1
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Wong DCJ, Wang Z, Perkins J, Jin X, Marsh GE, John EG, Peakall R. The road less taken: Dihydroflavonol 4-reductase inactivation and delphinidin anthocyanin loss underpins a natural intraspecific flower colour variation. Mol Ecol 2024:e17334. [PMID: 38651763 DOI: 10.1111/mec.17334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 02/22/2024] [Accepted: 03/20/2024] [Indexed: 04/25/2024]
Abstract
Visual cues are of critical importance for the attraction of animal pollinators, however, little is known about the molecular mechanisms underpinning intraspecific floral colour variation. Here, we combined comparative spectral analysis, targeted metabolite profiling, multi-tissue transcriptomics, differential gene expression, sequence analysis and functional analysis to investigate a bee-pollinated orchid species, Glossodia major with common purple- and infrequent white-flowered morphs. We found uncommon and previously unreported delphinidin-based anthocyanins responsible for the conspicuous and pollinator-perceivable colour of the purple morph and three genetic changes underpinning the loss of colour in the white morph - (1) a loss-of-function (LOF; frameshift) mutation affecting dihydroflavonol 4-reductase (DFR1) coding sequence due to a unique 4-bp insertion, (2) specific downregulation of functional DFR1 expression and (3) the unexpected discovery of chimeric Gypsy transposable element (TE)-gene (DFR) transcripts with potential consequences to the genomic stability and post-transcriptional or epigenetic regulation of DFR. This is one of few known cases where regulatory changes and LOF mutation in an anthocyanin structural gene, rather than transcription factors, are important. Furthermore, if TEs prove to be a frequent source of mutation, the interplay between environmental stress-induced TE evolution and pollinator-mediated selection for adaptive colour variation may be an overlooked mechanism maintaining floral colour polymorphism in nature.
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Zemin Wang
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - James Perkins
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Xin Jin
- State Key Laboratory of Aridland Crop Science, Gansu Agricultural University, Lanzhou, China
- College of Life Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Grace Emma Marsh
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Emma Grace John
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, Australian Capital Territory, Australia
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2
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Zhang C, Dai Z, Ferrier T, Orduña L, Santiago A, Peris A, Wong DCJ, Kappel C, Savoi S, Loyola R, Amato A, Kozak B, Li M, Liang A, Carrasco D, Meyer-Regueiro C, Espinoza C, Hilbert G, Figueroa-Balderas R, Cantu D, Arroyo-Garcia R, Arce-Johnson P, Claudel P, Errandonea D, Rodríguez-Concepción M, Duchêne E, Huang SSC, Castellarin SD, Tornielli GB, Barrieu F, Matus JT. MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries. Plant Cell 2023; 35:4238-4265. [PMID: 37648264 PMCID: PMC10689149 DOI: 10.1093/plcell/koad228] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 08/13/2023] [Accepted: 08/30/2023] [Indexed: 09/01/2023]
Abstract
Variegation is a rare type of mosaicism not fully studied in plants, especially fruits. We examined red and white sections of grape (Vitis vinifera cv. 'Béquignol') variegated berries and found that accumulation of products from branches of the phenylpropanoid and isoprenoid pathways showed an opposite tendency. Light-responsive flavonol and monoterpene levels increased in anthocyanin-depleted areas in correlation with increasing MYB24 expression. Cistrome analysis suggested that MYB24 binds to the promoters of 22 terpene synthase (TPS) genes, as well as 32 photosynthesis/light-related genes, including carotenoid pathway members, the flavonol regulator HY5 HOMOLOGUE (HYH), and other radiation response genes. Indeed, TPS35, TPS09, the carotenoid isomerase gene CRTISO2, and HYH were activated in the presence of MYB24 and MYC2. We suggest that MYB24 modulates ultraviolet and high-intensity visible light stress responses that include terpene and flavonol synthesis and potentially affects carotenoids. The MYB24 regulatory network is developmentally triggered after the onset of berry ripening, while the absence of anthocyanin sunscreens accelerates its activation, likely in a dose-dependent manner due to increased radiation exposure. Anthocyanins and flavonols in variegated berry skins act as effective sunscreens but for different wavelength ranges. The expression patterns of stress marker genes in red and white sections of 'Béquignol' berries strongly suggest that MYB24 promotes light stress amelioration but only partly succeeds during late ripening.
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Affiliation(s)
- Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Zhanwu Dai
- Beijing Key Laboratory of Grape Science and Enology and Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Thilia Ferrier
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Arnau Peris
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT 2601, Australia
| | - Christian Kappel
- Institute for Biochemistry and Biology, University of Potsdam, Potsdam-Golm 14476, Germany
| | - Stefania Savoi
- Department of Agricultural, Forest and Food Sciences, University of Turin, Turin 10124, Italy
| | - Rodrigo Loyola
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alessandra Amato
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Bartosz Kozak
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Akun Liang
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - David Carrasco
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Carlos Meyer-Regueiro
- Departamento de Genética Molecular y Microbiología, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Carmen Espinoza
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago 8380453, Chile
| | - Ghislaine Hilbert
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - Rosa Figueroa-Balderas
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, CA 95616, USA
| | - Rosa Arroyo-Garcia
- Centre for Plant Biotechnology and Genomics (CBGP), Universidad Politécnica de Madrid-INIA, 28223, Pozuelo de Alarcón, Madrid, Spain
| | - Patricio Arce-Johnson
- Instituto de Ciencias Aplicadas, Facultad de Ingeniería Universidad Autónoma deChile
| | | | - Daniel Errandonea
- Departamento de Física Aplicada-ICMUV-MALTA Consolider Team, Universitat de València, Burjassot 46100, Valencia, Spain
| | - Manuel Rodríguez-Concepción
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-Universitat Politècnica de València, Valencia 46022, Spain
| | - Eric Duchêne
- SVQV, University of Strasbourg, INRAE, Colmar 68000, France
| | - Shao-shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY 10003, USA
| | - Simone Diego Castellarin
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia V1V 1V7, Canada
| | | | - Francois Barrieu
- EGFV, Bordeaux Sciences Agro, University of Bordeaux, INRAE, ISVV, 210 Chemin de Leysotte, 33140 Villenave d'Ornon, France
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna 46980, Valencia, Spain
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3
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Orduña L, Santiago A, Navarro-Payá D, Zhang C, Wong DCJ, Matus JT. Aggregated gene co-expression networks predict transcription factor regulatory landscapes in grapevine. J Exp Bot 2023; 74:6522-6540. [PMID: 37668374 DOI: 10.1093/jxb/erad344] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2023] [Accepted: 08/30/2023] [Indexed: 09/06/2023]
Abstract
Gene co-expression networks (GCNs) have not been extensively studied in non-model plants. However, the rapid accumulation of transcriptome datasets in certain species represents an opportunity to explore underutilized network aggregation approaches. In fact, aggregated GCNs (aggGCNs) highlight robust co-expression interactions and improve functional connectivity. We applied and evaluated two different aggregation methods on public grapevine RNA-Seq datasets from three different tissues (leaf, berry, and 'all organs'). Our results show that co-occurrence-based aggregation generally yielded the best-performing networks. We applied aggGCNs to study several transcription factor gene families, showing their capacity for detecting both already-described and novel regulatory relationships between R2R3-MYBs, bHLH/MYC, and multiple specialized metabolic pathways. Specifically, transcription factor gene- and pathway-centered network analyses successfully ascertained the previously established role of VviMYBPA1 in controlling the accumulation of proanthocyanidins while providing insights into its novel role as a regulator of p-coumaroyl-CoA biosynthesis as well as the shikimate and aromatic amino acid pathways. This network was validated using DNA affinity purification sequencing data, demonstrating that co-expression networks of transcriptional activators can serve as a proxy of gene regulatory networks. This study presents an open repository to reproduce networks in other crops and a GCN application within the Vitviz platform, a user-friendly tool for exploring co-expression relationships.
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Affiliation(s)
- Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
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Wong DCJ, Pichersky E, Peakall R. Many different flowers make a bouquet: Lessons from specialized metabolite diversity in plant-pollinator interactions. Curr Opin Plant Biol 2023; 73:102332. [PMID: 36652780 DOI: 10.1016/j.pbi.2022.102332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/04/2022] [Accepted: 12/08/2022] [Indexed: 06/10/2023]
Abstract
Flowering plants have evolved extraordinarily diverse metabolites that underpin the floral visual and olfactory signals enabling plant-pollinator interactions. In some cases, these metabolites also provide unusual rewards that specific pollinators depend on. While some metabolites are shared by most flowering plants, many have evolved in restricted lineages in response to the specific selection pressures encountered within different niches. The latter are designated as specialized metabolites. Recent investigations continue to uncover a growing repertoire of unusual specialized metabolites. Increased accessibility to cutting-edge multi-omics technologies (e.g. genome, transcriptome, proteome, metabolome) is now opening new doors to simultaneously uncover the molecular basis of their synthesis and their evolution across diverse plant lineages. Drawing upon the recent literature, this perspective discusses these aspects and, where known, their ecological and evolutionary relevance. A primer on omics-guided approaches to discover the genetic and biochemical basis of functional specialized metabolites is also provided.
