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Savoi S, Santiago A, Orduña L, Matus JT. Transcriptomic and metabolomic integration as a resource in grapevine to study fruit metabolite quality traits. FRONTIERS IN PLANT SCIENCE 2022; 13:937927. [PMID: 36340350 PMCID: PMC9630917 DOI: 10.3389/fpls.2022.937927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 09/09/2022] [Indexed: 06/16/2023]
Abstract
Transcriptomics and metabolomics are methodologies being increasingly chosen to perform molecular studies in grapevine (Vitis vinifera L.), focusing either on plant and fruit development or on interaction with abiotic or biotic factors. Currently, the integration of these approaches has become of utmost relevance when studying key plant physiological and metabolic processes. The results from these analyses can undoubtedly be incorporated in breeding programs whereby genes associated with better fruit quality (e.g., those enhancing the accumulation of health-promoting compounds) or with stress resistance (e.g., those regulating beneficial responses to environmental transition) can be used as selection markers in crop improvement programs. Despite the vast amount of data being generated, integrative transcriptome/metabolome meta-analyses (i.e., the joint analysis of several studies) have not yet been fully accomplished in this species, mainly due to particular specificities of metabolomic studies, such as differences in data acquisition (i.e., different compounds being investigated), unappropriated and unstandardized metadata, or simply no deposition of data in public repositories. These meta-analyses require a high computational capacity for data mining a priori, but they also need appropriate tools to explore and visualize the integrated results. This perspective article explores the universe of omics studies conducted in V. vinifera, focusing on fruit-transcriptome and metabolome analyses as leading approaches to understand berry physiology, secondary metabolism, and quality. Moreover, we show how omics data can be integrated in a simple format and offered to the research community as a web resource, giving the chance to inspect potential gene-to-gene and gene-to-metabolite relationships that can later be tested in hypothesis-driven research. In the frame of the activities promoted by the COST Action CA17111 INTEGRAPE, we present the first grapevine transcriptomic and metabolomic integrated database (TransMetaDb) developed within the Vitis Visualization (VitViz) platform (https://tomsbiolab.com/vitviz). This tool also enables the user to conduct and explore meta-analyses utilizing different experiments, therefore hopefully motivating the community to generate Findable, Accessible, Interoperable and Reusable (F.A.I.R.) data to be included in the future.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Grugliasco, Italy
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, Spain
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Peng Y, Gu X, Zhou Q, Huang J, Liu Z, Zhou Y, Zheng Y. Molecular and physiologic mechanisms of advanced ripening by trunk girdling at early veraison of 'Summer Black' grape. FRONTIERS IN PLANT SCIENCE 2022; 13:1012741. [PMID: 36330263 PMCID: PMC9623158 DOI: 10.3389/fpls.2022.1012741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2022] [Accepted: 09/23/2022] [Indexed: 06/16/2023]
Abstract
Although the effects of girdling on grape berry development have been widely studied, the underlying mechanisms are poorly understood, especially at the molecular level. This study investigated the effect of trunk girdling on grape (Vitis L.) berry maturation. Girdling was performed on 5-year-old 'Summer Black' grapevines at early veraison, and transcriptional and physiologic analyses were performed. Trunk girdling promoted sugar accumulation and color development in berries and accelerated berry ripening by 25 days. Genes related to sucrose cleavage and polysaccharide degradation were upregulated at the transcriptional level, which was associated with increased monosaccharide accumulation and berry softening. Anthocyanin biosynthesis and accumulation were also enhanced by trunk girdling through the upregulation of anthocyanin biosynthesis genes including phenylalanine ammonia-lyase and UDP-glucose:flavonoid 3-O-glucosyltransferase (UFGT). The increased expression of two VvUFGT genes was accompanied by the upregulation of VvMYBA2 under girdling. The upregulation of genes involved in ethylene biosynthesis and hormone (abscisic acid and brassinosteroid) responses and downregulation of genes involved in indoleacetic acid biosynthesis and response may have also promoted berry ripening in the girdling group. A total of 120 differentially expressed transcription factor genes from 29 gene families including MYB, ERF, and MYB-related were identified in the girdling group, which may participate in the regulation of berry development and ripening. These results provide molecular-level insight into the positive effects of trunk girdling on berry development in grapes.
