Abstract
Oomycetes comprise a diverse group of organisms that morphologically resemble fungi but belong to the stramenopile lineage within the supergroup of chromalveolates. Recent studies have shown that plant pathogenic oomycetes have expanded gene families that are possibly linked to their pathogenic lifestyle. We analyzed the protein domain organization of 67 eukaryotic species including four oomycete and five fungal plant pathogens. We detected 246 expanded domains in fungal and oomycete plant pathogens. The analysis of genes differentially expressed during infection revealed a significant enrichment of genes encoding expanded domains as well as signal peptides linking a substantial part of these genes to pathogenicity. Overrepresentation and clustering of domain abundance profiles revealed domains that might have important roles in host-pathogen interactions but, as yet, have not been linked to pathogenicity. The number of distinct domain combinations (bigrams) in oomycetes was significantly higher than in fungi. We identified 773 oomycete-specific bigrams, with the majority composed of domains common to eukaryotes. The analyses enabled us to link domain content to biological processes such as host-pathogen interaction, nutrient uptake, or suppression and elicitation of plant immune responses. Taken together, this study represents a comprehensive overview of the domain repertoire of fungal and oomycete plant pathogens and points to novel features like domain expansion and species-specific bigram types that could, at least partially, explain why oomycetes are such remarkable plant pathogens.
Highlights
Oomycetes are a diverse group of organisms that live as saprophytes or as pathogens of plants, insects, fish, vertebrates, and microbes (Govers and Gijzen, 2006)
We quantified and examined domain properties observed in oomycetes and especially emphasized differences and common themes within fungal- and oomycete plant pathogens and their probable contribution to a pathogenic lifestyle
We observed that oomycete plant pathogens, in particular Phytophthora spp., have significantly higher numbers of unique bigram types compared to species with a similar number of domain types (Fig. 2a)
Summary
Oomycetes are a diverse group of organisms that live as saprophytes or as pathogens of plants, insects, fish, vertebrates, and microbes (Govers and Gijzen, 2006). Plant pathogenic oomycetes include a large number of different species that vary in their lifestyle, from obligate biotrophic, hemi-biotrophic to necrotrophic They show great differences in host selectivity ranging from broad to very narrow (Erwin and Ribeiro, 1996; Agrios, 2005). The genomes of oomycetes sequenced so far are variable in size and content, ranging from 65 Mb in Phytophthora ramorum to 240 Mb in P. infestans (Haas et al, 2009) and only include plant pathogenic species. Analysis of these genomes revealed that several gene families facilitating the infection process are expanded (Martens et al, 2008). Comparative genomics provides an important framework to functionally characterize oomycete gene products and generate hypotheses on the basic cellular functions as well as the complex interactions of these plant pathogens with their hosts and environment
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