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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5
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Hou Y, Wong DCJ, Li Q, Zhou H, Zhu Z, Gong L, Liang J, Ren H, Liang Z, Wang Q, Xin H. Dissecting the effect of ethylene in the transcriptional regulation of chilling treatment in grapevine leaves. Plant Physiol Biochem 2023; 196:1084-1097. [PMID: 36921558 DOI: 10.1016/j.plaphy.2023.03.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/07/2023] [Accepted: 03/09/2023] [Indexed: 06/18/2023]
Abstract
Ethylene (ETH) plays important roles in various development programs and stress responses in plants. In grapevines, ETH increased dramatically under chilling stress and is known to positively regulate cold tolerance. However, the role of ETH in transcriptional regulation during chilling stress of grapevine leaves is still not clear. To address this gap, targeted hormone profiling and transcriptomic analysis were performed on leaves of Vitis amurensis under chilling stress with and without aminoethoxyvinylglycine (AVG, a inhibitor of ETH synthesis) treatment. APETALA2/ETHYLENE RESPONSIVE FACTOR (AP2/ERF) and WRKY transcription factors (TF) were only the two highly enriched TF families that were consistently up-regulated during chilling stress but inhibited by AVG. The comparison of leaf transcriptomes between chilling treatment and chilling with AVG allowed the identification of potential ETH-regulated genes. Potential genes that are positively regulated by ETH are enriched in solute transport, protein biosynthesis, phytohormone action, antioxidant and carbohydrate metabolism. Conversely, genes related to the synthesis and signaling of ETH, indole-3-acetic acid (IAA), abscisic acid (ABA) were up-regulated by chilling treatment but inhibited by AVG. The contents of ETH, ABA and IAA also paralleled with the transcriptome data, which suggests that the response of ABA and IAA during chilling stress may regulate by ETH signaling, and together may belong to an integrated network of hormonal signaling pathways underpinning chilling stress response in grapevine leaves. Together, these findings provide new clues for further studying the complex regulatory mechanism of ETH under low-temperature stress in plants more generally and new opportunities for breeding cold-resilient grapevines.
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Affiliation(s)
- Yujun Hou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture/Center of Economic Botany, Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
| | - Qingyun Li
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture/Center of Economic Botany, Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Huimin Zhou
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture/Center of Economic Botany, Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Zhenfei Zhu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture/Center of Economic Botany, Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Linzhong Gong
- Institute of Fruit and Tea, Hubei Academy of Agricultural Sciences, Wuhan, 430064, China
| | - Ju Liang
- Turpan Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang, 830091, China
| | - Hongsong Ren
- Turpan Institute of Agricultural Sciences, Xinjiang Academy of Agricultural Sciences, Xinjiang, 830091, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Science and Enology, And CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Science, Beijing, 100093, China
| | - Qingfeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture/Center of Economic Botany, Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture/Center of Economic Botany, Core Botanical Gardens/Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China; Sino-Africa Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, China; University of Chinese Academy of Sciences, Beijing, 100049, China.
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6
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Wong DCJ, Perkins J, Peakall R. Conserved pigment pathways underpin the dark insectiform floral structures of sexually deceptive Chiloglottis (Orchidaceae). Front Plant Sci 2022; 13:976283. [PMID: 36275580 PMCID: PMC9581149 DOI: 10.3389/fpls.2022.976283] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 08/24/2022] [Indexed: 06/10/2023]
Abstract
Sexually deceptive plants achieve pollination by enticing specific male insects as pollinators using a combination of olfactory, visual, and morphological mimicry. The sexually deceptive orchid genus Chiloglottis is comprised of some 30 species with predominantly dull green-red flowers except for the dark insectiform calli/callus structure from the labellum lamina. This unique structure mimics the female of the pollinator and potentially enhances the visibility of the mimic. However, the chemical and genetic basis for the color of these structures remains poorly understood across the genus. The goal of this study was to investigate the flower color biochemistry and patterns of gene expression across the anthocyanin and flavonol glycoside biosynthetic pathway within the calli structures across the three distinct clades of Chiloglottis (Formicifera, Reflexa, and Valida) using chemical and transcriptome analysis. Our phylogenomic analysis confirmed the close sister relationship between the Reflexa/Formicifera clades and reaffirms the basal position of the Valida clade. Additionally, the biochemical basis of the dark calli/callus structures is conserved across the genus. Nonetheless, the proportion of methoxylated anthocyanin and flavonol glycoside derivatives and the mean gene expression levels appear to differentiate the Reflexa and Formicifera clades from the Valida clade. In future studies, it will be of interest to tease apart the role of phylogeny, environment, pollinators, and other factors as potential drivers of the observed biochemistry and gene expression differences. It will also be important to characterize the function of candidate genes such as DFR, LDOX, and FLS in this fascinating case of flower color mimicry.
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Wong DCJ, Peakall R. Orchid Phylotranscriptomics: The Prospects of Repurposing Multi-Tissue Transcriptomes for Phylogenetic Analysis and Beyond. Front Plant Sci 2022; 13:910362. [PMID: 35712597 PMCID: PMC9196242 DOI: 10.3389/fpls.2022.910362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 04/21/2022] [Indexed: 06/10/2023]
Abstract
The Orchidaceae is rivaled only by the Asteraceae as the largest plant family, with the estimated number of species exceeding 25,000 and encompassing more than 700 genera. To gain insights into the mechanisms driving species diversity across both global and local scales, well-supported phylogenies targeting different taxonomic groups and/or geographical regions will be crucial. High-throughput sequencing technologies have revolutionized the field of molecular phylogenetics by simplifying the process of obtaining genome-scale sequence data. Consequently, there has been an explosive growth of such data in public repositories. Here we took advantage of this unprecedented access to transcriptome data from predominantly non-phylogenetic studies to assess if it can be repurposed to gain rapid and accurate phylogenetic insights across the orchids. Exhaustive searches revealed transcriptomic data for more than 100 orchid species spanning 5 subfamilies, 13 tribes, 21 subtribes, and 50 genera that were amendable for exploratory phylotranscriptomic analysis. Next, we performed re-assembly of the transcriptomes before strategic selection of the final samples based on a gene completeness evaluation. Drawing on these data, we report phylogenetic analyses at both deep and shallow evolutionary scales via maximum likelihood and shortcut coalescent species tree methods. In this perspective, we discuss some key outcomes of this study and conclude by highlighting other complementary, albeit rarely explored, insights beyond phylogenetic analysis that repurposed multi-tissue transcriptome can offer.
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8
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Orduña L, Li M, Navarro-Payá D, Zhang C, Santiago A, Romero P, Ramšak Ž, Magon G, Höll J, Merz P, Gruden K, Vannozzi A, Cantu D, Bogs J, Wong DCJ, Huang SSC, Matus JT. Direct regulation of shikimate, early phenylpropanoid, and stilbenoid pathways by Subgroup 2 R2R3-MYBs in grapevine. Plant J 2022; 110:529-547. [PMID: 35092714 DOI: 10.1111/tpj.15686] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 01/17/2022] [Accepted: 01/19/2022] [Indexed: 05/08/2023]
Abstract
The stilbenoid pathway is responsible for the production of resveratrol in grapevine (Vitis vinifera L.). A few transcription factors (TFs) have been identified as regulators of this pathway but the extent of this control has not been deeply studied. Here we show how DNA affinity purification sequencing (DAP-Seq) allows for the genome-wide TF-binding site interrogation in grape. We obtained 5190 and 4443 binding events assigned to 4041 and 3626 genes for MYB14 and MYB15, respectively (approximately 40% of peaks located within −10 kb of transcription start sites). DAP-Seq of MYB14/MYB15 was combined with aggregate gene co-expression networks (GCNs) built from more than 1400 transcriptomic datasets from leaves, fruits, and flowers to narrow down bound genes to a set of high confidence targets. The analysis of MYB14, MYB15, and MYB13, a third uncharacterized member of Subgroup 2 (S2), showed that in addition to the few previously known stilbene synthase (STS) targets, these regulators bind to 30 of 47 STS family genes. Moreover, all three MYBs bind to several PAL, C4H, and 4CL genes, in addition to shikimate pathway genes, the WRKY03 stilbenoid co-regulator and resveratrol-modifying gene candidates among which ROMT2-3 were validated enzymatically. A high proportion of DAP-Seq bound genes were induced in the activated transcriptomes of transient MYB15-overexpressing grapevine leaves, validating our methodological approach for delimiting TF targets. Overall, Subgroup 2 R2R3-MYBs appear to play a key role in binding and directly regulating several primary and secondary metabolic steps leading to an increased flux towards stilbenoid production. The integration of DAP-Seq and reciprocal GCNs offers a rapid framework for gene function characterization using genome-wide approaches in the context of non-model plant species and stands up as a valid first approach for identifying gene regulatory networks of specialized metabolism.