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Affiliation(s)
- Yanjie Peng
- College of Life Science, Leshan Normal University, Leshan, China
- Institution of Biodiversity Conservation and Utilization in Mount Emei, Leshan Normal University, Leshan, China
| | - Xingjia Gu
- College of Life Science, Leshan Normal University, Leshan, China
| | - Qi Zhou
- Justices, Equity, Diversity, and Inclusion Department, California Association of Resource Conservation Districts, Folsom, CA, United States
| | - Jiao Huang
- College of Life Science, Leshan Normal University, Leshan, China
- Institution of Biodiversity Conservation and Utilization in Mount Emei, Leshan Normal University, Leshan, China
| | - Zhong Liu
- College of Life Science, Leshan Normal University, Leshan, China
- Institution of Biodiversity Conservation and Utilization in Mount Emei, Leshan Normal University, Leshan, China
| | - Yong Zhou
- College of Life Science, Leshan Normal University, Leshan, China
- Institution of Biodiversity Conservation and Utilization in Mount Emei, Leshan Normal University, Leshan, China
- Academy of Mount Emei, Leshan Normal University, Leshan, China
| | - Ying Zheng
- Research Institution of Industrial Crop, Leshan Academy of Agricultural Sciences, Leshan, China
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Gong P, Kang J, Sadeghnezhad E, Bao R, Ge M, Zhuge Y, Shangguan L, Fang J. Transcriptional Profiling of Resistant and Susceptible Cultivars of Grapevine ( Vitis L.) Reveals Hypersensitive Responses to Plasmopara viticola. Front Microbiol 2022; 13:846504. [PMID: 35572700 PMCID: PMC9097084 DOI: 10.3389/fmicb.2022.846504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 03/24/2022] [Indexed: 11/13/2022] Open
Abstract
Grapevine downy mildew is the most serious disease of grapevine cultivars that affects the rate of resistance/susceptibility to Plasmopara viticola. In this study, we used the susceptible cultivar "Zitian Seedless" and the resistant cultivar "Kober 5BB" as materials to determine the transcriptome differences and phenotypes of the leaves after inoculation with downy mildew. The differences in microstructures and molecular levels were compared and analyzed. Fluorescence staining and microscopic observations confirmed that hypersensitive cell death occurred around the stomata in "Kober 5BB" infected by downy mildew zoospores. Meanwhile, transcriptomic profiling indicated that there were 11,713 and 6,997 gene expression differences between the resistant and susceptible cultivars at 72 h after inoculation when compared to control (0 h), respectively. The differentially expressed genes of the two cultivars are significantly enriched in different pathways, including response to plant-pathogen interaction, mitogen-activated protein kinase (MAPK) signaling pathway, plant hormone signal transduction, phenylpropanoid, and flavonoid biosynthesis. Furthermore, the results of functional enrichment analysis showed that H2O2 metabolism, cell death, reactive oxygen response, and carbohydrate metabolism are also involved in the defense response of "Kober 5BB," wherein a total of 322 key genes have been identified. The protein interaction network showed that metacaspases (MCAs), vacuolar processing enzymes (VPEs), and Papain-like cysteine proteases (PLCPs) play an important role in the execution of hypersensitive responses (HR). In conclusion, we demonstrated that HR cell death is the key strategy in the process of grape defense against downy mildew, which may be mediated or activated by Caspase-like proteases.
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Affiliation(s)
- Peijie Gong
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jun Kang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ehsan Sadeghnezhad
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Ruoxuan Bao
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Mengqing Ge
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Yaxian Zhuge
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Lingfei Shangguan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, China
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House MA, Young LW, Robinson SJ, Booker HM. Transcriptomic Analysis of Early Flowering Signals in ‘Royal’ Flax. PLANTS 2022; 11:plants11070860. [PMID: 35406840 PMCID: PMC9002848 DOI: 10.3390/plants11070860] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Revised: 03/11/2022] [Accepted: 03/16/2022] [Indexed: 11/29/2022]
Abstract
Canada is one of the world’s leading producers and exporters of flax seed, with most production occurring in the Prairie Provinces. However, reduced season length and risk of frost restricts production in the northern grain belt of the Canadian Prairies. To expand the growing region of flax and increase production in Canada, flax breeders need to develop earlier-flowering varieties capable of avoiding the risk of abiotic stress. A thorough understanding of flowering control of flax is essential for the efficient breeding of such lines. We identified 722 putative flax flowering genes that span all major flowering-time pathways. Frequently, we found multiple flax homologues for a single Arabidopsis flowering gene. We used RNA sequencing to quantify the expression of genes in the shoot apical meristem (SAM) at 10, 15, 19, and 29 days after planting (dap) using the ‘Royal’ cultivar. We observed the expression of 80% of putative flax flowering genes and the differential expression of only 30%; these included homologues of major flowering regulators, such as SOC1, FUL, and AP1. We also found enrichment of differentially expressed genes (DEGs) in transcription factor (TF) families involved in flowering. Finally, we identified the candidates’ novel flowering genes amongst the uncharacterized flax genes. Our transcriptomic dataset provides a useful resource for investigating the regulatory control of the transition to flowering in flax and for the breeding of northern-adapted varieties.
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Affiliation(s)
- Megan A. House
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Lester W. Young
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
| | - Stephen J. Robinson
- Agriculture and Agri-Food Canada, Saskatoon Research and Development Centre, 107 Science Place, Saskatoon, SK S7N 0X2, Canada;
| | - Helen M. Booker
- Department of Plant Sciences, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada; (M.A.H.); (L.W.Y.)
- Department of Plant Agriculture, Ontario Agricultural College, University of Guelph, 50 Stone Rd E, Guelph, ON N1G 2W1, Canada
- Correspondence: ; Tel.: +1-519-824-4120 (ext. 56829)
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Wang P, Ge M, Yu A, Song W, Fang J, Leng X. Effects of ethylene on berry ripening and anthocyanin accumulation of 'Fujiminori' grape in protected cultivation. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2022; 102:1124-1136. [PMID: 34329497 DOI: 10.1002/jsfa.11449] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Revised: 05/19/2021] [Accepted: 07/30/2021] [Indexed: 06/13/2023]
Abstract
BACKGROUND Although the grape berries are deliberated as a non-climacteric fruit, ethylene seems to be involved in grape berry ripening. However, the precise role of ethylene in regulating the ripening of non-climacteric fruits is poorly understood. RESULTS Exogenous ethephon (ETH) can stimulate the concentration of internal ethylene and accelerate the accumulation of anthocyanins in berries of 'Fujiminori', including malvidin-, delphinidin-, and petunidin-derivatives (3',4',5'-trihydroxylated anthocyanins) and cyanidin-derivatives (3',4'-dihydroxylated anthocyanins). The content of 3',4',5'-trihydroxylated anthocyanins was extremely higher than 3',4'-dihydroxylated anthocyanins, and ethylene did not affect the composition of anthocyanins in grape. Furthermore, we observed the expression of anthocyanin structural and regulatory genes as well as ethylene biosynthesis and response genes in response to ETH treatment. The anthocyanins accumulation is significantly associated with increased expression of anthocyanin structural (VvPAL, Vv4CH, VvCHS, VvCHI, VvF3H, and VvUFGT) and regulatory genes (VvMYBA1, VvMYBA2, and VvMYBA3), which persisted over the 12 days. In addition, exogenous ETH affected the endogenous ethylene biosynthesis (VvACO2 and VvACO4) and the downstream ethylene regulatory network (VvERS1, VvETR2, VvCTR1, and VvERF005). CONCLUSIONS These findings bring new insights into the physiological and molecular function of ethylene during berry development and ripening in grapes. © 2021 Society of Chemical Industry.
