizes the progress that has been made in recent years by these modern techniques and approaches.
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Affiliation(s)
- Surjit S Dudeja
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Pooja Suneja-Madan
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Minakshi Paul
- Department of Bio & Nanotechnology, Guru Jambeshwar University of Science & Technology, Hisar, India
| | - Rajat Maheswari
- Department of Microbiology, Maharishi Dayanand University, Rohtak, India
| | - Erika Kothe
- Microbial Communication, Institute of Microbiology, Faculty for Biosciences, Friedrich Schiller University of Jena, Jena, Germany
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Tang M, Li Z, Luo D, Wei F, Kashif MH, Lu H, Hu Y, Yue J, Huang Z, Tan W, Li R, Chen P. A comprehensive integrated transcriptome and metabolome analyses to reveal key genes and essential metabolic pathways involved in CMS in kenaf. PLANT CELL REPORTS 2021; 40:223-236. [PMID: 33128088 DOI: 10.1007/s00299-020-02628-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/20/2020] [Accepted: 10/15/2020] [Indexed: 06/11/2023]
Abstract
Numbers of critical genes and pathways were found from the levels of transcriptome and metabolome, which were useful information for understanding of kenaf CMS mechanism. Cytoplasmic male sterility (CMS) is a maternally inherited trait in higher plants that leads to the inability to produce or release functional pollen. However, there is lack of comprehensive studies to reveal the molecular basis of CMS occurrence in kenaf. Herein, we performed transcriptome and UPLC-MS-based metabolome analyses in the anthers of a CMS (UG93A) and its maintainer (UG93B) to sort out essential genes and metabolites responding to CMS in kenaf. Transcriptome characterized 7769 differentially expressed genes (DEGs) between these two materials, and pathway enrichment analysis indicated that these DEGs were involved mainly in pentose and glucuronate interconversions, starch and sucrose metabolism, taurine and hypotaurine metabolism. In the metabolome assay, a total of 116 significantly different metabolites (SDMs) were identified between the CMS and its maintainer line, and these SDMs were involved in eight KEGG pathways, including flavone and flavonol biosynthesis, glycerophospholipid metabolism, flavonoid biosynthesis, glycosylphosphatidylinositol-anchor biosynthesi. Integrated analyses of transcriptome and metabolome showed that 50 genes had strong correlation coefficient values (R2 > 0.9) with ten metabolites enriched in six pathways; notably, most genes and metabolites of flavonoid biosynthesis pathways and flavone and flavonol biosynthesis pathways involved in flavonoids biosynthetic pathways were downregulated in CMS compared to those in maintainer. Taken together, the decreased accumulation of flavonoids resulted from the compromised biosynthesis pathways coupled with energy deficiency in the anthers may contribute largely to CMS in UG93A of kenaf.
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Affiliation(s)
- Meiqiong Tang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China
| | - Zengqiang Li
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Dengjie Luo
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Fan Wei
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
- Guangxi Botanical Garden of Medicinal Plants, Guangxi Key Laboratory Resources Protection and Genetic Improvement, Nanning, China
| | - Muhammad Haneef Kashif
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Hai Lu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Yali Hu
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Jiao Yue
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Zhen Huang
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Wenye Tan
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China
| | - Ru Li
- College of Life Science and Technology, Guangxi University, Nanning, China
| | - Peng Chen
- Key Laboratory of Plant Genetics and Breeding, College of Agriculture, Guangxi University, Nanning, China.
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Baslam M, Mitsui T, Sueyoshi K, Ohyama T. Recent Advances in Carbon and Nitrogen Metabolism in C3 Plants. Int J Mol Sci 2020; 22:E318. [PMID: 33396811 PMCID: PMC7795015 DOI: 10.3390/ijms22010318] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 12/23/2020] [Accepted: 12/23/2020] [Indexed: 12/19/2022] Open
Abstract
C and N are the most important essential elements constituting organic compounds in plants. The shoots and roots depend on each other by exchanging C and N through the xylem and phloem transport systems. Complex mechanisms regulate C and N metabolism to optimize plant growth, agricultural crop production, and maintenance of the agroecosystem. In this paper, we cover the recent advances in understanding C and N metabolism, regulation, and transport in plants, as well as their underlying molecular mechanisms. Special emphasis is given to the mechanisms of starch metabolism in plastids and the changes in responses to environmental stress that were previously overlooked, since these changes provide an essential store of C that fuels plant metabolism and growth. We present general insights into the system biology approaches that have expanded our understanding of core biological questions related to C and N metabolism. Finally, this review synthesizes recent advances in our understanding of the trade-off concept that links C and N status to the plant's response to microorganisms.
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Affiliation(s)
- Marouane Baslam
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
| | - Toshiaki Mitsui
- Laboratory of Biochemistry, Faculty of Agriculture, Niigata University, Niigata 950-2181, Japan; (M.B.); (T.M.)