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Affiliation(s)
- Luis Orduña
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Miaomiao Li
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA
| | - David Navarro-Payá
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Chen Zhang
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Antonio Santiago
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Pablo Romero
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
| | - Živa Ramšak
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Gabriele Magon
- Department of Agronomy, Food, Natural resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, 35020, Italy
| | - Janine Höll
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Patrick Merz
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Kristina Gruden
- Department of Biotechnology and Systems Biology, National Institute of Biology, Večna pot 111, 1000, Ljubljana, Slovenia
| | - Alessandro Vannozzi
- Department of Agronomy, Food, Natural resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, 35020, Italy
| | - Dario Cantu
- Department of Viticulture and Enology, University of California Davis, Davis, California, USA
| | - Jochen Bogs
- Dienstleistungszentrum Ländlicher Raum Rheinpfalz, Viticulture and Enology Group, Neustadt/W, Germany
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
| | - Shao-Shan Carol Huang
- Center for Genomics and Systems Biology, Department of Biology, New York University, USA
| | - José Tomás Matus
- Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, Paterna, 46908, Valencia, Spain
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9
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Wong DCJ, Perkins J, Peakall R. Anthocyanin and Flavonol Glycoside Metabolic Pathways Underpin Floral Color Mimicry and Contrast in a Sexually Deceptive Orchid. Front Plant Sci 2022; 13:860997. [PMID: 35401591 PMCID: PMC8983864 DOI: 10.3389/fpls.2022.860997] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 02/17/2022] [Indexed: 06/10/2023]
Abstract
Sexually deceptive plants secure pollination by luring specific male insects as pollinators using a combination of olfactory, visual, and morphological mimicry. Flower color is a key component to this attraction, but its chemical and genetic basis remains poorly understood. Chiloglottis trapeziformis is a sexually deceptive orchid which has predominantly dull green-red flowers except for the central black callus projecting from the labellum lamina. The callus mimics the female of the pollinator and the stark color contrast between the black callus and dull green or red lamina is thought to enhance the visibility of the mimic. The goal of this study was to investigate the chemical composition and genetic regulation of temporal and spatial color patterns leading to visual mimicry, by integrating targeted metabolite profiling and transcriptomic analysis. Even at the very young bud stage, high levels of anthocyanins were detected in the dark callus, with peak accumulation by the mature bud stage. In contrast, anthocyanin levels in the lamina peaked as the buds opened and became reddish-green. Coordinated upregulation of multiple genes, including dihydroflavonol reductase and leucoanthocyanidin dioxygenase, and the downregulation of flavonol synthase genes (FLS) in the callus at the very young bud stage underpins the initial high anthocyanin levels. Conversely, within the lamina, upregulated FLS genes promote flavonol glycoside over anthocyanin production, with the downstream upregulation of flavonoid O-methyltransferase genes further contributing to the accumulation of methylated flavonol glycosides, whose levels peaked in the mature bud stage. Finally, the peak anthocyanin content of the reddish-green lamina of the open flower is underpinned by small increases in gene expression levels and/or differential upregulation in the lamina in select anthocyanin genes while FLS patterns showed little change. Differential expression of candidate genes involved in specific transport, vacuolar acidification, and photosynthetic pathways may also assist in maintaining the distinct callus and contrasting lamina color from the earliest bud stage through to the mature flower. Our findings highlight that flower color in this sexually deceptive orchid is achieved by complex tissue-specific coordinated regulation of genes and biochemical pathways across multiple developmental stages.
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10
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Peakall R, Wong DCJ, Phillips RD, Ruibal M, Eyles R, Rodriguez-Delgado C, Linde CC. A multitiered sequence capture strategy spanning broad evolutionary scales: Application for phylogenetic and phylogeographic studies of orchids. Mol Ecol Resour 2021; 21:1118-1140. [PMID: 33453072 DOI: 10.1111/1755-0998.13327] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2020] [Revised: 12/22/2020] [Accepted: 01/05/2021] [Indexed: 11/30/2022]
Abstract
With over 25,000 species, the drivers of diversity in the Orchidaceae remain to be fully understood. Here, we outline a multitiered sequence capture strategy aimed at capturing hundreds of loci to enable phylogenetic resolution from subtribe to subspecific levels in orchids of the tribe Diurideae. For the probe design, we mined subsets of 18 transcriptomes, to give five target sequence sets aimed at the tribe (Sets 1 & 2), subtribe (Set 3), and within subtribe levels (Sets 4 & 5). Analysis included alternative de novo and reference-guided assembly, before target sequence extraction, annotation and alignment, and application of a homology-aware k-mer block phylogenomic approach, prior to maximum likelihood and coalescence-based phylogenetic inference. Our evaluation considered 87 taxa in two test data sets: 67 samples spanning the tribe, and 72 samples involving 24 closely related Caladenia species. The tiered design achieved high target loci recovery (>89%), with the median number of recovered loci in Sets 1-5 as follows: 212, 219, 816, 1024, and 1009, respectively. Interestingly, as a first test of the homologous k-mer approach for targeted sequence capture data, our study revealed its potential for enabling robust phylogenetic species tree inferences. Specifically, we found matching, and in one case improved phylogenetic resolution within species complexes, compared to conventional phylogenetic analysis involving target gene extraction. Our findings indicate that a customized multitiered sequence capture strategy, in combination with promising yet underutilized phylogenomic approaches, will be effective for groups where interspecific divergence is recent, but information on deeper phylogenetic relationships is also required.
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Affiliation(s)
- Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Ryan D Phillips
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia.,Department of Ecology, Environment and Evolution, La Trobe University, Melbourne, Vic., Australia
| | - Monica Ruibal
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Rodney Eyles
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Claudia Rodriguez-Delgado
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Celeste C Linde
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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11
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Azaman SNA, Wong DCJ, Tan SW, Yusoff FM, Nagao N, Yeap SK. De novo transcriptome analysis of Chlorella sorokiniana: effect of glucose assimilation, and moderate light intensity. Sci Rep 2020; 10:17331. [PMID: 33060668 PMCID: PMC7562877 DOI: 10.1038/s41598-020-74410-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2020] [Accepted: 10/01/2020] [Indexed: 02/01/2023] Open
Abstract
Chlorella can produce an unusually wide range of metabolites under various nutrient availability, carbon source, and light availability. Glucose, an essential molecule for the growth of microorganisms, also contributes significantly to the metabolism of various metabolic compounds produced by Chlorella. In addition, manipulation of light intensity also induces the formation of secondary metabolites such as pigments, and carotenoids in Chlorella. This study will focus on the effect of glucose addition, and moderate light on the regulation of carotenoid, lipid, starch, and other key metabolic pathways in Chlorella sorokiniana. To gain knowledge about this, we performed transcriptome profiling on C. sorokiniana strain NIES-2168 in response to moderate light stress supplemented with glucose under mixotrophic conditions. A total of 60,982,352 raw paired-end (PE) reads 100 bp in length was obtained from both normal, and mixotrophic samples of C. sorokiniana. After pre-processing, 93.63% high-quality PE reads were obtained, and 18,310 predicted full-length transcripts were assembled. Differential gene expression showed that a total of 937, and 1124 genes were upregulated, and downregulated in mixotrophic samples, respectively. Transcriptome analysis revealed that the mixotrophic condition caused upregulation of genes involved in carotenoids production (specifically lutein biosynthesis), fatty acid biosynthesis, TAG accumulation, and the majority of the carbon fixation pathways. Conversely, starch biosynthesis, sucrose biosynthesis, and isoprenoid biosynthesis were downregulated. Novel insights into the pathways that link the enhanced production of valuable metabolites (such as carotenoids in C. sorokiniana) grown under mixotrophic conditions is presented.
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Affiliation(s)
- Siti Nor Ani Azaman
- Centre of Foundation Studies for Agricultural Sciences, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, 2600, Australia
| | - Sheau Wei Tan
- Laboratory of Vaccine and Biomolecules (VacBio), Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Fatimah M Yusoff
- International Institute of Aquaculture and Aquatic Sciences (I-AQUAS), Universiti Putra Malaysia, Port Dickson, Negeri Sembilan, Malaysia
- Department of Aquaculture, Faculty of Agriculture, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
| | - Norio Nagao
- Aquatic Animal Health and Therapeutics Laboratory (AquaHealth), Institute of Bioscience, Universiti Putra Malaysia, Serdang, Selangor, Malaysia
- , 102 Naname-go, Shinkamigoto-cho, Minami Matsuura-Gun, Nagasaki, 857-4214, Japan
| | - Swee Keong Yeap
- China-ASEAN College of Marine Sciences, Xiamen University Malaysia, Sepang, Selangor, Malaysia.
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12
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Perkins ML, Schuetz M, Unda F, Smith RA, Sibout R, Hoffmann NJ, Wong DCJ, Castellarin SD, Mansfield SD, Samuels L. Dwarfism of high-monolignol Arabidopsis plants is rescued by ectopic LACCASE overexpression. Plant Direct 2020; 4:e00265. [PMID: 33005856 PMCID: PMC7520647 DOI: 10.1002/pld3.265] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/24/2020] [Accepted: 08/14/2020] [Indexed: 05/24/2023]
Abstract
Lignin is a key secondary cell wall chemical constituent, and is both a barrier to biomass utilization and a potential source of bioproducts. The Arabidopsis transcription factors MYB58 and MYB63 have been shown to upregulate gene expression of the general phenylpropanoid and monolignol biosynthetic pathways. The overexpression of these genes also results in dwarfism. The vascular integrity, soluble phenolic profiles, cell wall lignin, and transcriptomes associated with these MYB-overexpressing lines were characterized. Plants with high expression of MYB58 and MYB63 had increased ectopic lignin and the xylem vessels were regular and open, suggesting that the stunted growth is not associated with loss of vascular conductivity. MYB58 and MYB63 overexpression lines had characteristic soluble phenolic profiles with large amounts of monolignol glucosides and sinapoyl esters, but decreased flavonoids. Because loss of function lac4 lac17 mutants also accumulate monolignol glucosides, we hypothesized that LACCASE overexpression might decrease monolignol glucoside levels in the MYB-overexpressing plant lines. When laccases related to lignification (LAC4 or LAC17) were co-overexpressed with MYB63 or MYB58, the dwarf phenotype was rescued. Moreover, the overexpression of either LAC4 or LAC17 led to wild-type monolignol glucoside levels, as well as wild-type lignin levels in the rescued plants. Transcriptomes of the rescued double MYB63-OX/LAC17-OX overexpression lines showed elevated, but attenuated, expression of the MYB63 gene itself and the direct transcriptional targets of MYB63. Contrasting the dwarfism from overabundant monolignol production with dwarfism from lignin mutants provides insight into some of the proposed mechanisms of lignin modification-induced dwarfism.