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Affiliation(s)
- Peipei Wang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Mengqing Ge
- College of Horticulture, Nanjing Agricultural University, Nanjing, China
| | - Aishui Yu
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Wei Song
- Fruit Industry Development and Service Center of Qixia, Yantai, China
| | - Jinggui Fang
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
| | - Xiangpeng Leng
- College of Horticulture, Qingdao Agricultural University, Qingdao, China
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Yin X, Gao Y, Song S, Hassani D, Lu J. Identification, characterization and functional analysis of grape (Vitis vinifera L.) mitochondrial transcription termination factor (mTERF) genes in responding to biotic stress and exogenous phytohormone. BMC Genomics 2021; 22:136. [PMID: 33637035 PMCID: PMC7913399 DOI: 10.1186/s12864-021-07446-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2020] [Accepted: 02/15/2021] [Indexed: 11/29/2022] Open
Abstract
Background Mitochondrial transcription termination factor (mTERF) is a large gene family which plays a significant role during plant growth under various environmental stresses. However, knowledge of mTERF genes in grapevine (Vitis L.) is limited. Results In this research, a comprehensive analysis of grape mTERF (VvmTERF) genes, including chromosome locations, phylogeny, protein motifs, gene structures, gene duplications, synteny analysis and expression profiles, was conducted. As a result, a total of 25 mTERF genes were identified from the grape genome, which are distributed on 13 chromosomes with diverse densities and segmental duplication events. The grape mTERF gene family is classified into nine clades based on phylogenetic analysis and structural characteristics. These VvmTERF genes showed differential expression patterns in response to multiple phytohormone treatments and biotic stresses, including treatments with abscisic acid and methyl jasmonate, and inoculation of Plasmopara viticola and Erysiphe necator. Conclusions These research findings, as the first of its kind in grapevine, will provide useful information for future development of new stress tolerant grape cultivars through genetic manipulation of VvmTERF genes. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07446-z.
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Affiliation(s)
- Xiangjing Yin
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yu Gao
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Shiren Song
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Danial Hassani
- Joint International Research Laboratory of Metabolic and Developmental Sciences, Key Laboratory of Urban Agriculture (South) Ministry of Agriculture, Plant Biotechnology Research Center, Fudan-SJTU-Nottingham Plant Biotechnology R&D Center, School of Agriculture and Biology, Shanghai Jiao Tong University (SJTU), Shanghai, 200240, China
| | - Jiang Lu
- Center for Viticulture and Enology, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, 200240, China.
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Zhong H, Zhang F, Pan M, Wu X, Zhang W, Han S, Xie H, Zhou X, Wang M, Ai CM, He T. Comparative phenotypic and transcriptomic analysis of Victoria and flame seedless grape cultivars during berry ripening. FEBS Open Bio 2020; 10:2616-2630. [PMID: 33090714 PMCID: PMC7714085 DOI: 10.1002/2211-5463.12996] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 09/07/2020] [Accepted: 10/05/2020] [Indexed: 11/18/2022] Open
Abstract
Grape berry development is a highly coordinated and intricate process. Herein, we analyzed the phenotypic and transcriptomic patterns of Victoria (VT) and Flame Seedless (FS) grape varieties during berry development. Physiological analysis and transcriptomic sequencing were performed at four berry developmental phases. VT berry size was comparatively larger to the FS variety. At maturity, 80 days postanthesis (DPA), the FS soluble solids were 61.8% higher than VT. Further, 4889 and 2802 differentially expressed genes were identified from VT and FS 40 DPA to 80 DPA development stages, respectively. VvSWEET15, VvHXK, and MYB44 genes were up‐regulated during the postanthesis period, while bHLH14, linked to glucose metabolism, was gradually down‐regulated during berry development. These genes may have significant roles in berry development, ripening, and sugar accumulation.
