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Background   Phytophthora infestans  is the most devastating pathogen of potato and a model organism for the oomycetes. It exhibits high evolutionary potential and rapidly adapts to host plants. The  P. infestans  genome experienced a repeat-driven expansion relative to the genomes of  Phytophthora sojae  and  Phytophthora ramorum  and shows a discontinuous distribution of gene density. Effector genes, such as members of the RXLR and Crinkler (CRN) families, localize to expanded, repeat-rich and gene-sparse regions of the genome. This distinct genomic environment is thought to contribute to genome plasticity and host adaptation.    Results  We used  in silico  approaches to predict and describe the repertoire of  P. infestans  secreted proteins (the secretome). We defined the "plastic secretome" as a subset of the genome that (i) encodes predicted secreted proteins, (ii) is excluded from genome segments orthologous to the  P. sojae  and  P. ramorum  genomes and (iii) is encoded by genes residing in gene sparse regions of  P. infestans  genome. Although including only ~3%  of P. infestans  genes, the plastic secretome contains ~62% of known effector genes and shows >2 fold enrichment in genes induced  in planta . We highlight 19 plastic secretome genes induced  in planta  but distinct from previously described effectors. This list includes a trypsin-like serine protease, secreted oxidoreductases, small cysteine-rich proteins and repeat containing proteins that we propose to be novel candidate virulence factors.    Conclusions  This work revealed a remarkably diverse plastic secretome. It illustrates the value of combining genome architecture with comparative genomics to identify novel candidate virulence factors from pathogen genomes.

Analyses of genome architecture and gene expression reveal novel candidate virulence factors in the secretome of Phytophthora infestans