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Kuni Sueyoshi
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
| | - Takuji Ohyama
- Department of Life and Food Sciences, Graduate School of Science and Technology, Niigata University, Niigata 950-2181, Japan;
- Faculty of Applied Biosciences, Tokyo University of Agriculture, Tokyo 156-8502, Japan
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Gao Y, Zhang X, Ren G, Wu C, Qin P, Yao Y. Peptides from Extruded Lupin ( Lupinus albus L.) Regulate Inflammatory Activity via the p38 MAPK Signal Transduction Pathway in RAW 264.7 Cells. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2020; 68:11702-11709. [PMID: 32869636 DOI: 10.1021/acs.jafc.0c02476] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
In this study, protein was extracted from extruded lupin and submitted to gastroduodenal digests to obtain lupin peptides, which were characterized using ultraperformance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS). After this, IQDKEGIPPDQQR (IQD), the lupine peptide monomer characterized after UPLC-MS/MS, was screened out by macrophage inflammatory cytokine production assay. RNA-sequencing analysis was performed to explore the mechanisms underlying the anti-inflammatory activity associated with this peptide. The results indicated that lupin peptides effectively inhibited the lipopolysaccharide-induced overproduction of proinflammatory mediators. IQD inhibited the production of tumor necrosis factor-α, interleukin (IL)-6, IL-1β, and monocyte chemoattractant protein-1 by 51.20, 38.52, 44.70, and 40.43%, respectively. RNA-sequencing results showed that IQD inhibited the inflammatory response by regulating the gene expression of the p38 mitogen-activated protein kinase pathway and inhibiting downstream inflammatory cytokines. These bioactive peptides may be used to develop new ingredients for anti-inflammatory nutritional supplements.
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Affiliation(s)
- Yue Gao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Xuna Zhang
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Guixing Ren
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Caie Wu
- College of Light Industry and Food Engineering, Nanjing Forestry University, Nanjing 210037, Jiangsu Province, China
| | - Peiyou Qin
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
| | - Yang Yao
- Institute of Crop Science, Chinese Academy of Agricultural Sciences, No. 80 South Xueyuan Road, Haidian District, Beijing 100081, China
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Jiang T, Zhang M, Wen C, Xie X, Tian W, Wen S, Lu R, Liu L. Integrated metabolomic and transcriptomic analysis of the anthocyanin regulatory networks in Salvia miltiorrhiza Bge. flowers. BMC PLANT BIOLOGY 2020; 20:349. [PMID: 32703155 PMCID: PMC7379815 DOI: 10.1186/s12870-020-02553-7] [Citation(s) in RCA: 49] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2020] [Accepted: 07/15/2020] [Indexed: 05/05/2023]
Abstract
BACKGROUND The objectives of this study were to reveal the anthocyanin biosynthesis metabolic pathway in white and purple flowers of Salvia miltiorrhiza using metabolomics and transcriptomics, to identify different anthocyanin metabolites, and to analyze the differentially expressed genes involved in anthocyanin biosynthesis. RESULTS We analyzed the metabolomics and transcriptomics data of S. miltiorrhiza flowers. A total of 1994 differentially expressed genes and 84 flavonoid metabolites were identified between the white and purple flowers of S. miltiorrhiza. Integrated analysis of transcriptomics and metabolomics showed that cyanidin 3,5-O-diglucoside, malvidin 3,5-diglucoside, and cyanidin 3-O-galactoside were mainly responsible for the purple flower color of S. miltiorrhiza. A total of 100 unigenes encoding 10 enzymes were identified as candidate genes involved in anthocyanin biosynthesis in S. miltiorrhiza flowers. Low expression of the ANS gene decreased the anthocyanin content but enhanced the accumulation of flavonoids in S. miltiorrhiza flowers. CONCLUSIONS Our results provide valuable information on the anthocyanin metabolites and the candidate genes involved in the anthocyanin biosynthesis pathways in S. miltiorrhiza.
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Affiliation(s)
- Tao Jiang
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Meidi Zhang
- Institute of Chinese Herbal Medicines, Hubei Academy of Agricultural Sciences, Enshi, 445000, Hubei, China
| | - Chunxiu Wen
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Xiaoliang Xie
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Wei Tian
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Saiqun Wen
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Ruike Lu
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China
| | - Lingdi Liu
- Institute of Cash Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050051, Hebei, China.
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Qiang T, Liu J, Dong Y, Ma Y, Zhang B, Wei X, Liu H, Xiao P. Transcriptome Sequencing and Chemical Analysis Reveal the Formation Mechanism of White Florets in Carthamus tinctorius L. PLANTS 2020; 9:plants9070847. [PMID: 32635570 PMCID: PMC7412316 DOI: 10.3390/plants9070847] [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: 06/09/2020] [Revised: 06/26/2020] [Accepted: 07/02/2020] [Indexed: 12/12/2022]
Abstract
Carthamus tinctorius L. (safflower), an economic crop and herb, has been extensively studied for its diverse chemical constituents and pharmacological effects, but the mechanism of safflower pigments (SP) leading to different colors of florets has not been clarified. In the present study, we compared the contents of SP in two varieties of safflower with white and red florets, named Xinhonghua No. 7 (WXHH) and Yunhong No. 2 (RYH). The results showed the contents of SP in RYH were higher than WXHH. To investigate genes related to SP, we obtained six cDNA libraries of florets from the two varieties by transcriptome sequencing. A total of 225,008 unigenes were assembled and 40 unigenes related to safflower pigment biosynthesis were annotated, including 7 unigenes of phenylalanine ammonia-lyase (PAL), 20 unigenes of 4-coumarate-CoA ligase (4CL), 1 unigene of trans-cinnamate 4-monooxygenase (C4H), 7 unigenes of chalcone synthase (CHS), 4 unigenes of chalcone isomerase (CHI), and 1 unigene of flavanone 3-hydroxylase (F3H). Based on expression levels we selected 16 differentially expressed unigenes (DEGs) and tested them using reverse transcription-quantitative real-time polymerase chain reaction (RT-qPCR), which was consistent with the sequencing results. Consequently, we speculated that in WXHH, 3 PALs, 3 4CLs, 1 C4H, 1 CHS, and 1 CHI, which were down-regulated, and 1 F3H, which was up-regulated, may play a key role in the formation of white florets.