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Affiliation(s)
- Haixia Zhong
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, China.,Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Fuchun Zhang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Mingqi Pan
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xinyu Wu
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Wen Zhang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Shouan Han
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Hui Xie
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Xiaoming Zhou
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Min Wang
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Caikasimu Maikeer Ai
- Institute of Horticulture Crops, Xinjiang Academy of Agricultural Sciences, Urumqi, China
| | - Tianming He
- College of Forestry and Horticulture, Xinjiang Agricultural University, Urumqi, China
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Shangguan L, Chen M, Fang X, Xie Z, Gong P, Huang Y, Wang Z, Fang J. Comparative transcriptome analysis provides insight into regulation pathways and temporal and spatial expression characteristics of grapevine (Vitis vinifera) dormant buds in different nodes. BMC PLANT BIOLOGY 2020; 20:390. [PMID: 32842963 PMCID: PMC7449092 DOI: 10.1186/s12870-020-02583-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Accepted: 07/29/2020] [Indexed: 05/31/2023]
Abstract
BACKGROUND Bud dormancy is a strategic mechanism plants developed as an adaptation to unfavorable environments. The grapevine (Vitis vinifera) is one of the most ancient fruit vine species and vines are planted all over the world due to their great economic benefits. To better understand the molecular mechanisms underlying bud dormancy between adjacent months, the transcriptomes of 'Rosario Bianco' grape buds of 6 months and three nodes were analyzed using RNA-sequencing technology and pair-wise comparison. From November to April of the following year, pairwise comparisons were conducted between adjacent months. RESULTS A total of 11,647 differentially expressed genes (DEGs) were obtained from five comparisons. According to the results of cluster analysis of the DEG profiles and the climatic status of the sampling period, the 6 months were divided into three key processes (November to January, January to March, and March to April). Pair-wise comparisons of DEG profiles of adjacent months and three main dormancy processes showed that the whole grapevine bud dormancy period was mainly regulated by the antioxidant system, secondary metabolism, cell cycle and division, cell wall metabolism, and carbohydrates metabolism. Additionally, several DEGs, such as VvGA2OX6 and VvSS3, showed temporally and spatially differential expression patterns, which normalized to a similar trend during or before April. CONCLUSION Considering these results, the molecular mechanisms underlying bud dormancy in the grapevine can be hypothesized, which lays the foundation for further research.
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Affiliation(s)
- Lingfei Shangguan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China.
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China.
| | - Mengxia Chen
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China
| | - Xiang Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China
| | - Zhenqiang Xie
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China
- Department of Agriculture and Horticulture, Jiangsu Vocational College of Agriculture and Forestry, Jurong, 212499, Jiangsu Province, China
| | - Peijie Gong
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China
| | - Yuxiang Huang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China
| | - Zicheng Wang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095, Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095, China
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Wang W, Bai Y, Koilkonda P, Guan L, Zhuge Y, Wang X, Liu Z, Jia H, Wang C, Fang J. Genome-wide identification and characterization of gibberellin metabolic and signal transduction (GA MST) pathway mediating seed and berry development (SBD) in grape (Vitis vinifera L.). BMC PLANT BIOLOGY 2020; 20:384. [PMID: 32825825 PMCID: PMC7441673 DOI: 10.1186/s12870-020-02591-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 08/12/2020] [Indexed: 05/13/2023]
Abstract
BACKGROUND Grape is highly sensitive to gibberellin (GA), which is crucial during seed and berry development (SBD) either by itself or by interacting with other hormones, such as auxin, Abscisic acid (ABA), and Cytokinin (CK). However, no systematic analysis of GA metabolic and signal transduction (MST) pathway has been undertaken in grapevine. RESULTS In this study, total endogenous GA3 content significantly decreased during SBD, and a total of 48 known genes in GA metabolic (GAM; 31) and signal transduction (ST; 17) pathways were identified in this process. In the GAM pathway, out of 31 genes, VvGA20ox1-1, VvGA3ox4-1, and VvGA2ox1-1 may be the major factors interacting at the green-berry stage (GBS) accompanied with higher accumulation rate. GA biosynthesis was greater than GA inactivation at GBS, confirming the importance of seeds in GA synthesis. The visible correlation between endogenous GA3 content and gene expression profiles suggested that the transcriptional regulation of GA biosynthesis pathway genes was a key mechanism of GA accumulation at the stone-hardening stage (SHS). Interestingly, we observed a negative feedback regulation between VvGA3oxs-VvGAI1-4, VvGA2oxs-VvGAI1-4, and VvGID1B-VvGAI1-4 in maintaining the balance of GA3 content in berries. Moreover, 11 miRNAs may be involved in the modulation of GA MST pathway by mediating their target genes, such as VvGA3ox, VvGID1B, and VvGAMYB. Many genes in auxin, ABA, and CK MST pathways were further identified and found to have a special pattern in the berry, and the crosstalk between GA and these hormones may modulate the complex process during SBD through the interaction gene network of the multihormone pathway. Lastly, based on the expression characterization of multihormone MST pathway genes, a proposed model of the GA-mediated multihormone regulatory network during SBD was proposed. CONCLUSIONS Our results provided novel insights into GA-mediated regulatory networks during SBD in grape. The complexity of GA-mediated multihormone ST in SBD was also elucidated, thereby providing valuable information for future functional characterizations of specific genes in grape.