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Affiliation(s)
| | - Mathias Schuetz
- Department of BotanyUniversity of British ColumbiaVancouverCanada
| | - Faride Unda
- Department of Wood ScienceUniversity of British ColumbiaVancouverCanada
| | - Rebecca A. Smith
- Department of BotanyUniversity of British ColumbiaVancouverCanada
- Department of Energy's Great Lakes Bioenergy Research CenterDepartment of BiochemistryUniversity of Wisconsin‐MadisonMadisonWIUSA
| | - Richard Sibout
- Department of BotanyUniversity of British ColumbiaVancouverCanada
- UR1268 BIA (Biopolymères Interactions Assemblages)INRANantesFrance
| | | | | | | | | | - Lacey Samuels
- Department of BotanyUniversity of British ColumbiaVancouverCanada
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13
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Wong DCJ. Network aggregation improves gene function prediction of grapevine gene co-expression networks. Plant Mol Biol 2020; 103:425-441. [PMID: 32266646 DOI: 10.1007/s11103-020-01001-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 03/21/2020] [Indexed: 05/08/2023]
Abstract
Aggregation across multiple networks highlights robust co-expression interactions and improves the functional connectivity of grapevine gene co-expression networks. In recent years, the rapid accumulation of transcriptome datasets from diverse experimental conditions has enabled the widespread use of gene co-expression network (GCN) analysis in plants. In grapevine, GCN analysis has shown great promise for gene function prediction, however, measurable progress is currently lacking. Using accumulated microarray datasets from the grapevine whole-genome array (33 experiments, 1359 samples), we explored how meta-analysis through aggregation influences the functional connectivity (performance) of derived networks using guilt-by-association neighbor voting. Two annotation schemes, i.e. MapMan BIN and Pfam, at two sparsity thresholds, i.e. top 100 (stringent) and 300 (relaxed) ranked genes were evaluated. We observed that aggregating across multiple networks improves performance dramatically, with the aggregate outperforming the majority of functional terms across individual networks. Network sparsity and size (i.e. the number of samples and aggregates) were key factors influencing performance while the choice of annotation scheme had little. Systematic comparison with various state-of-the-art microarray and RNA-seq networks was also performed, however, none outperformed the aggregate microarray network despite having good predictive performance. Repeating these series of tests using a functional enrichment-based performance metric also showed remarkably consistent findings with guilt-by-association neighbor voting. To demonstrate its functionality, we explore the function and transcriptional regulation of grapevine EXPANSIN genes. We envisage that network aggregation will offer new and unique opportunities for gene function prediction in future grapevine functional genomics studies. To this end, we make the aggregate networks and associated metadata publicly available at VTC-Agg (https://sites.google.com/view/vtc-agg).
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT, 2601, Australia.
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14
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Dimopoulos N, Tindjau R, Wong DCJ, Matzat T, Haslam T, Song C, Gambetta GA, Kunst L, Castellarin SD. Drought stress modulates cuticular wax composition of the grape berry. J Exp Bot 2020; 71:3126-3141. [PMID: 31985780 PMCID: PMC7260727 DOI: 10.1093/jxb/eraa046] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 01/24/2020] [Indexed: 05/08/2023]
Abstract
Drought events are a major challenge for many horticultural crops, including grapes, which are often cultivated in dry and warm climates. It is not understood how the cuticle contributes to the grape berry response to water deficit (WD); furthermore, the cuticular waxes and the related biosynthetic pathways are poorly characterized in this fruit. In this study, we identified candidate wax-related genes from the grapevine genome by phylogenetic and transcriptomic analyses. Developmental and stress response expression patterns of these candidates were characterized across pre-existing RNA sequencing data sets and confirmed a high responsiveness of the pathway to environmental stresses. We then characterized the developmental and WD-induced changes in berry cuticular wax composition, and quantified differences in berry transpiration. Cuticular aliphatic wax content was modulated during development and an increase was observed under WD, with wax esters being strongly up-regulated. These compositional changes were related to up-regulated candidate genes of the aliphatic wax biosynthetic pathway, including CER10, CER2, CER3, CER1, CER4, and WSD1. The effect of WD on berry transpiration was not significant. This study indicates that changes in cuticular wax amount and composition are part of the metabolic response of the grape berry to WD, but these changes do not reduce berry transpiration.
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Affiliation(s)
- Nicolas Dimopoulos
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Ricco Tindjau
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Darren C J Wong
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Till Matzat
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Tegan Haslam
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Changzheng Song
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
| | - Gregory A Gambetta
- EGFV, Bordeaux-Sciences Agro, INRA, Univ. Bordeaux, ISVV, Villenave d’Ornon, France
| | - Ljerka Kunst
- Department of Botany, The University of British Columbia, Vancouver, BC, Canada
| | - Simone D Castellarin
- Wine Research Centre, Faculty of Land and Food Systems, The University of British Columbia, Vancouver, BC, Canada
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15
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Kreynes AE, Yong Z, Liu XM, Wong DCJ, Castellarin SD, Ellis BE. Biological impacts of phosphomimic AtMYB75. Planta 2020; 251:60. [PMID: 32030477 DOI: 10.1007/s00425-020-03350-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/27/2020] [Indexed: 05/04/2023]
Abstract
The phosphorylation status of MYB75 at T-131 affects protein stability, flavonoid profiles, and patterns of gene expression. The Arabidopsis transcription factor Myeloblastosis protein 75 (MYB75, AT1G56650) is known to act as a positive transcriptional regulator of genes required for flavonoid and anthocyanin biosynthesis. MYB75 was also shown to negatively regulate lignin and other secondary cell wall biosynthetic genes (Bhargava et al. in Plant Physiol 154(3):1428-1438, 2010). While transcriptional regulation of MYB75 has been described in numerous publications, little is known about post-translational control of MYB75 protein function. In a recent publication, light-induced activation of a MAP kinase (MPK4, AT4G01370) in Arabidopsis was reported to lead to MYB75 phosphorylation at two canonical MPK target sites, threonines, T-126 and T-131. This double phosphorylation event positively influenced MYB75 protein stability (Li et al. in Plant Cell 28(11):2866-2883, 2016). We have examined this phenomenon through use of phosphomutant forms of MYB75 and found that MYB75 is phosphorylated primarily at T-131, and that the phosphorylation of MYB75 recombinant protein in vitro can be catalyzed by multiple MAP kinases, including MPK3 (AT3G45640), MPK6 (AT2G43790), MPK4 and MPK11 (AT1G01560). We also demonstrate that MYB75 can bind to a large number of Arabidopsis MPK's in vitro, suggesting it could be a target of multiple signalling pathways. The impact of MYB75 phosphorylation at T-131 on the function of this transcription factor, in terms of localization, stability, and protein-protein interactions with known binding partners was examined in transgenic lines expressing phosphomimic and phosphonull versions of MYB75, to capture the behaviour of permanently phosphorylated and unphosphorylated MYB75 protein, respectively. In addition, we describe how ectopic over-expression of different phosphovariant forms of MYB75 (MYB75WT, MYB75T131A, and MYB75T131E) affects flavonoid biochemical profiles and global changes of gene expression in the corresponding transgenic Arabidopsis plants.
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Affiliation(s)
- Anna E Kreynes
- Michael Smith Laboratories, Department of Botany, and Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Zhenhua Yong
- Michael Smith Laboratories, Department of Botany, and Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xiao-Min Liu
- Michael Smith Laboratories, Department of Botany, and Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Darren C J Wong
- Michael Smith Laboratories, Department of Botany, and Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Simone D Castellarin
- Michael Smith Laboratories, Department of Botany, and Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Brian E Ellis
- Michael Smith Laboratories, Department of Botany, and Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
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16
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Livingston SJ, Quilichini TD, Booth JK, Wong DCJ, Rensing KH, Laflamme-Yonkman J, Castellarin SD, Bohlmann J, Page JE, Samuels AL. Cannabis glandular trichomes alter morphology and metabolite content during flower maturation. Plant J 2020; 101:37-56. [PMID: 31469934 DOI: 10.1111/tpj.14516] [Citation(s) in RCA: 106] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Revised: 07/28/2019] [Accepted: 08/19/2019] [Indexed: 05/18/2023]
Abstract
The cannabis leaf is iconic, but it is the flowers of cannabis that are consumed for the psychoactive and medicinal effects of their specialized metabolites. Cannabinoid metabolites, together with terpenes, are produced in glandular trichomes. Superficially, stalked and sessile trichomes in cannabis only differ in size and whether they have a stalk. The objectives of this study were: to define each trichome type using patterns of autofluorescence and secretory cell numbers, to test the hypothesis that stalked trichomes develop from sessile-like precursors, and to test whether metabolic specialization occurs in cannabis glandular trichomes. A two-photon microscopy technique using glandular trichome intrinsic autofluorescence was developed which demonstrated that stalked glandular trichomes possessed blue autofluorescence correlated with high cannabinoid levels. These stalked trichomes had 12-16 secretory disc cells and strongly monoterpene-dominant terpene profiles. In contrast, sessile trichomes on mature flowers and vegetative leaves possessed red-shifted autofluorescence, eight secretory disc cells and less monoterpene-dominant terpene profiles. Moreover, intrinsic autofluorescence patterns and disc cell numbers supported a developmental model where stalked trichomes develop from apparently sessile trichomes. Transcriptomes of isolated floral trichomes revealed strong expression of cannabinoid and terpene biosynthetic genes, as well as uncharacterized genes highly co-expressed with CBDA synthase. Identification and characterization of two previously unknown and highly expressed monoterpene synthases highlighted the metabolic specialization of stalked trichomes for monoterpene production. These unique properties and highly expressed genes of cannabis trichomes determine the medicinal, psychoactive and sensory properties of cannabis products.