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Affiliation(s)
- Tingyan Qiang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (T.Q.); (J.L.); (Y.D.); (B.Z.); (X.W.); (P.X.)
| | - Jiushi Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (T.Q.); (J.L.); (Y.D.); (B.Z.); (X.W.); (P.X.)
| | - Yuqing Dong
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (T.Q.); (J.L.); (Y.D.); (B.Z.); (X.W.); (P.X.)
| | - Yinbo Ma
- Molecular Genetics and Genomics Laboratory, Department of Horticulture, Chungnam National University, Daejeon 34134, Korea;
| | - Bengang Zhang
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (T.Q.); (J.L.); (Y.D.); (B.Z.); (X.W.); (P.X.)
| | - Xueping Wei
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (T.Q.); (J.L.); (Y.D.); (B.Z.); (X.W.); (P.X.)
| | - Haitao Liu
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (T.Q.); (J.L.); (Y.D.); (B.Z.); (X.W.); (P.X.)
- Correspondence: ; Tel.: +86-10-57833196
| | - Peigen Xiao
- Institute of Medicinal Plant Development, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100193, China; (T.Q.); (J.L.); (Y.D.); (B.Z.); (X.W.); (P.X.)
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21
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Jiang C, Fan Z, Li Z, Niu D, Li Y, Zheng M, Wang Q, Jin H, Guo J. Bacillus cereus AR156 triggers induced systemic resistance against Pseudomonas syringae pv. tomato DC3000 by suppressing miR472 and activating CNLs-mediated basal immunity in Arabidopsis. MOLECULAR PLANT PATHOLOGY 2020; 21:854-870. [PMID: 32227587 PMCID: PMC7214473 DOI: 10.1111/mpp.12935] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 02/28/2020] [Accepted: 02/28/2020] [Indexed: 05/18/2023]
Abstract
Small RNAs play an important role in plant innate immunity. However, their regulatory function in induced systemic resistance (ISR) triggered by plant growth-promoting rhizobacteria remains unclear. Here, using Arabidopsis as a model system, one plant endogenous small RNA, miR472, was identified as an important regulator involved in the process of Bacillus cereus AR156 ISR against Pseudomonas syringae pv. tomato (Pst) DC3000. The results revealed that miR472 was down-regulated with B. cereus AR156 treatment by comparing small RNA profiles and northern blot analysis of Arabidopsis with or without B. cereus AR156 treatment. Plants overexpressing miR472 showed higher susceptibility to Pst DC3000; by contrast, plant lines with miR472 knocked down/out showed the opposite. The transcriptome sequencing revealed thousands of differentially expressed genes in the transgenic plants. Target prediction showed that miR472 targets lots of coiled coil nucleotide-binding site (NBS) and leucine-rich repeat (LRR) type resistance genes and the expression of these targets was negatively correlated with the expression of miR472. In addition, transgenic plants with knocked-out target genes exhibited decreased resistance to Pst DC3000 invasion. Quantitative reverse transcription PCR results indicated that target genes of miR472 were expressed during the process of B. cereus AR156-triggered ISR. Taken together, our results demonstrate that the miR472-mediated silencing pathway is an important regulatory checkpoint occurring via post-transcriptional control of NBS-LRR genes during B. cereus AR156-triggered ISR in Arabidopsis.
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Affiliation(s)
- Chunhao Jiang
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zhihang Fan
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Zijie Li
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
| | - Dongdong Niu
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
| | - Yan Li
- Department of Plant PathologyCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Mingzi Zheng
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
| | - Qi Wang
- Department of Plant PathologyCollege of Plant ProtectionChina Agricultural UniversityBeijingChina
| | - Hailing Jin
- Department of Plant Pathology and MicrobiologyUniversity of CaliforniaRiversideCAUSA
| | - Jianhua Guo
- Department of Plant PathologyCollege of Plant ProtectionNanjing Agricultural UniversityNanjingChina
- Key Laboratory of Monitoring and Management of Crop Diseases and Pest InsectsMinistry of AgricultureNanjingChina
- Engineering Center of Bioresource Pesticide in Jiangsu ProvinceNanjingChina
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22
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Duan HR, Wang LR, Cui GX, Zhou XH, Duan XR, Yang HS. Identification of the regulatory networks and hub genes controlling alfalfa floral pigmentation variation using RNA-sequencing analysis. BMC PLANT BIOLOGY 2020; 20:110. [PMID: 32164566 PMCID: PMC7068929 DOI: 10.1186/s12870-020-2322-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2019] [Accepted: 02/28/2020] [Indexed: 05/11/2023]
Abstract
BACKGROUND To understand the gene expression networks controlling flower color formation in alfalfa, flowers anthocyanins were identified using two materials with contrasting flower colors, namely Defu and Zhongtian No. 3, and transcriptome analyses of PacBio full-length sequencing combined with RNA sequencing were performed, across four flower developmental stages. RESULTS Malvidin and petunidin glycoside derivatives were the major anthocyanins in the flowers of Defu, which were lacking in the flowers of Zhongtian No. 3. The two transcriptomic datasets provided a comprehensive and systems-level view on the dynamic gene expression networks underpinning alfalfa flower color formation. By weighted gene coexpression network analyses, we identified candidate genes and hub genes from the modules closely related to floral developmental stages. PAL, 4CL, CHS, CHR, F3'H, DFR, and UFGT were enriched in the important modules. Additionally, PAL6, PAL9, 4CL18, CHS2, 4 and 8 were identified as hub genes. Thus, a hypothesis explaining the lack of purple color in the flower of Zhongtian No. 3 was proposed. CONCLUSIONS These analyses identified a large number of potential key regulators controlling flower color pigmentation, thereby providing new insights into the molecular networks underlying alfalfa flower development.