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Affiliation(s)
- Wenran Wang
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
- China Agricultural University, College of Horticulture, Beijing, 100193 China
| | - Yunhe Bai
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Padmalatha Koilkonda
- Division of Crop Sciences, ICAR-Central Research Institute for Dryland Agriculture, Santoshnagar, Hyderabad, Telangana 500059 India
| | - Le Guan
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Yaxian Zhuge
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Xicheng Wang
- Institute of Pomology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 China
| | - Zhongjie Liu
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Haifeng Jia
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Chen Wang
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
| | - Jinggui Fang
- Nanjing Agricultural University, College of Horticulture, Nanjing, 210095 PR China
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Shangguan L, Fang X, Jia H, Chen M, Zhang K, Fang J. Characterization of DNA methylation variations during fruit development and ripening of Vitis vinifera (cv. 'Fujiminori'). PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2020; 26:617-637. [PMID: 32255927 PMCID: PMC7113366 DOI: 10.1007/s12298-020-00759-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/21/2019] [Accepted: 01/03/2020] [Indexed: 05/04/2023]
Abstract
The fruit is the most important economical organ in the grape; accordingly, to investigate the grapevine genomic methylation landscape and examine its functional significance during fruit development, we generated whole genome DNA methylation maps for various developmental stages in the fruit of grapevine. In this study, thirteen DNA methylation-related genes and their expression profiles were identified and analyzed. The methylation levels for mC, mCG, mCHG, and mCHH contexts in 65 days after flowering (65DAF) fruit (véraison stage) were higher than those in 40DAF (green stage) and 90DAF (mature stage) fruits. Relative to methylation in the mC context, methylation levels in the mCHH context were higher than those of mCG and mCHG. The DNA methylation level in the ncRNA regions was significantly higher than that in exon, gene, intron, and mRNA regions. The differentially methylated regions (DMRs) and differentially methylated promoters (DMPs) in 65DAF_vs_40DAF were both higher than those in 90DAF_vs_65DAF and 90DAF_vs_40DAF. Most DMRs (or DMPs) were involved in metabolic processes and cell processes, binding, and catalytic activity. These results indicated that DNA methylation represses gene expression during grape fruit development, and it broadens our understanding of the landscape and function of DNA methylation in grapevine genomes.
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Affiliation(s)
- Lingfei Shangguan
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Xiang Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
| | - Haifeng Jia
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Mengxia Chen
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Kekun Zhang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
| | - Jinggui Fang
- Department of Horticulture, Nanjing Agricultural University, Nanjing, 210095 Jiangsu Province, China
- Fruit Crop Genetic Improvement and Seedling Propagation Engineering Center of Jiangsu Province, Nanjing, 210095 China
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11
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Wei H, Wang P, Chen J, Li C, Wang Y, Yuan Y, Fang J, Leng X. Genome-wide identification and analysis of B-BOX gene family in grapevine reveal its potential functions in berry development. BMC PLANT BIOLOGY 2020; 20:72. [PMID: 32054455 PMCID: PMC7020368 DOI: 10.1186/s12870-020-2239-3] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2019] [Accepted: 01/03/2020] [Indexed: 05/26/2023]
Abstract
BACKGROUND The B-BOX (BBX) proteins are the class of zinc-finger transcription factors and can regulate plant growth, development, and endure stress response. In plants, the BBX gene family has been identified in Arabidopsis, rice, and tomato. However, no systematic analysis of BBX genes has been undertaken in grapevine. RESULTS In this study, 24 grapevine BBX (VvBBX) genes were identified by comprehensive bioinformatics analysis. Subsequently, the chromosomal localizations, gene structure, conserved domains, phylogenetic relationship, gene duplication, and cis-acting elements were analyzed. Phylogenetic analysis divided VvBBX genes into five subgroups. Numerous cis-acting elements related to plant development, hormone and/or stress responses were identified in the promoter of the VvBBX genes. The tissue-specific expressional dynamics of VvBBX genes demonstrated that VvBBXs might play important role in plant growth and development. The transcript analysis from transcriptome data and qRT-PCR inferred that 11 VvBBX genes were down-regulated in different fruit developmental stages, while three VvBBX genes were up-regulated. It is also speculated that VvBBX genes might be involved in multiple hormone signaling (ABA, ethylene, GA3, and CPPU) as transcriptional regulators to modulate berry development and ripening. VvBBX22 seems to be responsive to multiple hormone signaling, including ABA, ethylene GA3, and CPPU. Some VvBBX genes were strongly induced by Cu, salt, waterlogging, and drought stress treatment. Furthermore, the expression of VvBBX22 proposed its involvement in multiple functions, including leaf senescence, abiotic stress responses, fruit development, and hormone response. CONCLUSIONS Our results will provide the reference for functional studies of BBX gene family, and highlight its functions in grapevine berry development and ripening. The results will help us to better understand the complexity of the BBX gene family in abiotic stress tolerance and provide valuable information for future functional characterization of specific genes in grapevine.
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Affiliation(s)
- Hongru Wei
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
| | - Peipei Wang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
| | - Jianqing Chen
- College of Horticulture, Fujian Agriculture and Forestry University, Fuzhou, 350002 China
| | - Changjun Li
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
| | - Yongzhang Wang
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
| | - Yongbing Yuan
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Nanjing, 210095 China
- Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
| | - Xiangpeng Leng
- Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
- Institute of Grape Science and Engineering, College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 People’s Republic of China
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12
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Leng X, Wei H, Xu X, Ghuge SA, Jia D, Liu G, Wang Y, Yuan Y. Genome-wide identification and transcript analysis of TCP transcription factors in grapevine. BMC Genomics 2019; 20:786. [PMID: 31664916 PMCID: PMC6819353 DOI: 10.1186/s12864-019-6159-2] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/09/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND The plant-specific TCP transcription factors play different functions in multiple processes of plant growth and development. TCP family genes have been identified in several plant species, but no comprehensive analysis of the TCP family in grapevine has been undertaken to date, especially their roles in fruit development. RESULTS A total of 18 non-redundant grapevine TCP (VvTCP) genes distributing on 11 chromosomes were identified. Phylogenetic and structural analysis showed that VvTCP genes were divided into two main classes - class I and class II. The Class II genes were further classified into two subclasses, the CIN subclass and the CYC/TB1 subclass. Segmental duplication was a predominant duplication event which caused the expansion of VvTCP genes. The cis-acting elements analysis and tissue-specific expression patterns of VvTCP genes demonstrated that these VvTCP genes might play important roles in plant growth and development. Expression patterns of VvTCP genes during fruit development and ripening were analyzed by RNA-Seq and qRT-PCR. Among them, 11 VvTCP genes were down-regulated during different fruit developmental stages, while only one VvTCP genes were up-regulated, suggesting that most VvTCP genes were probably related to early development in grapevine fruit. Futhermore, the expression of most VvTCP genes can be inhibited by drought and waterlogging stresses. CONCLUSIONS Our study establishes the first genome-wide analysis of the grapevine TCP gene family and provides valuable information for understanding the classification and functions of the TCP genes in grapevine.