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Affiliation(s)
- Samuel J Livingston
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Teagen D Quilichini
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Anandia Laboratories Inc., Vancouver, British Columbia, Canada
| | - Judith K Booth
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
| | - Darren C J Wong
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | | | | | - Simone D Castellarin
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Joerg Bohlmann
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada
- Wine Research Centre, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jonathan E Page
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
- Anandia Laboratories Inc., Vancouver, British Columbia, Canada
| | - A Lacey Samuels
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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Sun X, Zhang L, Wong DCJ, Wang Y, Zhu Z, Xu G, Wang Q, Li S, Liang Z, Xin H. The ethylene response factor VaERF092 from Amur grape regulates the transcription factor VaWRKY33, improving cold tolerance. Plant J 2019; 99:988-1002. [PMID: 31063661 DOI: 10.1111/tpj.14378] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 04/19/2019] [Accepted: 04/25/2019] [Indexed: 05/08/2023]
Abstract
Cold stress is a major limiting factor in grape (Vitis) productivity. In this study, we characterized a cold-responsive ethylene response factor (ERF) transcription factor, VaERF092, from Amur grape (Vitis amurensis). VaERF092 expression was induced by both low temperatures and the ethylene precursor 1-aminocyclopropane-1-carboxylate (ACC), but was suppressed by treatment with the ethylene inhibitor aminoethoxyvinylglycine (AVG) under cold conditions. Ectopic expression of VaERF092 in Arabidopsis thaliana enhanced cold tolerance. Co-expression network analysis of V. vinifera genes indicated that WRKY33 might be a downstream target of VaERF092. This hypothesis was supported by the fact that VaWRKY33 was expressed temporally after VaERF092 expression and could also be induced by cold and ACC, and inhibited by AVG. Yeast one-hybrid, transient β-glucuronidase (GUS) and dual-luciferase reporter assays provided evidence for an interaction between VaERF092 and a GCC-box element in the VaWRKY33 promoter. In addition, heterologous overexpression of VaWRKY33 in A. thaliana resulted in enhanced cold tolerance. VaERF092- and VaWRKY33 overexpressing grape calli showed lower low-temperature exothermic values than the empty vector (EV) calli, indicating enhanced tolerance to cold. Together, these results indicated that VaERF092 regulates VaWRKY33 through binding to its promoter GCC-box, leading to enhanced cold stress tolerance.
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Affiliation(s)
- Xiaoming Sun
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Langlang Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT, 2601, Australia
| | - Yi Wang
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhenfei Zhu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Guangzhao Xu
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Qingfeng Wang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
| | - Shaohua Li
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Zhenchang Liang
- Beijing Key Laboratory of Grape Sciences and Enology, CAS Key Laboratory of Plant Resources, Institute of Botany, Chinese Academy of Sciences, Beijing, 100093, China
| | - Haiping Xin
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, 430074, China
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18
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Wong DCJ, Amarasinghe R, Falara V, Pichersky E, Peakall R. Duplication and selection in β-ketoacyl-ACP synthase gene lineages in the sexually deceptive Chiloglottis (Orchidaceace). Ann Bot 2019; 123:1053-1066. [PMID: 30789664 PMCID: PMC6589519 DOI: 10.1093/aob/mcz013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/05/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND AND AIMS The processes of gene duplication, followed by divergence and selection, probably underpin the evolution of floral volatiles crucial to plant-insect interactions. The Australian sexually deceptive Chiloglottis orchids use a class of 2,5-dialkylcyclohexan-1,3-dione volatiles or 'chiloglottones' to attract specific male wasp pollinators. Here, we explore the expression and evolution of fatty acid pathway genes implicated in chiloglottone biosynthesis. METHODS Both Chiloglottis seminuda and C. trapeziformis produce chiloglottone 1, but only the phylogenetically distinct C. seminuda produces this volatile from both the labellum callus and glandular sepal tips. Transcriptome sequencing and tissue-specific contrasts of the active and non-active floral tissues was performed. The effects of the fatty acid synthase inhibitor cerulenin on chiloglottone production were tested. Patterns of selection and gene evolution were investigated for fatty acid pathway genes. KEY RESULTS Tissue-specific differential expression of fatty acid pathway transcripts was evident between active and non-active floral tissues. Cerulenin significantly inhibits chiloglottone 1 production in the active tissues of C. seminuda. Phylogenetic analysis of plant β-ketoacyl synthase I (KASI), a protein involved in fatty acid biosynthesis, revealed two distinct clades, one of which is unique to the Orchidaceae (KASI-2B). Selection analysis indicated a strong signal of positive selection at the split of KASI-2B followed by relaxed purifying selection in the Chiloglottis clade. CONCLUSIONS By capitalizing on a phylogenetically distinct Chiloglottis from earlier studies, we show that the transcriptional and biochemical dynamics linked to chiloglottone biosynthesis in active tissues are conserved across Chiloglottis. A combination of tissue-specific expression and relaxed purifying selection operating at specific fatty acid pathway genes may hold the key to the evolution of chiloglottones.
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Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
- For correspondence. E-mail ,
| | - Ranamalie Amarasinghe
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
| | - Vasiliki Falara
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, USA
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, Australia
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19
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Degu A, Hochberg U, Wong DCJ, Alberti G, Lazarovitch N, Peterlunger E, Castellarin SD, Herrera JC, Fait A. Swift metabolite changes and leaf shedding are milestones in the acclimation process of grapevine under prolonged water stress. BMC Plant Biol 2019; 19:69. [PMID: 30744556 PMCID: PMC6371445 DOI: 10.1186/s12870-019-1652-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 01/14/2019] [Indexed: 05/06/2023]
Abstract
BACKGROUND Grape leaves provide the biochemical substrates for berry development. Thus, understanding the regulation of grapevine leaf metabolism can aid in discerning processes fundamental to fruit development and berry quality. Here, the temporal alterations in leaf metabolism in Merlot grapevine grown under sufficient irrigation and water deficit were monitored from veraison until harvest. RESULTS The vines mediated water stress gradually and involving multiple strategies: osmotic adjustment, transcript-metabolite alteration and leaf shedding. Initially stomatal conductance and leaf water potential showed a steep decrease together with the induction of stress related metabolism, e.g. up-regulation of proline and GABA metabolism and stress related sugars, and the down-regulation of developmental processes. Later, progressive soil drying was associated with an incremental contribution of Ca2+ and sucrose to the osmotic adjustment concomitant with the initiation of leaf shedding. Last, towards harvest under progressive stress conditions following leaf shedding, incremental changes in leaf water potential were measured, while the magnitude of perturbation in leaf metabolism lessened. CONCLUSIONS The data present evidence that over time grapevine acclimation to water stress diversifies in temporal responses encompassing the alteration of central metabolism and gene expression, osmotic adjustments and reduction in leaf area. Together these processes mitigate leaf water stress and aid in maintaining the berry-ripening program.
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Affiliation(s)
- Asfaw Degu
- The French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer campus, Midreshet Ben Gurion, Israel
- College of Agriculture and Environmental Sciences, Bahir Dar University, Bahir Dar, Ethiopia
| | - Uri Hochberg
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
- Intitute of Soil, Water and Environmental Sciences, Agricultural Research Organization Rishon LeZion, Rishon LeZion, Israel
| | - Darren C. J. Wong
- Wine Research Centre, The University of British Columbia, Vancouver, Canada
| | - Giorgio Alberti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Naftali Lazarovitch
- The French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer campus, Midreshet Ben Gurion, Israel
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | | | - Jose C. Herrera
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
- Division of Viticulture and Pomology, Department of Crop Sciences, University of Natural Resources and Life Sciences Vienna (BOKU), Tulln, Austria
| | - Aaron Fait
- The French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institute for Desert Research, Ben-Gurion University of the Negev, Sede Boqer campus, Midreshet Ben Gurion, Israel
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20
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Wong DCJ. Harnessing Integrated Omics Approaches for Plant Specialized Metabolism Research: New Insights into Shikonin Biosynthesis. Plant Cell Physiol 2019; 60:4-6. [PMID: 30476245 DOI: 10.1093/pcp/pcy230] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 11/21/2018] [Indexed: 06/09/2023]
Affiliation(s)
- Darren C J Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
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21
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Chen Y, Grimplet J, David K, Castellarin SD, Terol J, Wong DCJ, Luo Z, Schaffer R, Celton JM, Talon M, Gambetta GA, Chervin C. Ethylene receptors and related proteins in climacteric and non-climacteric fruits. Plant Sci 2018; 276:63-72. [PMID: 30348329 DOI: 10.1023/a:1011357320259] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 05/22/2023]
Abstract
Fruits have been traditionally classified into two categories based on their capacity to produce and respond to ethylene during ripening. Fruits whose ripening is associated to a peak of ethylene production and a respiration burst are referred to as climacteric, while those that are not are referred to as non-climacteric. However, an increasing body of literature supports an important role for ethylene in the ripening of both climacteric and non-climacteric fruits. Genome and transcriptomic data have become available across a variety of fruits and we leverage these data to compare the structure and transcriptional regulation of the ethylene receptors and related proteins. Through the analysis of four economically important fruits, two climacteric (tomato and apple), and two non-climacteric (grape and citrus), this review compares the structure and transcriptional regulation of the ethylene receptors and related proteins in both types of fruit, establishing a basis for the annotation of ethylene-related genes. This analysis reveals two interesting differences between climacteric and non-climacteric fruit: i) a higher number of ETR genes are found in climacteric fruits, and ii) non-climacteric fruits are characterized by an earlier ETR expression peak relative to sugar accumulation.
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Affiliation(s)
- Yi Chen
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain.
| | - Karine David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Simone Diego Castellarin
- University of British Columbia, Wine Research Centre, 2205 East Mall, Vancouver, BC, V6T1Z4, Canada.
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia.
| | - Zhiwei Luo
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Robert Schaffer
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences, INRA, BP 60057, 49071 Beaucouze Cedex, France.