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Affiliation(s)
- Hui-Rong Duan
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Li-Rong Wang
- College of Ecological Environment and Resources, Qinghai Nationalities University, Xining, China
| | - Guang-Xin Cui
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xue-Hui Zhou
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Xiao-Rong Duan
- Shanxi Electric Power Research Institute, State Grid Corporation of China, Taiyuan, China
| | - Hong-Shan Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Science, Chinese Academy of Agricultural Sciences, Lanzhou, China.
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23
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Lin W, Li Y, Lu Q, Lu H, Li J. Combined Analysis of the Metabolome and Transcriptome Identified Candidate Genes Involved in Phenolic Acid Biosynthesis in the Leaves of Cyclocarya paliurus. Int J Mol Sci 2020; 21:ijms21041337. [PMID: 32079236 PMCID: PMC7073005 DOI: 10.3390/ijms21041337] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 02/10/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022] Open
Abstract
To assess changes of metabolite content and regulation mechanism of the phenolic acid biosynthesis pathway at different developmental stages of leaves, this study performed a combined metabolome and transcriptome analysis of Cyclocarya paliurus leaves at different developmental stages. Metabolite and transcript profiling were conducted by ultra-performance liquid chromatography quadrupole time-of-flight tandem mass spectrometer and high-throughput RNA sequencing, respectively. Transcriptome identification showed that 58 genes were involved in the biosynthesis of phenolic acid. Among them, 10 differentially expressed genes were detected between every two developmental stages. Identification and quantification of metabolites indicated that 14 metabolites were located in the phenolic acid biosynthetic pathway. Among them, eight differentially accumulated metabolites were detected between every two developmental stages. Association analysis between metabolome and transcriptome showed that six differentially expressed structural genes were significantly positively correlated with metabolite accumulation and showed similar expression trends. A total of 128 transcription factors were identified that may be involved in the regulation of phenolic acid biosynthesis; these include 12 MYBs and 10 basic helix–loop–helix (bHLH) transcription factors. A regulatory network of the phenolic acid biosynthesis was established to visualize differentially expressed candidate genes that are involved in the accumulation of metabolites with significant differences. The results of this study contribute to the further understanding of phenolic acid biosynthesis during the development of leaves of C. paliurus.
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Affiliation(s)
- Weida Lin
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China; (W.L.); (H.L.)
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China; (Y.L.); (Q.L.)
| | - Yueling Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China; (Y.L.); (Q.L.)
| | - Qiuwei Lu
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China; (Y.L.); (Q.L.)
| | - Hongfei Lu
- College of Life Science, Zhejiang Sci-Tech University, Hangzhou 310018, China; (W.L.); (H.L.)
| | - Junmin Li
- Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou 318000, China; (Y.L.); (Q.L.)
- Correspondence:
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24
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Zhang L, Chen F, Zhang X, Li Z, Zhao Y, Lohaus R, Chang X, Dong W, Ho SYW, Liu X, Song A, Chen J, Guo W, Wang Z, Zhuang Y, Wang H, Chen X, Hu J, Liu Y, Qin Y, Wang K, Dong S, Liu Y, Zhang S, Yu X, Wu Q, Wang L, Yan X, Jiao Y, Kong H, Zhou X, Yu C, Chen Y, Li F, Wang J, Chen W, Chen X, Jia Q, Zhang C, Jiang Y, Zhang W, Liu G, Fu J, Chen F, Ma H, Van de Peer Y, Tang H. The water lily genome and the early evolution of flowering plants. Nature 2020; 577:79-84. [PMID: 31853069 PMCID: PMC7015852 DOI: 10.1038/s41586-019-1852-5] [Citation(s) in RCA: 199] [Impact Index Per Article: 49.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Accepted: 10/31/2019] [Indexed: 12/16/2022]
Abstract
Water lilies belong to the angiosperm order Nymphaeales. Amborellales, Nymphaeales and Austrobaileyales together form the so-called ANA-grade of angiosperms, which are extant representatives of lineages that diverged the earliest from the lineage leading to the extant mesangiosperms1-3. Here we report the 409-megabase genome sequence of the blue-petal water lily (Nymphaea colorata). Our phylogenomic analyses support Amborellales and Nymphaeales as successive sister lineages to all other extant angiosperms. The N. colorata genome and 19 other water lily transcriptomes reveal a Nymphaealean whole-genome duplication event, which is shared by Nymphaeaceae and possibly Cabombaceae. Among the genes retained from this whole-genome duplication are homologues of genes that regulate flowering transition and flower development. The broad expression of homologues of floral ABCE genes in N. colorata might support a similarly broadly active ancestral ABCE model of floral organ determination in early angiosperms. Water lilies have evolved attractive floral scents and colours, which are features shared with mesangiosperms, and we identified their putative biosynthetic genes in N. colorata. The chemical compounds and biosynthetic genes behind floral scents suggest that they have evolved in parallel to those in mesangiosperms. Because of its unique phylogenetic position, the N. colorata genome sheds light on the early evolution of angiosperms.