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Affiliation(s)
- Xiangpeng Leng
- 0000 0000 9526 6338grid.412608.9Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Qingdao, 266109 People’s Republic of China
| | - Hongru Wei
- 0000 0000 9526 6338grid.412608.9Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Qingdao, 266109 People’s Republic of China
| | - Xiaozhao Xu
- 0000 0000 9526 6338grid.412608.9Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Qingdao, 266109 People’s Republic of China
| | - Sandip A. Ghuge
- 0000 0001 0465 9329grid.410498.0Institute of Plant Sciences, The Volcani Center, Agricultural Research Organization, 50250 Bet-Dagan, Israel
| | - Dongjie Jia
- 0000 0000 9526 6338grid.412608.9Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Qingdao, 266109 People’s Republic of China
| | - Gengsen Liu
- 0000 0000 9526 6338grid.412608.9Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Qingdao, 266109 People’s Republic of China
| | - Yongzhang Wang
- 0000 0000 9526 6338grid.412608.9Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Qingdao, 266109 People’s Republic of China
| | - Yongbing Yuan
- 0000 0000 9526 6338grid.412608.9Qingdao Key Lab of Modern Agriculture Quality and Safety Engineering, College of Horticulture, Qingdao Agricultural University, Changcheng Road 700, Qingdao, 266109 People’s Republic of China
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13
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Bhatia G, Sharma S, Upadhyay SK, Singh K. Long Non-coding RNAs Coordinate Developmental Transitions and Other Key Biological Processes in Grapevine. Sci Rep 2019; 9:3552. [PMID: 30837504 PMCID: PMC6401051 DOI: 10.1038/s41598-019-38989-7] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 01/15/2019] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are transcripts >200 nucleotides that have prominently surfaced as dynamic regulatory molecules. Using computational approaches, we identified and characterized 56,441 lncRNAs in grapevine (Vitis vinifera) by harnessing RNA-seq data from 10 developmental stages of leaf, inflorescence, and berry tissues. We conducted differential expression analysis and determined tissue- and developmental stage-specificity of lncRNAs in grapevine, which indicated their spatiotemporal regulation. Functional annotation using co-expression analysis revealed their involvement in regulation of developmental transitions in sync with transcription factors (TFs). Further, pathway enrichment analysis revealed lncRNAs associated with biosynthetic and secondary metabolic pathways. Additionally, we identified 115, 560, and 133 lncRNAs as putative miRNA precursors, targets, and endogenous target mimics, respectively, which provided an insight into the interplay of regulatory RNAs. We also explored lncRNA-mediated regulation of extra-chromosomal genes-i.e., mitochondrial and chloroplast coding sequences and observed their involvement in key biological processes like 'photosynthesis' and 'oxidative phosphorylation'. In brief, these transcripts coordinate important biological functions via interactions with both coding and non-coding RNAs as well as TFs in grapevine. Our study would facilitate future experiments in unraveling regulatory mechanisms of development in this fruit crop of economic importance.
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Affiliation(s)
- Garima Bhatia
- Department of Biotechnology, Panjab University, 160014, Chandigarh, India
| | - Shailesh Sharma
- National Institute of Animal Biotechnology (NIAB), D. No. 1-121/1, 4th and 5th Floors, Axis Clinicals Building, Opp. to Talkie Town, Miyapur, Hyderabad, 500 049, Telangana, India
| | | | - Kashmir Singh
- Department of Biotechnology, Panjab University, 160014, Chandigarh, India.
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14
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Kou M, Liu YJ, Li ZY, Zhang YG, Tang W, Yan H, Wang X, Chen XG, Su ZX, Arisha MH, Li Q, Ma DF. A novel glutathione S-transferase gene from sweetpotato, IbGSTF4, is involved in anthocyanin sequestration. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2019; 135:395-403. [PMID: 30634134 DOI: 10.1016/j.plaphy.2018.12.028] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/26/2018] [Accepted: 12/30/2018] [Indexed: 05/11/2023]
Abstract
Anthocyanins are synthesized by multi-enzyme complexes localized at the cytoplasmic surface of the endoplasmic reticulum (synthesis site), and transported to the destination site, the vacuole. Three mechanisms for the vacuolar accumulation of anthocyanin in plant species have been proposed. Previous studies have indicated that glutathione S-transferase (GST) genes from model and ornamental plants are involved in anthocyanin transportation. In the present study, an anthocyanin-related GST, IbGSTF4, was identified and characterized based on transcriptome results. Phylogenetic analysis revealed that IbGSTF4 was most closely correlated to PhAN9 and CkmGST3, the anthocyanin-related GST of Petunia hybrida and Cyclamen. Furthermore, the expression analysis revealed that IbGSTF4 is strongly expressed in pigmented tissues, when compared to green organs, which is in agreement to the ability to correlate with anthocyanin accumulation. A GST activity assay uncovered that the IbGST4 protein owned similar activities with the GST family. Furthermore, the molecular functional complementation of Arabidopsis thaliana mutant tt19 demonstrated that IbGSTF4 might play a vital role in the vacuole sequestration of anthocyanin in sweetpotato. Moreover, the dual luciferase assay revealed that the LUC driven by the promoter of IbGSTF4 could not be directly activated by IbMYB1, suggesting that the regulatory mechanism of anthocyanin accumulation and sequestration in sweetpotato was intricate.
