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.

Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families / Pilati, Stefania; Malacarne, Giulia; Navarro-Payá, David; Tomè, Gabriele; Riscica, Laura; Cavecchia, Valter; Matus, José Tomás; Moser, Claudio; Blanzieri, Enrico. - In: BIOMOLECULES. - ISSN 2218-273X. - 11:12(2021), p. 1744. [10.3390/biom11121744]

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

Pilati, Stefania;Malacarne, Giulia;Tomè, Gabriele;Cavecchia, Valter;Moser, Claudio;Blanzieri, Enrico
2021-01-01

Abstract

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.
2021
12
Pilati, Stefania; Malacarne, Giulia; Navarro-Payá, David; Tomè, Gabriele; Riscica, Laura; Cavecchia, Valter; Matus, José Tomás; Moser, Claudio; Blanzieri, Enrico
Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families / Pilati, Stefania; Malacarne, Giulia; Navarro-Payá, David; Tomè, Gabriele; Riscica, Laura; Cavecchia, Valter; Matus, José Tomás; Moser, Claudio; Blanzieri, Enrico. - In: BIOMOLECULES. - ISSN 2218-273X. - 11:12(2021), p. 1744. [10.3390/biom11121744]
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Utilizza questo identificativo per citare o creare un link a questo documento: https://hdl.handle.net/11572/373199
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