Abstract
Rust fungi are obligate biotrophic pathogens that cause considerable damage on crop plants. Puccinia graminis f. sp. tritici, the causal agent of wheat stem rust, and Melampsora larici-populina, the poplar leaf rust pathogen, have strong deleterious impacts on wheat and poplar wood production, respectively. Filamentous pathogens such as rust fungi secrete molecules called disease effectors that act as modulators of host cell physiology and can suppress or trigger host immunity. Current knowledge on effectors from other filamentous plant pathogens can be exploited for the characterisation of effectors in the genome of recently sequenced rust fungi. We designed a comprehensive in silico analysis pipeline to identify the putative effector repertoire from the genome of two plant pathogenic rust fungi. The pipeline is based on the observation that known effector proteins from filamentous pathogens have at least one of the following properties: (i) contain a secretion signal, (ii) are encoded by in planta induced genes, (iii) have similarity to haustorial proteins, (iv) are small and cysteine rich, (v) contain a known effector motif or a nuclear localization signal, (vi) are encoded by genes with long intergenic regions, (vii) contain internal repeats, and (viii) do not contain PFAM domains, except those associated with pathogenicity. We used Markov clustering and hierarchical clustering to classify protein families of rust pathogens and rank them according to their likelihood of being effectors. Using this approach, we identified eight families of candidate effectors that we consider of high value for functional characterization. This study revealed a diverse set of candidate effectors, including families of haustorial expressed secreted proteins and small cysteine-rich proteins. This comprehensive classification of candidate effectors from these devastating rust pathogens is an initial step towards probing plant germplasm for novel resistance components.
Highlights
Rust fungi are a diverse monophyletic group of obligate plant pathogens that infect numerous economically important cereal crops and constitute a serious threat to global food security [1]
Poplar plantations are susceptible to widespread infestation by the leaf rust fungus, with the threat exacerbated by artificial cultivation methods such as dense planting and breeding for uniformity, which limits genetic diversity [3]
A total of 1222 tribes containing at least one secreted protein were produced by analysis of the combined proteomes of M. larici-populina and P. graminis f. sp. tritici
Summary
Rust fungi are a diverse monophyletic group of obligate plant pathogens that infect numerous economically important cereal crops and constitute a serious threat to global food security [1]. The Ug99 race and its variants are estimated to be virulent on over 90% of the wheat grown globally, presenting a substantial threat to wheat production [2]. Rust fungi present a serious threat to the production of bioenergy and fundamental plant products derived from the poplar tree. Poplar plantations are susceptible to widespread infestation by the leaf rust fungus, with the threat exacerbated by artificial cultivation methods such as dense planting and breeding for uniformity, which limits genetic diversity [3]. The integration of new resistance (R) genes through plant breeding programs remains the main sustainable solution to dealing with these notorious and destructive plant pathogens
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