New Cross-Talks between Pathways Involved in Grapevine Infection with ‘<i>Candidatus</i> Phytoplasma solani’ Revealed by Temporal Network Modelling

• Main Authors: Blaž Škrlj, Maruša Pompe Novak, Günter Brader, Barbara Anžič, Živa Ramšak, Kristina Gruden, Jan Kralj, Aleš Kladnik, Nada Lavrač, Thomas Roitsch, Marina Dermastia
• Format: Article
• Language: English
• Published: MDPI AG 2021-03-01
• Series: Plants
• Subjects: network analysis; phytoplasma; bois noir; community detection; enrichment analysis
• Online Access: https://www.mdpi.com/2223-7747/10/4/646

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 ‘<i>Candidatus</i> 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 ‘<i>Ca</i>. 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 ‘<i>Ca</i>. P. solani’ to date. To confirm the capabilities of the proposed method, selected predictions were empirically evaluated.