New cross-talks between pathways involved in grapevine infection with ʼCandidatus Phytoplasma solaniʼ revealed by temporal network modelling

Škrlj, Blaž (author), Pompe Novak, Maruša (author), Brader, Günter (author), Anžič, Barbara (author), Ramšak, Živa (author), Gruden, Kristina (author), Kralj, Jan (author), Kladnik, Aleš (author), Lavrač, Nada (author), Roitsch, Thomas (author), Dermastia, Marina (author)

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

• Language: English
• Keywords: community detection, enrichment analysis, network analysis, phytoplasma, bois noir
• Work type: Article
• Typology: 1.01 - Original Scientific Article
• Organization: BF - Biotechnical Faculty
• Publication status: Published
• Publication version: Version of Record
• Year: 2021
• Number of pages: 18 str.
• Numbering: Vol. 10, iss. 4, art. 646
• PID: 20.500.12556/RUL-135237
• UDC: 577
• ISSN on article: 2223-7747
• DOI: 10.3390/plants10040646
• COBISS.SI-ID: 58899971
• Publication date in RUL: 02.03.2022

Record is a part of a journal

• Title: Plants
• Shortened title: Plants
• Publisher: MDPI
• ISSN: 2223-7747
• COBISS.SI-ID: 523345433

Licences

• License: CC BY 4.0, Creative Commons Attribution 4.0 International
• Link: http://creativecommons.org/licenses/by/4.0/
• Description: This is the standard Creative Commons license that gives others maximum freedom to do what they want with the work as long as they credit the author.
• Licensing start date: 01.04.2021

Secondary language

• Language: Slovenian
• Keywords: analiza omrežij, fitoplazme, počrnelost lesa