Original Research ARTICLE
PHI-Nets: A network resource for Ascomycete fungal pathogens to annotate and identify putative virulence interacting proteins and siRNAs
- 1Rothamsted Research (BBSRC), United Kingdom
- 2King's College London, United Kingdom
Interactions between proteins underlie all aspects of complex biological mechanisms, therefore methodologies based on complex networks analysis can facilitate identification of promising candidate genes involved in phenotypes of interest and put this information into appropriate context. To facilitate discovery and gain additional insights into globally important pathogenic fungi, we have reconstructed computationally inferred interactomes using an interolog and domain-based approach for 15 diverse Ascomycete fungal species, specifically Aspergillus fumigatus, Bipolaris sorokiniana, Blumeria graminis f.sp hordei, Botrytis cinerea, Colletotrichum gloeosporioides, Colletotrichum graminicola, Fusarium graminearum, Fusarium oxysporum f. sp. lycopersici, Fusarium verticillioides, Leptosphaeria maculans, Magnaporthe oryzae, Saccharomyces cerevisiae, Sclerotinia sclerotiorum, Verticillium dahliae, and Zymoseptoria tritici. The topological properties of networks corresponding to individual species interactomes were studied using a combination of community structure detection and functional cartography analysis and were then associated to functional patterns of annotated genes linked to disease-causing ability of each pathogen. In addition, for the best annotated organism, namely F. graminearum, the distribution of annotated genes with respect to network structure was profiled using a random walk with restart algorithm, which suggested possible co-location of virulence-related genes in the protein-protein interaction network.
In a second ‘use case’ study involving two networks, namely Botrytis cinerea and Fusarium graminearum, previously identified small silencing plant RNAs were mapped to their targets. The F. graminearum phenotypic network analysis implicates eight B. cinerea targets and 35 F. graminearum predicted interacting proteins as prime candidate virulence genes for further testing. All 15 networks have been made accessible for download at www.phi-base.org, providing a rich resource for major crop plant pathogens.
Keywords: biological networks, pathogenic fungi, interactome inference, small interfering RNA, PHI-base, gene function inference fungal species, specifically Aspergillus fumigatus, Bipolaris sorokiniana, Blumeria graminis fsp hordei, Botrytis cinerea, Colletotrichum gloeosporioides, Colletotrichum graminicola, Fusarium graminearum, Fusarium oxysporum f sp lycopersici, Fusarium verticillioides, Leptosphaeria maculans, Magnaporthe oryzae, Saccharomyces cerevisiae, Sclerotinia sclerotiorum, Verticillium dahliae, and Zymoseptoria tritici Network cartography
Received: 01 Sep 2019;
Accepted: 08 Nov 2019.
Copyright: © 2019 Urban, Lysenko, Janowska-Sedja, Rawlings, Hammond-Kosack and Tsoka. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Dr. Martin Urban, Rothamsted Research (BBSRC), Harpenden, United Kingdom, email@example.com