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Gregory Alan Gambetta
- Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, 33140 Villenave d'Ornon, France.
| | - Christian Chervin
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
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22
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Chen Y, Grimplet J, David K, Castellarin SD, Terol J, Wong DCJ, Luo Z, Schaffer R, Celton JM, Talon M, Gambetta GA, Chervin C. Ethylene receptors and related proteins in climacteric and non-climacteric fruits. Plant Sci 2018; 276:63-72. [PMID: 30348329 DOI: 10.1016/j.plantsci.2018.07.012] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 07/23/2018] [Accepted: 07/27/2018] [Indexed: 05/10/2023]
Abstract
Fruits have been traditionally classified into two categories based on their capacity to produce and respond to ethylene during ripening. Fruits whose ripening is associated to a peak of ethylene production and a respiration burst are referred to as climacteric, while those that are not are referred to as non-climacteric. However, an increasing body of literature supports an important role for ethylene in the ripening of both climacteric and non-climacteric fruits. Genome and transcriptomic data have become available across a variety of fruits and we leverage these data to compare the structure and transcriptional regulation of the ethylene receptors and related proteins. Through the analysis of four economically important fruits, two climacteric (tomato and apple), and two non-climacteric (grape and citrus), this review compares the structure and transcriptional regulation of the ethylene receptors and related proteins in both types of fruit, establishing a basis for the annotation of ethylene-related genes. This analysis reveals two interesting differences between climacteric and non-climacteric fruit: i) a higher number of ETR genes are found in climacteric fruits, and ii) non-climacteric fruits are characterized by an earlier ETR expression peak relative to sugar accumulation.
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Affiliation(s)
- Yi Chen
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
| | - Jérôme Grimplet
- Departamento de Viticultura, Instituto de Ciencias de la Vid y del Vino, CSIC, Universidad de La Rioja, Gobierno de la Rioja, Logroño, Spain.
| | - Karine David
- School of Biological Sciences, The University of Auckland, Private Bag 92019, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Simone Diego Castellarin
- University of British Columbia, Wine Research Centre, 2205 East Mall, Vancouver, BC, V6T1Z4, Canada.
| | - Javier Terol
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Darren C J Wong
- Ecology and Evolution, Research School of Biology, Australian National University, Acton, ACT 2601, Australia.
| | - Zhiwei Luo
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Robert Schaffer
- Plant & Food Research, Private Bag 92169, Auckland Mail Centre, Auckland 1142, New Zealand.
| | - Jean-Marc Celton
- Institut de Recherche en Horticulture et Semences, INRA, BP 60057, 49071 Beaucouze Cedex, France.
| | - Manuel Talon
- Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV-315, km 10,7, Moncada, Valencia, Spain.
| | - Gregory Alan Gambetta
- Bordeaux Science Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, 33140 Villenave d'Ornon, France.
| | - Christian Chervin
- Université de Toulouse, Genomics & Biotechnology of Fruits, INRA, Toulouse INP, ENSAT, BP 32607, F-31326 Castanet-Tolosan, France.
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23
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Wong DCJ, Amarasinghe R, Pichersky E, Peakall R. Evidence for the Involvement of Fatty Acid Biosynthesis and Degradation in the Formation of Insect Sex Pheromone-Mimicking Chiloglottones in Sexually Deceptive Chiloglottis Orchids. Front Plant Sci 2018; 9:839. [PMID: 29971087 PMCID: PMC6018206 DOI: 10.3389/fpls.2018.00839] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2018] [Accepted: 05/30/2018] [Indexed: 05/24/2023]
Abstract
Hundreds of orchid species secure pollination by sexually luring specific male insects as pollinators by chemical and morphological mimicry. Yet, the biochemical pathways involved in the synthesis of the insect sex pheromone-mimicking volatiles in these sexually deceptive plants remain poorly understood. Here, we explore the biochemical pathways linked to the chemical mimicry of female sex pheromones (chiloglottones) employed by the Australian sexually deceptive Chiloglottis orchids to lure their male pollinator. By strategically exploiting the transcriptomes of chiloglottone 1-producing Chiloglottis trapeziformis at distinct floral tissues and at key floral developmental stages, we identified two key transcriptional trends linked to the stage- and tissue-dependent distribution profiles of chiloglottone in the flower: (i) developmental upregulation of fatty acid biosynthesis and β-oxidation genes such as KETOACYL-ACP SYNTHASE, FATTY ACYL-ACP THIOESTERASE, and ACYL-COA OXIDASE during the transition from young to mature buds and flowers and (ii) the tissue-specific induction of fatty acid pathway genes in the callus (the insectiform odor-producing structure on the labellum of the flower) compared to the labellum remains (non-odor-producing) regardless of development stage of the flower. Enzyme inhibition experiments targeting KETOACYL-ACP SYNTHASE activity alone in three chiloglottone-producing species (C. trapeziformis, C. valida, and C. aff. valida) significantly inhibited chiloglottone biosynthesis up to 88.4% compared to the controls. These findings highlight the role of coordinated (developmental stage- and tissue-dependent) fatty acid gene expression and enzyme activities for chiloglottone production in Chiloglottis orchids.
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Affiliation(s)
- Darren C. J. Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Ranamalie Amarasinghe
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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24
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Wong DCJ, Ariani P, Castellarin S, Polverari A, Vandelle E. Co-expression network analysis and cis-regulatory element enrichment determine putative functions and regulatory mechanisms of grapevine ATL E3 ubiquitin ligases. Sci Rep 2018; 8:3151. [PMID: 29453355 PMCID: PMC5816651 DOI: 10.1038/s41598-018-21377-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2017] [Accepted: 02/02/2018] [Indexed: 02/06/2023] Open
Abstract
Arabidopsis thaliana Toxicos en Levadura (ATL) proteins are a subclass of the RING-H2 zinc finger binding E3 ubiquitin ligases. The grapevine (Vitis vinifera) ATL family was recently characterized, revealing 96 members that are likely to be involved in several physiological processes through protein ubiquitination. However, the final targets and biological functions of most ATL E3 ligases are still unknown. We analyzed the co-expression networks among grapevine ATL genes across a set of transcriptomic data related to defense and abiotic stress, combined with a condition-independent dataset. This revealed strong correlations between ATL proteins and diverse signal transduction components and transcriptional regulators, in particular those involved in immunity. An enrichment analysis of cis-regulatory elements in ATL gene promoters and related co-expressed genes highlighted the importance of hormones in the regulation of ATL gene expression. Our work identified several ATL proteins as candidates for further studies aiming to decipher specific grapevine resistance mechanisms activated in response to pathogens.
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Affiliation(s)
- Darren C J Wong
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
- Ecology and Evolution, Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Pietro Ariani
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, 37134, Italy
| | - Simone Castellarin
- Wine Research Centre, University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4, Canada
| | - Annalisa Polverari
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, 37134, Italy.
| | - Elodie Vandelle
- Dipartimento di Biotecnologie, Università degli Studi di Verona, Verona, 37134, Italy.
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25
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Wong DCJ, Pichersky E, Peakall R. The Biosynthesis of Unusual Floral Volatiles and Blends Involved in Orchid Pollination by Deception: Current Progress and Future Prospects. Front Plant Sci 2017; 8:1955. [PMID: 29181016 PMCID: PMC5693887 DOI: 10.3389/fpls.2017.01955] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 10/30/2017] [Indexed: 05/23/2023]
Abstract
Flowers have evolved diverse strategies to attract animal pollinators, with visual and olfactory floral cues often crucial for pollinator attraction. While most plants provide reward (e.g., nectar, pollen) in return for the service of pollination, 1000s of plant species, particularly in the orchid family, offer no apparent reward. Instead, they exploit their often specific pollinators (one or few) by mimicking signals of female insects, food source, and oviposition sites, among others. A full understanding of how these deceptive pollination strategies evolve and persist remains an open question. Nonetheless, there is growing evidence that unique blends that often contain unusual compounds in floral volatile constituents are often employed to secure pollination by deception. Thus, the ability of plants to rapidly evolve new pathways for synthesizing floral volatiles may hold the key to the widespread evolution of deceptive pollination. Yet, until now the biosynthesis of these volatile compounds has been largely neglected. While elucidating the biosynthesis in non-model systems is challenging, nonetheless, these cases may also offer untapped potential for biosynthetic breakthroughs given that some of the compounds can be exclusive or dominant components of the floral scent and production is often tissue-specific. In this perspective article, we first highlight the chemical diversity underpinning some of the more widespread deceptive orchid pollination strategies. Next, we explore the potential metabolic pathways and biosynthetic steps that might be involved. Finally, we offer recommendations to accelerate the discovery of the biochemical pathways in these challenging but intriguing systems.