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Affiliation(s)
- Liangsheng Zhang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Fei Chen
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China ,0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Xingtan Zhang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Zhen Li
- 0000 0001 2069 7798grid.5342.0Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,0000000104788040grid.11486.3aVIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yiyong Zhao
- 0000 0001 0125 2443grid.8547.eState Key Laboratory of Genetic Engineering, Ministry of Education Key Laboratory of Biodiversity Sciences and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, China ,0000 0001 2097 4281grid.29857.31Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA USA
| | - Rolf Lohaus
- 0000 0001 2069 7798grid.5342.0Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,0000000104788040grid.11486.3aVIB Center for Plant Systems Biology, Ghent, Belgium
| | - Xiaojun Chang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China ,Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Wei Dong
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Simon Y. W. Ho
- 0000 0004 1936 834Xgrid.1013.3School of Life and Environmental Sciences, University of Sydney, Sydney, New South Wales Australia
| | - Xing Liu
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Aixia Song
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Junhao Chen
- 0000 0000 9152 7385grid.443483.cState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Wenlei Guo
- 0000 0000 9152 7385grid.443483.cState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Zhengjia Wang
- 0000 0000 9152 7385grid.443483.cState Key Laboratory of Subtropical Silviculture, School of Forestry and Biotechnology, Zhejiang A&F University, Hangzhou, China
| | - Yingyu Zhuang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Haifeng Wang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Xuequn Chen
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Juan Hu
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yanhui Liu
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Yuan Qin
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Kai Wang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
| | - Shanshan Dong
- Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Yang Liu
- Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China ,0000 0001 2034 1839grid.21155.32BGI-Shenzhen, Shenzhen, China
| | - Shouzhou Zhang
- Fairy Lake Botanical Garden, Shenzhen and Chinese Academy of Sciences, Shenzhen, China
| | - Xianxian Yu
- 0000 0000 8989 0732grid.412992.5School of Urban-Rural Planning and Landscape Architecture, Xuchang University, Xuchang, China
| | - Qian Wu
- 0000000119573309grid.9227.eKey Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China ,0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China
| | - Liangsheng Wang
- 0000000119573309grid.9227.eKey Laboratory of Plant Resources/Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China ,0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China
| | - Xueqing Yan
- 0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China ,0000000119573309grid.9227.eState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Yuannian Jiao
- 0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China ,0000000119573309grid.9227.eState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Hongzhi Kong
- 0000 0004 1797 8419grid.410726.6University of the Chinese Academy of Sciences, Beijing, China ,0000000119573309grid.9227.eState Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Xiaofan Zhou
- 0000 0000 9546 5767grid.20561.30Guangdong Province Key Laboratory of Microbial Signals and Disease Control, Integrative Microbiology Research Centre, South China Agricultural University, Guangzhou, China
| | - Cuiwei Yu
- Hangzhou Tianjing Aquatic Botanical Garden, Zhejiang Humanities Landscape Co. Ltd., Hangzhou, China
| | - Yuchu Chen
- Hangzhou Tianjing Aquatic Botanical Garden, Zhejiang Humanities Landscape Co. Ltd., Hangzhou, China
| | - Fan Li
- 0000 0004 1799 1111grid.410732.3National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Jihua Wang
- 0000 0004 1799 1111grid.410732.3National Engineering Research Center for Ornamental Horticulture, Key Laboratory for Flower Breeding of Yunnan Province, Floriculture Research Institute, Yunnan Academy of Agricultural Sciences, Kunming, China
| | - Wei Chen
- 0000 0001 0376 205Xgrid.411304.3Innovative Institute of Chinese Medicine and Pharmacy, Chengdu University of Traditional Chinese Medicine, Chengdu, China
| | - Xinlu Chen
- 0000 0001 2315 1184grid.411461.7Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Qidong Jia
- 0000 0001 2315 1184grid.411461.7Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN USA
| | - Chi Zhang
- 0000 0001 2315 1184grid.411461.7Department of Plant Sciences, University of Tennessee, Knoxville, TN USA
| | - Yifan Jiang
- 0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Wanbo Zhang
- 0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Guanhua Liu
- 0000 0001 0526 1937grid.410727.7Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Jianyu Fu
- 0000 0001 0526 1937grid.410727.7Key Laboratory of Tea Quality and Safety Control, Ministry of Agriculture and Rural Affairs, Tea Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China
| | - Feng Chen
- 0000 0000 9750 7019grid.27871.3bCollege of Horticulture, Nanjing Agricultural University, Nanjing, China ,0000 0001 2315 1184grid.411461.7Department of Plant Sciences, University of Tennessee, Knoxville, TN USA ,0000 0001 2315 1184grid.411461.7Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN USA
| | - Hong Ma
- 0000 0001 2097 4281grid.29857.31Department of Biology, Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA USA
| | - Yves Van de Peer
- 0000 0001 2069 7798grid.5342.0Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium ,0000000104788040grid.11486.3aVIB Center for Plant Systems Biology, Ghent, Belgium ,0000 0001 2107 2298grid.49697.35Centre for Microbial Ecology and Genomics, Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Haibao Tang
- 0000 0004 1760 2876grid.256111.0Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops, Key Laboratory of National Forestry and Grassland Administration for Orchid Conservation and Utilization, Fujian Agriculture and Forestry University, Fuzhou, China
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25
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Deng C, Li S, Feng C, Hong Y, Huang H, Wang J, Wang L, Dai S. Metabolite and gene expression analysis reveal the molecular mechanism for petal colour variation in six Centaurea cyanus cultivars. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 142:22-33. [PMID: 31255906 DOI: 10.1016/j.plaphy.2019.06.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 06/09/2019] [Accepted: 06/13/2019] [Indexed: 06/09/2023]
