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Article

Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

1
Research and Innovation Centre, Department of Genomics and Biology of Fruit Crops, Fondazione Edmund Mach, 38098 San Michele all’Adige, Italy
2
Institute for Integrative Systems Biology (I2SysBio), Universitat de València-CSIC, 46908 Paterna, Valencia, Spain
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Centre for Integrative Biology (CIBIO), University of Trento, 38123 Trento, Italy
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Department of Information Engineering and Computer Science, University of Trento, 38123 Trento, Italy
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CNR-Institute of Materials for Electronics and Magnetism, 38123 Trento, Italy
*
Author to whom correspondence should be addressed.
Academic Editor: Attila Fehér
Biomolecules 2021, 11(12), 1744; https://doi.org/10.3390/biom11121744
Received: 9 October 2021 / Revised: 11 November 2021 / Accepted: 16 November 2021 / Published: 23 November 2021
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. View Full-Text
Keywords: OneGenE; stilbenoids; lignin; causal inference; gene network; transcriptomics; peroxidase; laccase; dirigent protein OneGenE; stilbenoids; lignin; causal inference; gene network; transcriptomics; peroxidase; laccase; dirigent protein
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MDPI and ACS Style

Pilati, S.; Malacarne, G.; Navarro-Payá, D.; Tomè, G.; Riscica, L.; Cavecchia, V.; Matus, J.T.; Moser, C.; Blanzieri, E. Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families. Biomolecules 2021, 11, 1744. https://doi.org/10.3390/biom11121744

AMA Style

Pilati S, Malacarne G, Navarro-Payá D, Tomè G, Riscica L, Cavecchia V, Matus JT, Moser C, Blanzieri E. Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families. Biomolecules. 2021; 11(12):1744. https://doi.org/10.3390/biom11121744

Chicago/Turabian Style

Pilati, Stefania, Giulia Malacarne, David Navarro-Payá, Gabriele Tomè, Laura Riscica, Valter Cavecchia, José Tomás Matus, Claudio Moser, and Enrico Blanzieri. 2021. "Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families" Biomolecules 11, no. 12: 1744. https://doi.org/10.3390/biom11121744

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