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Affiliation(s)
- Darren C. J. Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
| | - Eran Pichersky
- Department of Molecular, Cellular and Developmental Biology, University of Michigan, Ann Arbor, MI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, Canberra, ACT, Australia
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26
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Wong DCJ, Amarasinghe R, Rodriguez-Delgado C, Eyles R, Pichersky E, Peakall R. Tissue-Specific Floral Transcriptome Analysis of the Sexually Deceptive Orchid Chiloglottis trapeziformis Provides Insights into the Biosynthesis and Regulation of Its Unique UV-B Dependent Floral Volatile, Chiloglottone 1. Front Plant Sci 2017; 8:1260. [PMID: 28769963 PMCID: PMC5515871 DOI: 10.3389/fpls.2017.01260] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 07/04/2017] [Indexed: 05/29/2023]
Abstract
The Australian sexually deceptive orchid, Chiloglottis trapeziformis, employs a unique UV-B-dependent floral volatile, chiloglottone 1, for specific male wasp pollinator attraction. Chiloglottone 1 and related variants (2,5-dialkylcyclohexane-1,3-diones), represent a unique class of specialized metabolites presumed to be the product of cyclization between two fatty acid (FA) precursors. However, the genes involved in the biosynthesis of precursors, intermediates, and transcriptional regulation remains to be discovered. Chiloglottone 1 production occurs in the aggregation of calli (callus) on the labellum under continuous UV-B light. Therefore, deep sequencing, transcriptome assembly, and differential expression (DE) analysis were performed across different tissue types and UV-B treatments. Transcripts expressed in the callus and labellum (∼23,000 transcripts) were highly specialized and enriched for a diversity of known and novel metabolic pathways. DE analysis between chiloglottone-emitting callus versus the remainder of the labellum showed strong coordinated induction of entire FA biosynthesis and β-oxidation pathways including genes encoding Ketoacyl-ACP Synthase, Acyl-CoA Oxidase, and Multifunctional Protein. Phylogenetic analysis revealed potential gene duplicates with tissue-specific differential regulation including two Acyl-ACP Thioesterase B and a Ketoacyl-ACP Synthase genes. UV-B treatment induced the activation of UVR8-mediated signaling and large-scale transcriptome changes in both tissues, however, neither FA biosynthesis/β-oxidation nor other lipid metabolic pathways showed clear indications of concerted DE. Gene co-expression network analysis identified three callus-specific modules enriched with various lipid metabolism categories. These networks also highlight promising candidates involved in the cyclization of chiloglottone 1 intermediates (e.g., Bet v I and dimeric α,β barrel proteins) and orchestrating regulation of precursor pathways (e.g., AP2/ERF) given a strong co-regulation with FA biosynthesis/β-oxidation genes. Possible alternative biosynthetic routes for precursors (e.g., aldehyde dehydrogenases) were also indicated. Our comprehensive study constitutes the first step toward understanding the biosynthetic pathways involved in chiloglottone 1 production in Chiloglottis trapeziformis - supporting the roles of FA metabolism in planta, gene duplication as a potential source of new genes, and co-regulation of novel pathway genes in a tissue-specific manner. This study also provides a new and valuable resource for future discovery and comparative studies in plant specialized metabolism of other orchids and non-model plants.
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Affiliation(s)
- Darren C. J. Wong
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Ranamalie Amarasinghe
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Claudia Rodriguez-Delgado
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Rodney Eyles
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
| | - Eran Pichersky
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann ArborMI, United States
| | - Rod Peakall
- Ecology and Evolution, Research School of Biology, The Australian National University, CanberraACT, Australia
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Savoi S, Wong DCJ, Degu A, Herrera JC, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries ( Vitis vinifera L.) Exposed to Water Deficit. Front Plant Sci 2017; 8:1124. [PMID: 28740499 DOI: 10.2174/9781608059300117010001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/12/2017] [Indexed: 05/24/2023]
Abstract
Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
| | - Darren C J Wong
- Wine Research Centre, The University of British Columbia, VancouverBC, Canada
| | - Asfaw Degu
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Jose C Herrera
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Barbara Bucchetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Aaron Fait
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all'Adige, Italy
- Center Agriculture Food Environment, University of TrentoSan Michele all'Adige, Italy
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28
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Wong DCJ, Matus JT. Constructing Integrated Networks for Identifying New Secondary Metabolic Pathway Regulators in Grapevine: Recent Applications and Future Opportunities. Front Plant Sci 2017; 8:505. [PMID: 28446914 PMCID: PMC5388765 DOI: 10.3389/fpls.2017.00505] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 03/22/2017] [Indexed: 05/19/2023]
Abstract
Representing large biological data as networks is becoming increasingly adopted for predicting gene function while elucidating the multifaceted organization of life processes. In grapevine (Vitis vinifera L.), network analyses have been mostly adopted to contribute to the understanding of the regulatory mechanisms that control berry composition. Whereas, some studies have used gene co-expression networks to find common pathways and putative targets for transcription factors related to development and metabolism, others have defined networks of primary and secondary metabolites for characterizing the main metabolic differences between cultivars throughout fruit ripening. Lately, proteomic-related networks and those integrating genome-wide analyses of promoter regulatory elements have also been generated. The integration of all these data in multilayered networks allows building complex maps of molecular regulation and interaction. This perspective article describes the currently available network data and related resources for grapevine. With the aim of illustrating data integration approaches into network construction and analysis in grapevine, we searched for berry-specific regulators of the phenylpropanoid pathway. We generated a composite network consisting of overlaying maps of co-expression between structural and transcription factor genes, integrated with the presence of promoter cis-binding elements, microRNAs, and long non-coding RNAs (lncRNA). This approach revealed new uncharacterized transcription factors together with several microRNAs potentially regulating different steps of the phenylpropanoid pathway, and one particular lncRNA compromising the expression of nine stilbene synthase (STS) genes located in chromosome 10. Application of network-based approaches into multi-omics data will continue providing supplementary resources to address important questions regarding grapevine fruit quality and composition.
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Affiliation(s)
- Darren C. J. Wong
- Ecology and Evolution, Research School of Biology, Australian National UniversityActon, ACT, Australia
| | - José Tomás Matus
- Centre for Research in Agricultural Genomics, CSIC-IRTA-UAB-UBBarcelona, Spain
- *Correspondence: José Tomás Matus
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Savoi S, Wong DCJ, Degu A, Herrera JC, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD. Multi-Omics and Integrated Network Analyses Reveal New Insights into the Systems Relationships between Metabolites, Structural Genes, and Transcriptional Regulators in Developing Grape Berries ( Vitis vinifera L.) Exposed to Water Deficit. Front Plant Sci 2017; 8:1124. [PMID: 28740499 PMCID: PMC5502274 DOI: 10.3389/fpls.2017.01124] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/12/2017] [Indexed: 05/19/2023]
Abstract
Grapes are one of the major fruit crops and they are cultivated in many dry environments. This study comprehensively characterizes the metabolic response of grape berries exposed to water deficit at different developmental stages. Increases of proline, branched-chain amino acids, phenylpropanoids, anthocyanins, and free volatile organic compounds have been previously observed in grape berries exposed to water deficit. Integrating RNA-sequencing analysis of the transcriptome with large-scale analysis of central and specialized metabolites, we reveal that these increases occur via a coordinated regulation of key structural pathway genes. Water deficit-induced up-regulation of flavonoid genes is also coordinated with the down-regulation of many stilbene synthases and a consistent decrease in stilbenoid concentration. Water deficit activated both ABA-dependent and ABA-independent signal transduction pathways by modulating the expression of several transcription factors. Gene-gene and gene-metabolite network analyses showed that water deficit-responsive transcription factors such as bZIPs, AP2/ERFs, MYBs, and NACs are implicated in the regulation of stress-responsive metabolites. Enrichment of known and novel cis-regulatory elements in the promoters of several ripening-specific/water deficit-induced modules further affirms the involvement of a transcription factor cross-talk in the berry response to water deficit. Together, our integrated approaches show that water deficit-regulated gene modules are strongly linked to key fruit-quality metabolites and multiple signal transduction pathways may be critical to achieve a balance between the regulation of the stress-response and the berry ripening program. This study constitutes an invaluable resource for future discoveries and comparative studies, in grapes and other fruits, centered on reproductive tissue metabolism under abiotic stress.
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Affiliation(s)
- Stefania Savoi
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all’Adige, Italy
| | - Darren C. J. Wong
- Wine Research Centre, The University of British Columbia, VancouverBC, Canada
| | - Asfaw Degu
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Jose C. Herrera
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Barbara Bucchetti
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Enrico Peterlunger
- Department of Agricultural, Food, Environmental and Animal Sciences, University of UdineUdine, Italy
| | - Aaron Fait
- The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the NegevSede Boqer, Israel
| | - Fulvio Mattivi
- Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund MachSan Michele all’Adige, Italy
- Center Agriculture Food Environment, University of TrentoSan Michele all’Adige, Italy
| | - Simone D. Castellarin
- Wine Research Centre, The University of British Columbia, VancouverBC, Canada
- *Correspondence: Simone D. Castellarin,
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Wong DCJ, Lopez Gutierrez R, Dimopoulos N, Gambetta GA, Castellarin SD. Combined physiological, transcriptome, and cis-regulatory element analyses indicate that key aspects of ripening, metabolism, and transcriptional program in grapes (Vitis vinifera L.) are differentially modulated accordingly to fruit size. BMC Genomics 2016; 17:416. [PMID: 27245662 PMCID: PMC4886440 DOI: 10.1186/s12864-016-2660-z] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2016] [Accepted: 04/25/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In wine grape production, management practices have been adopted to optimize grape and wine quality attributes by producing, or screening for, berries of smaller size. Fruit size and composition are influenced by numerous factors that include both internal (e.g. berry hormone metabolism) and external (e.g. environment and cultural practices) factors. Combined physiological, biochemical, and transcriptome analyses were performed to improve our current understanding of metabolic and transcriptional pathways related to berry ripening and composition in berries of different sizes. RESULTS The comparison of berry physiology between small and large berries throughout development (from 31 to 121 days after anthesis, DAA) revealed significant differences in firmness, the rate of softening, and sugar accumulation at specific developmental stages. Small berries had significantly higher skin to berry weight ratio, lower number of seeds per berry, and higher anthocyanin concentration compared to large berries. RNA-sequencing analyses of berry skins at 47, 74, 103, and 121 DAA revealed a total of 3482 differentially expressed genes between small and large berries. Abscisic acid, auxin, and ethylene hormone pathway genes were differentially modulated between berry sizes. Fatty acid degradation and stilbenoid pathway genes were upregulated at 47 DAA while cell wall degrading and modification genes were downregulated at 74 DAA in small compared to large berries. In the late ripening stage, concerted upregulation of the general phenylpropanoid and stilbenoid pathway genes and downregulation of flavonoid pathway genes were observed in skins of small compared to large berries. Cis-regulatory element analysis of differentially expressed hormone, fruit texture, flavor, and aroma genes revealed an enrichment of specific regulatory motifs related to bZIP, bHLH, AP2/ERF, NAC, MYB, and MADS-box transcription factors. CONCLUSIONS The study demonstrates that physiological and compositional differences between berries of different sizes parallel transcriptome changes that involve fruit texture, flavor, and aroma pathways. These results suggest that, in addition to direct effects brought about by differences in size, key aspects involved in the regulation of ripening likely contribute to different quality profiles between small and large berries.