Abstract
Centaurea cyanus is a popular garden plant native to Europe. Although their petals show abundant colour variations, the flavonoid profiling and the potential molecular mechanisms remain unclear. In the present study, we collected six cornflower cultivars with white, pink, red, blue, mauve and black petals. Ultra-performance liquid chromatography coupled with photodiode array and tandem mass spectrometry (UPLC-MS/MS) was used to investigate the comparative profiling of flavonoids both qualitatively and quantitatively. Ten anthocyanins, six flavones and two flavonols were separated and putatively identified. Except for white petals without any anthocyanins, both pink and red flowers contained pelargonidin derivatives, whereas blue, mauve and black petals accumulated cyanidins. The expression patterns of genes involved in the flavonoid biosynthesis were performed by real-time quantitative reverse transcription-PCR. The anthocyanin biosynthetic pathway in white petals was inhibited starting from flavanone 3-hydroxylase, resulting in the absence of anthocyanin accumulation. The open reading frame of flavonoid 3'-hydroxylase in pink and red petals was truncated; this led to loss of a haem binding site, a conserved motif in the cytochrome P450 family, and loss of conversion from dihydrokaempferol to dihydroquercetin. The significantly higher expression of structural genes corresponding to the hyper-accumulation of flavonoids in black petals may play an important role in black coloration. Remarkably, the mauve and blue petals accumulated the same cyanidin derivative but contained apigenin with different modifications on the 4' position, which may cause the coloration differences. The results obtained in this study will provide insights into the mechanisms of vivid colour diversities in cornflower.
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Affiliation(s)
- Chengyan Deng
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Shanshan Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chengyong Feng
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yan Hong
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - He Huang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Jiaying Wang
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China
| | - Liangsheng Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, The Chinese Academy of Sciences, Beijing, 100093, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Silan Dai
- Beijing Key Laboratory of Ornamental Plants Germplasm Innovation & Molecular Breeding, National Engineering Research Center for Floriculture, Beijing Laboratory of Urban and Rural Ecological Environment and College of Landscape Architecture, Beijing Forestry University, Beijing, 100083, China.
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26
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Guodong R, Jianguo Z, Xiaoxia L, Ying L. Identification of putative genes for polyphenol biosynthesis in olive fruits and leaves using full-length transcriptome sequencing. Food Chem 2019; 300:125246. [PMID: 31357017 DOI: 10.1016/j.foodchem.2019.125246] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/22/2019] [Accepted: 07/23/2019] [Indexed: 10/26/2022]
Abstract
Olive (Olea europaea) is a rich source of valuable bioactive polyphenols, which has attracted widespread interest. In this study, we combined targeted metabolome, Pacbio ISOseq transcriptome, and Illumina RNA-seq transcriptome to investigate the association between polyphenols and gene expression in the developing olive fruits and leaves. A total of 12 main polyphenols were measured, and 122 transcripts of 17 gene families, 101 transcripts of 9 gene families, and 106 transcripts of 6 gene families that encode for enzymes involved in flavonoid, oleuropein, and hydroxytyrosol biosynthesis were separately identified. Additionally, 232 alternative splicing events of 18 genes related to polyphenol synthesis were analyzed. This is the first time that the third generations of full-length transcriptome technology were used to study the gene expression pattern of olive fruits and leaves. The results of transcriptome combined with targeted metabolome can help us better understand the polyphenol biosynthesis pathways in the olive.
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Affiliation(s)
- Rao Guodong
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Zhang Jianguo
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China; Collaborative Innovation Center of Sustainable Forestry in Southern China, Nanjing Forestry University, Nanjing 210037, China; Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China.
| | - Liu Xiaoxia
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
| | - Luo Ying
- State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
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An Integrated Analysis of the Rice Transcriptome and Metabolome Reveals Differential Regulation of Carbon and Nitrogen Metabolism in Response to Nitrogen Availability. Int J Mol Sci 2019; 20:ijms20092349. [PMID: 31083591 PMCID: PMC6539487 DOI: 10.3390/ijms20092349] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 05/07/2019] [Accepted: 05/08/2019] [Indexed: 01/19/2023] Open
Abstract
Nitrogen (N) is an extremely important macronutrient for plant growth and development. It is the main limiting factor in most agricultural production. However, it is well known that the nitrogen use efficiency (NUE) of rice gradually decreases with the increase of the nitrogen application rate. In order to clarify the underlying metabolic and molecular mechanisms of this phenomenon, we performed an integrated analysis of the rice transcriptome and metabolome. Both differentially expressed genes (DEGs) and metabolite Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that carbon and nitrogen metabolism is significantly affected by nitrogen availability. Further analysis of carbon and nitrogen metabolism changes in rice under different nitrogen availability showed that high N inhibits nitrogen assimilation and aromatic metabolism pathways by regulating carbon metabolism pathways such as the tricarboxylic acid (TCA) cycle and the pentose phosphate pathway (PPP). Under low nitrogen, the TCA cycle is promoted to produce more energy and α-ketoglutarate, thereby enhancing nitrogen transport and assimilation. PPP is also inhibited by low N, which may be consistent with the lower NADPH demand under low nitrogen. Additionally, we performed a co-expression network analysis of genes and metabolites related to carbon and nitrogen metabolism. In total, 15 genes were identified as hub genes. In summary, this study reveals the influence of nitrogen levels on the regulation mechanisms for carbon and nitrogen metabolism in rice and provides new insights into coordinating carbon and nitrogen metabolism and improving nitrogen use efficiency in rice.
