Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene Families
The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept,...
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| Format: | Article |
| Language: | English |
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MDPI AG
2021-11-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/11/12/1744 |
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| author | Stefania Pilati Giulia Malacarne David Navarro-Payá Gabriele Tomè Laura Riscica Valter Cavecchia José Tomás Matus Claudio Moser Enrico Blanzieri |
| author_facet | Stefania Pilati Giulia Malacarne David Navarro-Payá Gabriele Tomè Laura Riscica Valter Cavecchia José Tomás Matus Claudio Moser Enrico Blanzieri |
| author_sort | Stefania Pilati |
| collection | DOAJ |
| description | The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs. |
| first_indexed | 2024-03-10T04:33:55Z |
| format | Article |
| id | doaj.art-a40d720bafc148aabbd8913ddbb6157b |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T04:33:55Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Biomolecules |
| spelling | doaj.art-a40d720bafc148aabbd8913ddbb6157b2023-11-23T03:58:28ZengMDPI AGBiomolecules2218-273X2021-11-011112174410.3390/biom11121744Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene FamiliesStefania Pilati0Giulia Malacarne1David Navarro-Payá2Gabriele Tomè3Laura Riscica4Valter Cavecchia5José Tomás Matus6Claudio Moser7Enrico Blanzieri8Research and Innovation Centre, Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, 38098 San Michele all’Adige, ItalyResearch and Innovation Centre, Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, 38098 San Michele all’Adige, ItalyInstitute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46908 Paterna, Valencia, SpainCentre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, ItalyDepartment of Information Engineering and Computer Science, University of Trento, 38123 Trento, ItalyCNR-Institute of Materials for Electronics and Magnetism, 38123 Trento, ItalyInstitute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46908 Paterna, Valencia, SpainResearch and Innovation Centre, Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, 38098 San Michele all’Adige, ItalyDepartment of Information Engineering and Computer Science, University of Trento, 38123 Trento, ItalyThe abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.https://www.mdpi.com/2218-273X/11/12/1744OneGenEstilbenoidslignincausal inferencegene networktranscriptomics |
| spellingShingle | Stefania Pilati Giulia Malacarne David Navarro-Payá Gabriele Tomè Laura Riscica Valter Cavecchia José Tomás Matus Claudio Moser Enrico Blanzieri Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene Families Biomolecules OneGenE stilbenoids lignin causal inference gene network transcriptomics |
| title | Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene Families |
| title_full | Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene Families |
| title_fullStr | Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene Families |
| title_full_unstemmed | Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene Families |
| title_short | Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in <i>Vitis vinifera</i> Sheds Light on the Laccase and Dirigent Gene Families |
| title_sort | vitis onegene a causality based approach to generate gene networks in i vitis vinifera i sheds light on the laccase and dirigent gene families |
| topic | OneGenE stilbenoids lignin causal inference gene network transcriptomics |
| url | https://www.mdpi.com/2218-273X/11/12/1744 |
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