New Cross-Talks between Pathways Involved in Grapevine Infection with ' Candidatus Phytoplasma solani' Revealed by Temporal Network Modelling

• Published in: Plants (Basel) Vol. 10; no. 4; p. 646
• Main Authors: Škrlj, Blaž, Novak, Maruša Pompe, Brader, Günter, Anžič, Barbara, Ramšak, Živa, Gruden, Kristina, Kralj, Jan, Kladnik, Aleš, Lavrač, Nada, Roitsch, Thomas, Dermastia, Marina
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 29-03-2021; MDPI
• Subjects: Algorithms; Binding sites; bois noir; Candidatus Phytoplasma solani; community detection; Community involvement; Computer networks; enrichment analysis; Gene expression; Metabolism; Methodology; Network analysis; Ontology; Phytoplasma; Semantics; Signal transduction; phytoplasma; network analysis; bois noir; community detection; enrichment analysis
• ISSN: 2223-7747; 2223-7747
• DOI: 10.3390/plants10040646

Understanding temporal biological phenomena is a challenging task that can be approached using network analysis. Here, we explored whether network reconstruction can be used to better understand the temporal dynamics of bois noir, which is associated with '
Phytoplasma solani', and is one of the most widespread phytoplasma diseases of grapevine in Europe. We proposed a methodology that explores the temporal network dynamics at the community level, i.e., densely connected subnetworks. The methodology offers both insights into the functional dynamics via enrichment analysis at the community level, and analyses of the community dissipation, as a measure that accounts for community degradation. We validated this methodology with cases on experimental temporal expression data of uninfected grapevines and grapevines infected with '
. P. solani'. These data confirm some known gene communities involved in this infection. They also reveal several new gene communities and their potential regulatory networks that have not been linked to '
. P. solani' to date. To confirm the capabilities of the proposed method, selected predictions were empirically evaluated.