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Jiang CH, Yao XF, Mi DD, Li ZJ, Yang BY, Zheng Y, Qi YJ, Guo JH. Comparative Transcriptome Analysis Reveals the Biocontrol Mechanism of Bacillus velezensis F21 Against Fusarium Wilt on Watermelon. Front Microbiol 2019; 10:652. [PMID: 31001229 PMCID: PMC6456681 DOI: 10.3389/fmicb.2019.00652] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 03/14/2019] [Indexed: 12/28/2022] Open
Abstract
The watermelon (Citrullus lanatus) is one of the most important horticultural crops for fruit production worldwide. However, the production of watermelon is seriously restricted by one kind of soilborne disease, Fusarium wilt, which is caused by Fusarium oxysporum f. sp. niveum (Fon). In this study, we identified an efficient PGPR strain B. velezensis F21, which could be used in watermelon production for Fon control. The results of biocontrol mechanisms showed that B. velezensis F21 could suppress the growth and spore germination of Fon in vitro. Moreover, B. velezensis F21 could also enhance plant basal immunity to Fon by increasing the expression of plant defense related genes and activities of some defense enzymes, such as CAT, POD, and SOD. To elucidate the detailed mechanisms regulating B. velezensis F21 biocontrol of Fusarium wilt in watermelon, a comparative transcriptome analysis using watermelon plant roots treated with B. velezensis F21 or sterile water alone and in combination with Fon inoculation was conducted. The transcriptome sequencing results revealed almost one thousand ripening-related differentially expressed genes (DEGs) in the process of B. velezensis F21 triggering ISR (induced systemic resistance) to Fon. In addition, the Gene Ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment indicated that numerous of transcription factors (TFs) and plant disease resistance genes were activated and validated by using quantitative real-time PCR (qRT-PCR), which showed significant differences in expression levels in the roots of watermelon with different treatments. In addition, genes involved in the MAPK signaling pathway and phytohormone signaling pathway were analyzed, and the results indicated that B. velezensis F21 could enhance plant disease resistance to Fon through the above related genes and phytohormone signal factors. Taken together, this study substantially expands transcriptome data resources and suggests a molecular framework for B. velezensis F21 inducing systemic resistance to Fon in watermelon. In addition, it also provides an effective strategy for the control of Fusarium wilt in watermelon.
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Affiliation(s)
- Chun-Hao Jiang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China.,State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, China
| | - Xie-Feng Yao
- Jiangsu Key Laboratory for Horticultural Crop Genetic Improvement, Institute of Vegetable Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Dan-Dan Mi
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Zi-Jie Li
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Bing-Ye Yang
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Ying Zheng
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
| | - Yi-Jun Qi
- Tsinghua Peking Center for Life Sciences, Center for Plant Biology, School of Life Sciences, Tsinghua University, Beijing, China
| | - Jian-Hua Guo
- Department of Plant Pathology, College of Plant Protection, Nanjing Agricultural University - Key Laboratory of Monitoring and Management of Crop Diseases and Pest Insects, Ministry of Agriculture - Engineering Center of Bioresource Pesticides in Jiangsu Province, Nanjing, China
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29
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Wu Q, Li PC, Zhang HJ, Feng CY, Li SS, Yin DD, Tian J, Xu WZ, Wang LS. Relationship between the flavonoid composition and flower colour variation in Victoria. PLANT BIOLOGY (STUTTGART, GERMANY) 2018; 20:674-681. [PMID: 29683547 DOI: 10.1111/plb.12835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Accepted: 04/17/2018] [Indexed: 05/07/2023]
Abstract
Victoria (Nymphaeaceae), an annual or perennial aquatic plant genus, contains only two species: V. amazonica (Poepp.) J. C. Sowerby and V. cruziana A. D. Orb. Both species have large floating leaves and variable flower colour. Both Victoria species are night bloomers, which have white petals on the first blooming night that then turn pink or ruby red on the second blooming day. The mechanism of the colour change of Victoria petals during anthesis is still unclear. In this study, flavonoids in Victoria petals of both species were evaluated and quantified by high-performance liquid chromatography with photodiode array detection (HPLC-DAD) and by ultra-performance liquid chromatography coupled with tandem mass spectrometry (UPLC-MS/MS) for the first time. In total, 14 flavonoids were detected in Victoria petals, including 4 anthocyanins and 10 flavonols. The flavonoid compositions differed across the two species, resulting in different colours between the inner and outer petals. With increased anthocyanin content across blooming days, the colour of Victoria flowers changed over time. The results of this study will improve understanding of the chemical mechanism of colour formation and lay the foundation for selective colour breeding in Victoria.
