Abstract
Interactions between proteins underlie all aspects of complex biological mechanisms. Therefore, methodologies based on complex network analyses can facilitate identification of promising candidate genes involved in phenotypes of interest and put this information into appropriate contexts. 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, across nine orders, 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. Network cartography analysis was associated with functional patterns of annotated genes linked to the 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 B. cinerea and F. 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.
Highlights
Global food security is threatened by numerous plant diseasecausing fungal pathogens, which infect agricultural and horticultural crops
To evaluate the quality of the different sources of inferred interactions, we have explored the numbers of co-localized interaction partners and the semantic similarity of their functional annotations in BP and molecular function (MF) aspects of the Gene Ontology (GO)
While B. cinerea is not a pathogen of wheat but of tomato and many other dicotyledonous hosts (Table 1), we suggest that the orthologous B. cinerea silencing RNAs (siRNAs) target genes in F. graminearum have a conserved function and may likely be virulence genes in this species
Summary
Global food security is threatened by numerous plant diseasecausing fungal pathogens, which infect agricultural and horticultural crops. New control mechanisms are urgently needed as pathogens (i) evolve resistance to the ever-narrowing range of available site specific and broad-spectrum fungicides, and (ii) regularly overcome the various disease resistance genes introduced by plant breeders. The necrotrophic Botrytis cinerea kills infected plant cells outright, whereas hemibiotrophic fungi such as Magnaporthe oryzae, Fusarium graminearum, Fusarium oxysporum, Colletotrichum spp., and Zymoseptoria tritici invade initially living host tissue until host cell death occurs. Biotrophic fungi, such as Blumeria graminis, keep host plants alive throughout the disease formation process. Differences in gene content of filamentous fungal pathogens can be attributed to the action of repetitive elements, transposons, and genome rearrangements in several lineages (Raffaele and Kamoun, 2012)
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