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Affiliation(s)
- Meng Kou
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Ya-Ju Liu
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Zong-Yun Li
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China
| | - Yun-Gang Zhang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Wei Tang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Hui Yan
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Xin Wang
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Xiao-Guang Chen
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | - Zai-Xing Su
- Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China
| | | | - Qiang Li
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China.
| | - Dai-Fu Ma
- School of Life Science, Jiangsu Normal University, Xuzhou 221116, PR China; Xuzhou Institute of Agricultural Sciences in Jiangsu Xuhuai District/Sweetpotato Research Institute, Chinese Academy of Agricultural Sciences/Key Laboratory of Biology and Genetic Breeding of Sweetpotato, Ministry of Agriculture, Xuzhou 221131, PR China.
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15
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Shangguan L, Fang X, Chen L, Cui L, Fang J. Genome-wide analysis of autophagy-related genes (ARGs) in grapevine and plant tolerance to copper stress. PLANTA 2018; 247:1449-1463. [PMID: 29541879 DOI: 10.1007/s00425-018-2864-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2017] [Accepted: 02/01/2018] [Indexed: 05/26/2023]
Abstract
Grapevine autophagy-related genes (ARGs) include 35 members that have unique evolutionary backgrounds and expression patterns, with some of them responding to abiotic stresses, including copper stress. Autophagy is one of the most crucial self-regulating phenomena in livings organisms, including animals, plants, yeasts, etc. In the genomes of plants, like Arabidopsis, rice, tobacco, and barley, more than 30 autophagy-related genes (ARGs) have been found. These ARGs are involved in plant development, programed cell death, and the stress response process. In plants, and particularly in grapevine, high copper stress results from the application of the Bordeaux mixture, a widely used fungicide. However, the function of autophagy in plant tolerance to copper stress is unknown. Accordingly, in this study, a genome-wide analysis was performed to identify Vitis vinifera ARGs (VvARGs), and 35 VvARGs were detected. A gene family analysis revealed that the tandem and segmental duplication events played significant roles in the VvARG gene family expansion. Moreover, there was more intense signature of purifying selection for the comparison between grape and rice than between grape and Arabidopsis. In response to copper treatment, both the autophagosome number and malondialdehyde concentration increased during the initial 4 h post-treatment, and reached maximal values at 24 h. An expression analysis indicated that most VvARGs responded to copper stress at 4 h post-treatment, and some VvARGs (e.g., VvATG6, VvATG8i, and VvATG18h) exhibited responses to most abiotic stresses. These results provide a detailed overview of the ARGs in grapevine and indicate multiple functions of autophagy in fruit development and abiotic stresses in grapevine. The key ARG (e.g., ATG8i) should be investigated in more detail in grapevine and other plant species.
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Affiliation(s)
- Lingfei Shangguan
- Horticultural Department, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xiang Fang
- Horticultural Department, Nanjing Agricultural University, Nanjing, 210095, China
| | - Lide Chen
- Horticultural Department, Nanjing Agricultural University, Nanjing, 210095, China
| | - Liwen Cui
- Horticultural Department, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinggui Fang
- Horticultural Department, Nanjing Agricultural University, Nanjing, 210095, China.
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16
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Enoki S, Hamaguchi Y, Suzuki S, Fujisawa H, Hattori T, Arita K, Yamaguchi C, Mikami M, Nagasaka S, Tanaka K. Physiological characterization of leaf and internode after bud break in Japanese indigenous Koshu grape by comparative RNA sequencing analysis. PLoS One 2018; 13:e0194807. [PMID: 29566077 PMCID: PMC5864062 DOI: 10.1371/journal.pone.0194807] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2017] [Accepted: 03/09/2018] [Indexed: 01/18/2023] Open
Abstract
Koshu is indigenous to Japan and considered the most important wine grape in Japan. Koshu grape berry possesses characteristics that make it unique from European V. vinifera as wine grape. However, the physiological characteristics of Koshu leaf and internode remain unknown. An understanding of those characteristics would contribute to improvements in Koshu cultivation, thereby enhancing grape berry and wine quality. To identify the genes responsible for the physiological characteristics of Koshu, we comprehensively analyzed leaf and internode differences at the transcriptome level between Koshu and Pinot Noir by RNA sequencing. A total of 248 and 131 differentially expressed genes (DEGs) were detected in leaves and internodes, respectively. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of these DEGs revealed that "flavonoid biosynthesis" and "glutathione metabolism" pathways were significantly enriched in Koshu leaves. On the other hand, when internodes were compared, "flavonoid"-related GO terms were specifically detected in Koshu. KEGG pathway enrichment analysis suggested that the expression of such genes as leucoanthocyanidin reductase and flavonol synthase in the flavonoid biosynthesis pathway was higher in Koshu than Pinot Noir. Measurement of the relative expression levels of these genes by RT-qPCR validated the results obtained by RNA sequencing. The characteristics of Koshu leaf and internode, which are expected to produce flavonoids with antibacterial activity and UV protection function, would suit Japanese climate as a survival strategy.
