title: Using hierarchical clustering of secreted protein families to classify and rank candidate effectors of rust fungi.
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.
authors.affiliation: The Sainsbury Laboratory, Norwich Research Park, Norwich, United Kingdom.
authors.forename: Diane G O
authors.initials: DG
authors.lastname: Saunders
authors.forename: Joe
authors.initials: J
authors.lastname: Win
authors.forename: Liliana M
authors.initials: LM
authors.lastname: Cano
authors.forename: Les J
authors.initials: LJ
authors.lastname: Szabo
authors.forename: Sophien
authors.initials: S
authors.lastname: Kamoun
authors.forename: Sylvain
authors.initials: S
authors.lastname: Raffaele
mesh_terms: D000595:Amino Acid Sequence; D016000:Cluster Analysis; D005656:Fungal Proteins / Q000145:classification* / Q000235:genetics / Q000378:metabolism*; D005658:Fungi / Q000235:genetics* / Q000378:metabolism*; D020869:Gene Expression Profiling; D056726:Genetic Association Studies; D008954:Models, Biological; D005810:Multigene Family / Q000235:genetics; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D018515:Plant Leaves / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D018547:Plant Stems / Q000235:genetics / Q000378:metabolism; D032107:Populus / Q000235:genetics / Q000378:metabolism / Q000382:microbiology; D020543:Proteome / Q000032:analysis / Q000235:genetics; D055571:Secretory Pathway / Q000235:genetics; D014908:Triticum / Q000235:genetics / Q000378:metabolism / Q000382:microbiology
chemical_list: D005656:Fungal Proteins; D020543:Proteome