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

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

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.

• Jezik: Angleški jezik
• Ključne besede: community detection, enrichment analysis, network analysis, phytoplasma, bois noir
• Vrsta gradiva: Članek v reviji
• Tipologija: 1.01 - Izvirni znanstveni članek
• Organizacija: BF - Biotehniška fakulteta
• Status publikacije: Objavljeno
• Različica publikacije: Objavljena publikacija
• Leto izida: 2021
• Št. strani: 18 str.
• Številčenje: Vol. 10, iss. 4, art. 646
• PID: 20.500.12556/RUL-135237
• UDK: 577
• ISSN pri članku: 2223-7747
• DOI: 10.3390/plants10040646
• COBISS.SI-ID: 58899971
• Datum objave v RUL: 02.03.2022

Gradivo je del revije

• Naslov: Plants
• Skrajšan naslov: Plants
• Založnik: MDPI
• ISSN: 2223-7747
• COBISS.SI-ID: 523345433

Licence

• Licenca: CC BY 4.0, Creative Commons Priznanje avtorstva 4.0 Mednarodna
• Povezava: http://creativecommons.org/licenses/by/4.0/deed.sl
• Opis: To je standardna licenca Creative Commons, ki daje uporabnikom največ možnosti za nadaljnjo uporabo dela, pri čemer morajo navesti avtorja.
• Začetek licenciranja: 01.04.2021

Sekundarni jezik

• Jezik: Slovenski jezik
• Ključne besede: analiza omrežij, fitoplazme, počrnelost lesa