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Affiliation(s)
- D C J Wong
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - R Lopez Gutierrez
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - N Dimopoulos
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada
| | - G A Gambetta
- Bordeaux Sciences Agro, Institut des Sciences de la Vigne et du Vin, Ecophysiologie et Génomique Fonctionnelle de la Vigne, UMR 1287, F-33140, Villenave d' Ornon, France
| | - S D Castellarin
- Wine Research Centre, University of British Columbia, Vancouver, BC, Canada.
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Savoi S, Wong DCJ, Arapitsas P, Miculan M, Bucchetti B, Peterlunger E, Fait A, Mattivi F, Castellarin SD. Transcriptome and metabolite profiling reveals that prolonged drought modulates the phenylpropanoid and terpenoid pathway in white grapes (Vitis vinifera L.). BMC Plant Biol 2016; 16:67. [PMID: 27001212 PMCID: PMC4802899 DOI: 10.1186/s12870-016-0760-1] [Citation(s) in RCA: 158] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2015] [Accepted: 03/15/2016] [Indexed: 05/19/2023]
Abstract
BACKGROUND Secondary metabolism contributes to the adaptation of a plant to its environment. In wine grapes, fruit secondary metabolism largely determines wine quality. Climate change is predicted to exacerbate drought events in several viticultural areas, potentially affecting the wine quality. In red grapes, water deficit modulates flavonoid accumulation, leading to major quantitative and compositional changes in the profile of the anthocyanin pigments; in white grapes, the effect of water deficit on secondary metabolism is still largely unknown. RESULTS In this study we investigated the impact of water deficit on the secondary metabolism of white grapes using a large scale metabolite and transcript profiling approach in a season characterized by prolonged drought. Irrigated grapevines were compared to non-irrigated grapevines that suffered from water deficit from early stages of berry development to harvest. A large effect of water deficit on fruit secondary metabolism was observed. Increased concentrations of phenylpropanoids, monoterpenes, and tocopherols were detected, while carotenoid and flavonoid accumulations were differentially modulated by water deficit according to the berry developmental stage. The RNA-sequencing analysis carried out on berries collected at three developmental stages-before, at the onset, and at late ripening-indicated that water deficit affected the expression of 4,889 genes. The Gene Ontology category secondary metabolic process was overrepresented within up-regulated genes at all the stages of fruit development considered, and within down-regulated genes before ripening. Eighteen phenylpropanoid, 16 flavonoid, 9 carotenoid, and 16 terpenoid structural genes were modulated by water deficit, indicating the transcriptional regulation of these metabolic pathways in fruit exposed to water deficit. An integrated network and promoter analyses identified a transcriptional regulatory module that encompasses terpenoid genes, transcription factors, and enriched drought-responsive elements in the promoter regions of those genes as part of the grapes response to drought. CONCLUSION Our study reveals that grapevine berries respond to drought by modulating several secondary metabolic pathways, and particularly, by stimulating the production of phenylpropanoids, the carotenoid zeaxanthin, and of volatile organic compounds such as monoterpenes, with potential effects on grape and wine antioxidant potential, composition, and sensory features.
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Affiliation(s)
- Stefania Savoi
- />Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
| | - Darren C. J. Wong
- />Wine Research Centre, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4 Canada
| | - Panagiotis Arapitsas
- />Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Mara Miculan
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
- />Istituto di Genomica Applicata, Parco Scientifco e Tecnologico Luigi Danieli, via Jacopo Linussio 51, 33100 Udine, Italy
| | - Barbara Bucchetti
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
| | - Enrico Peterlunger
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
| | - Aaron Fait
- />The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Israel
| | - Fulvio Mattivi
- />Department of Food Quality and Nutrition, Research and Innovation Centre, Fondazione Edmund Mach, Via E. Mach 1, 38010 San Michele all’Adige, Italy
| | - Simone D. Castellarin
- />Dipartimento di Scienze Agro-alimentari, Ambientali e Animali, University of Udine, Via delle Scienze 208, 33100 Udine, Italy
- />Wine Research Centre, The University of British Columbia, 2205 East Mall, Vancouver, BC V6T 1Z4 Canada
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Jia Y, Wong DCJ, Sweetman C, Bruning JB, Ford CM. New insights into the evolutionary history of plant sorbitol dehydrogenase. BMC Plant Biol 2015; 15:101. [PMID: 25879735 PMCID: PMC4404067 DOI: 10.1186/s12870-015-0478-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2014] [Accepted: 03/23/2015] [Indexed: 05/08/2023]
Abstract
BACKGROUND Sorbitol dehydrogenase (SDH, EC 1.1.1.14) is the key enzyme involved in sorbitol metabolism in higher plants. SDH genes in some Rosaceae species could be divided into two groups. L-idonate-5-dehydrogenase (LIDH, EC 1.1.1.264) is involved in tartaric acid (TA) synthesis in Vitis vinifera and is highly homologous to plant SDHs. Despite efforts to understand the biological functions of plant SDH, the evolutionary history of plant SDH genes and their phylogenetic relationship with the V. vinifera LIDH gene have not been characterized. RESULTS A total of 92 SDH genes were identified from 42 angiosperm species. SDH genes have been highly duplicated within the Rosaceae family while monocot, Brassicaceae and most Asterid species exhibit singleton SDH genes. Core Eudicot SDHs have diverged into two phylogenetic lineages, now classified as SDH Class I and SDH Class II. V. vinifera LIDH was identified as a Class II SDH. Tandem duplication played a dominant role in the expansion of plant SDH family and Class II SDH genes were positioned in tandem with Class I SDH genes in several plant genomes. Protein modelling analyses of V. vinifera SDHs revealed 19 putative active site residues, three of which exhibited amino acid substitutions between Class I and Class II SDHs and were influenced by positive natural selection in the SDH Class II lineage. Gene expression analyses also demonstrated a clear transcriptional divergence between Class I and Class II SDH genes in V. vinifera and Citrus sinensis (orange). CONCLUSIONS Phylogenetic, natural selection and synteny analyses provided strong support for the emergence of SDH Class II by positive natural selection after tandem duplication in the common ancestor of core Eudicot plants. The substitutions of three putative active site residues might be responsible for the unique enzyme activity of V. vinifera LIDH, which belongs to SDH Class II and represents a novel function of SDH in V. vinifera that may be true also of other Class II SDHs. Gene expression analyses also supported the divergence of SDH Class II at the expression level. This study will facilitate future research into understanding the biological functions of plant SDHs.
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Affiliation(s)
- Yong Jia
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, 5005, Australia.
| | - Darren C J Wong
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, 5005, Australia.
- Present address: Wine Research Center, Faculty of Land and Food Systems, University of British Columbia, Vancouver, V6T 1Z4, BC, Canada.
| | - Crystal Sweetman
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, 5005, Australia.
- Present address: School of Biological Sciences, Flinders University, GPO Box 2100, Adelaide, 5001, Australia.
| | - John B Bruning
- School of Biological Sciences, University of Adelaide, Adelaide, 5005, Australia.
| | - Christopher M Ford
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide, 5005, Australia.
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Wong DCJ, Sweetman C, Drew DP, Ford CM. VTCdb: a gene co-expression database for the crop species Vitis vinifera (grapevine). BMC Genomics 2013; 14:882. [PMID: 24341535 PMCID: PMC3904201 DOI: 10.1186/1471-2164-14-882] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 11/29/2013] [Indexed: 11/16/2022] Open
Abstract
Background Gene expression datasets in model plants such as Arabidopsis have contributed to our understanding of gene function and how a single underlying biological process can be governed by a diverse network of genes. The accumulation of publicly available microarray data encompassing a wide range of biological and environmental conditions has enabled the development of additional capabilities including gene co-expression analysis (GCA). GCA is based on the understanding that genes encoding proteins involved in similar and/or related biological processes may exhibit comparable expression patterns over a range of experimental conditions, developmental stages and tissues. We present an open access database for the investigation of gene co-expression networks within the cultivated grapevine, Vitis vinifera. Description The new gene co-expression database, VTCdb (http://vtcdb.adelaide.edu.au/Home.aspx), offers an online platform for transcriptional regulatory inference in the cultivated grapevine. Using condition-independent and condition-dependent approaches, grapevine co-expression networks were constructed using the latest publicly available microarray datasets from diverse experimental series, utilising the Affymetrix Vitis vinifera GeneChip (16 K) and the NimbleGen Grape Whole-genome microarray chip (29 K), thus making it possible to profile approximately 29,000 genes (95% of the predicted grapevine transcriptome). Applications available with the online platform include the use of gene names, probesets, modules or biological processes to query the co-expression networks, with the option to choose between Affymetrix or Nimblegen datasets and between multiple co-expression measures. Alternatively, the user can browse existing network modules using interactive network visualisation and analysis via CytoscapeWeb. To demonstrate the utility of the database, we present examples from three fundamental biological processes (berry development, photosynthesis and flavonoid biosynthesis) whereby the recovered sub-networks reconfirm established plant gene functions and also identify novel associations. Conclusions Together, we present valuable insights into grapevine transcriptional regulation by developing network models applicable to researchers in their prioritisation of gene candidates, for on-going study of biological processes related to grapevine development, metabolism and stress responses.
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Affiliation(s)
| | | | | | - Christopher M Ford
- School of Agriculture, Food and Wine, University of Adelaide, Adelaide 5064, South Australia, Australia.
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