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Affiliation(s)
- Shinichi Enoki
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Yamanashi, Japan
| | - Yu Hamaguchi
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
| | - Shunji Suzuki
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Yamanashi, Japan
| | - Hiroyuki Fujisawa
- Department of Agriculture, Tokyo University of Agriculture, Kanagawa, Japan
| | - Tomoki Hattori
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Yamanashi, Japan
| | - Kayo Arita
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Yamanashi, Japan
| | - Chiho Yamaguchi
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Yamanashi, Japan
| | - Masachika Mikami
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Yamanashi, Japan
| | - Shu Nagasaka
- Laboratory of Fruit Genetic Engineering, The Institute of Enology and Viticulture, University of Yamanashi, Yamanashi, Japan
| | - Keisuke Tanaka
- NODAI Genome Research Center, Tokyo University of Agriculture, Tokyo, Japan
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17
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Harris ZN, Kovacs LG, Londo JP. RNA-seq-based genome annotation and identification of long-noncoding RNAs in the grapevine cultivar 'Riesling'. BMC Genomics 2017; 18:937. [PMID: 29197332 PMCID: PMC5712117 DOI: 10.1186/s12864-017-4346-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 11/22/2017] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND The technological advances of RNA-seq and de novo transcriptome assembly have enabled genome annotation and transcriptome profiling in highly heterozygous species such as grapevine (Vitis vinifera L.). This work is an attempt to utilize a de novo-assembled transcriptome of the V. vinifera cultivar 'Riesling' to improve annotation of the grapevine reference genome sequence. RESULTS Here we show that the transcriptome assembly of a single V. vinifera cultivar is insufficient for a complete genome annotation of the grapevine reference genome constructed from V. vinifera PN40024. Further, we provide evidence that the gene models we identified cannot be completely anchored to the previously published V. vinifera PN40024 gene models. In addition to these findings, we present a computational pipeline for the de novo identification of lncRNAs. Our results demonstrate that, in grapevine, lncRNAs are significantly different from protein coding transcripts in such metrics as length, GC-content, minimum free energy, and length-corrected minimum free energy. CONCLUSIONS In grapevine, high-level heterozygosity necessitates that transcriptome characterization be based on cultivar-specific reference genome sequences. Our results strengthen the hypothesis that lncRNAs have thermodynamically different properties than protein-coding RNAs. The analyses of both coding and non-coding RNAs will be instrumental in uncovering inter-cultivar variation in wild and cultivated grapevine species.
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Affiliation(s)
- Zachary N. Harris
- Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO USA
- Present address: Saint Louis University, Department of Biology, 1 N. Grand Blvd, Saint Louis, MO USA
| | - Laszlo G. Kovacs
- Missouri State University, Biology Department, 901 S. National Ave, Springfield, MO USA
| | - Jason P. Londo
- United States Department of Agriculture, Agricultural Research Service, Grape Genetics Research Unit, 630 W. North Street, Geneva, NY USA
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18
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Leng X, Wang P, Wang C, Zhu X, Li X, Li H, Mu Q, Li A, Liu Z, Fang J. Genome-wide identification and characterization of genes involved in carotenoid metabolic in three stages of grapevine fruit development. Sci Rep 2017; 7:4216. [PMID: 28652583 PMCID: PMC5484692 DOI: 10.1038/s41598-017-04004-0] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 05/09/2017] [Indexed: 12/16/2022] Open
Abstract
Carotenoids not only play indispensable roles in plant growth and development but also enhance nutritional value and health benefits for humans. In this study, total carotenoids progressively decreased during fruit ripening. Fifty-four genes involving in mevalonate (MVA), 2-C-methyl-D-erythritol 4-phosphate (MEP), carotenoid biosynthesis and catabolism pathway were identified. The expression levels of most of the carotenoid metabolism related genes kept changing during fruit ripening generating a metabolic flux toward carotenoid synthesis. Down regulation of VvDXS, VvDXR, VvGGPPS and VvPSY and a dramatic increase in the transcription levels of VvCCD might be responsible for the reduction of carotenoids content. The visible correlation between carotenoid content and gene expression profiles suggested that transcriptional regulation of carotenoid biosynthesis pathway genes is a key mechanism of carotenoid accumulation. In addition, the decline of carotenoids was also accompanied with the reduction of chlorophyll content. The reduction of chlorophyll content might be due to the obstruction in chlorophyll synthesis and acceleration of chlorophyll degradation. These results will be helpful for better understanding of carotenoid biosynthesis in grapevine fruit and contribute to the development of conventional and transgenic grapevine cultivars for further enrichment of carotenoid content.
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Affiliation(s)
- Xiangpeng Leng
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China
| | - Peipei Wang
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China
| | - Chen Wang
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China
| | - Xudong Zhu
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China
| | - Xiaopeng Li
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China
| | - Hongyan Li
- Grape and Wine Research Institute, Guangxi Academy of Agricultural Sciences, Daxuedong Road 174, Nanning, 530007, P.R. China
| | - Qian Mu
- Shandong Aacademy of Grape, Gongyenan Road 103, Jinan, 250110, P.R. China
| | - Ao Li
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China
| | - Zhongjie Liu
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China
| | - Jinggui Fang
- College of Horticulture, Nanjing Agricultural University, Tongwei Road 6, Nanjing, 210095, P.R. China.
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