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Affiliation(s)
- Q Wu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - P-C Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - H-J Zhang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - C-Y Feng
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - S-S Li
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - D-D Yin
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, University of Chinese Academy of Sciences, Beijing, China
| | - J Tian
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - W-Z Xu
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - L-S Wang
- Key Laboratory of Plant Resources and Beijing Botanical Garden, Institute of Botany, Chinese Academy of Sciences, Beijing, China
- College of Agriculture, University of Chinese Academy of Sciences, Beijing, China
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30
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Okitsu N, Mizuno T, Matsui K, Choi SH, Tanaka Y. Molecular cloning of flavonoid biosynthetic genes and biochemical characterization of anthocyanin O-methyltransferase of Nemophila menziesii Hook. and Arn. PLANT BIOTECHNOLOGY (TOKYO, JAPAN) 2018; 35:9-16. [PMID: 31275032 PMCID: PMC6543731 DOI: 10.5511/plantbiotechnology.18.0104a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 01/04/2018] [Indexed: 05/27/2023]
Abstract
Blue flower color of Nemophila menziesii Hook. and Arn. is derived from a metalloanthocyanin, nemophilin, which comprises petunidin-3-O-[6-O-(trans-p-coumaroyl)-β-glucoside]-5-O-[6-O-(malonyl)-β-glucoside], apigenin-7-O-β-glucoside-4'-O-(6-O-malonyl)-β-glucoside, and Mg2+ and Fe3+ ions. The flavonoid biosynthetic pathway of nemophilin has not yet been characterized. RNA-Seq analysis of the petals yielded 61,491 contigs. These were searched using BLAST against petunia or torenia flavonoid biosynthetic proteins, which identified 11 putative full-length protein sequences belonging to the flavonoid biosynthetic pathway. RT-PCR using primers designed on the basis of these sequences yielded 14 sequences. Spatio-temporal transcriptome analysis indicated that genes involved in the early part of the pathway are strongly expressed during early-petal development and that those in the late part at late-flower opening stages, but they are rarely expressed in leaves. Flavanone 3-hydroxylase and flavonoid 3',5'-hydroxylase cDNAs were successfully expressed in yeast to confirm their activities. Recombinant anthocyanin O-methyltransferase cDNA (NmAMT6) produced using Escherichia coli was subjected to biochemical characterization. Km of NmAMT6 toward delphinidin 3-O-glucoside was 22 µM, which is comparable with Km values of anthocyanin O-methyltransferases from other plants. With delphinidin 3-O-glucoside as substrate, NmAMT6 almost exclusively yielded petunidin 3-O-glucoside rather than malvidin 3-O-glucoside. This specificity is consistent with the anthocyanin composition of Nemophila petals.
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Affiliation(s)
- Naoko Okitsu
- Research Institute, Suntory Global Innovation Center Ltd., Soraku-Gun, Kyoto 619-0284, Japan
| | - Takayuki Mizuno
- Department of Botany, National Museum of Nature and Science, Tsukuba, Ibaraki 305-0005, Japan
| | - Keisuke Matsui
- Research Institute, Suntory Global Innovation Center Ltd., Soraku-Gun, Kyoto 619-0284, Japan
| | - Sun Hee Choi
- Graduate School of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Yoshikazu Tanaka
- Research Institute, Suntory Global Innovation Center Ltd., Soraku-Gun, Kyoto 619-0284, Japan
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Chen F, Liu X, Yu C, Chen Y, Tang H, Zhang L. Water lilies as emerging models for Darwin's abominable mystery. HORTICULTURE RESEARCH 2017; 4:17051. [PMID: 28979789 PMCID: PMC5626932 DOI: 10.1038/hortres.2017.51] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2017] [Revised: 06/30/2017] [Accepted: 07/26/2017] [Indexed: 05/02/2023]
Abstract
Water lilies are not only highly favored aquatic ornamental plants with cultural and economic importance but they also occupy a critical evolutionary space that is crucial for understanding the origin and early evolutionary trajectory of flowering plants. The birth and rapid radiation of flowering plants has interested many scientists and was considered 'an abominable mystery' by Charles Darwin. In searching for the angiosperm evolutionary origin and its underlying mechanisms, the genome of Amborella has shed some light on the molecular features of one of the basal angiosperm lineages; however, little is known regarding the genetics and genomics of another basal angiosperm lineage, namely, the water lily. In this study, we reviewed current molecular research and note that water lily research has entered the genomic era. We propose that the genome of the water lily is critical for studying the contentious relationship of basal angiosperms and Darwin's 'abominable mystery'. Four pantropical water lilies, especially the recently sequenced Nymphaea colorata, have characteristics such as small size, rapid growth rate and numerous seeds and can act as the best model for understanding the origin of angiosperms. The water lily genome is also valuable for revealing the genetics of ornamental traits and will largely accelerate the molecular breeding of water lilies.
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Affiliation(s)
- Fei Chen
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Xing Liu
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Cuiwei Yu
- Zhejiang Humanities Landscape Co., LTD, Hangzhou 310030, China
| | - Yuchu Chen
- Zhejiang Humanities Landscape Co., LTD, Hangzhou 310030, China
| | - Haibao Tang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Liangsheng Zhang
- Center for Genomics and Biotechnology; State Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou 350002, China
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