Two addi tional CRNs have SignalP v2. 0 HMM scores of 0. 89 and 0. 76, respectively, which although below our stringent cutoff than of 0. 9 may still suggest potential signal peptides. Several of the remaining genes have incomplete ORFs and gene models, suggest ing a high frequency of CRN pseudogenes as previously noted in Ph. infestans. All 26 amino terminal regions were aligned to generate Inhibitors,Modulators,Libraries a sequence logo. These analyses revealed a conserved LxLYLAR K motif that is shared amongst P. ultimum CRN proteins and is followed by a conserved Inhibitors,Modulators,Libraries WL motif. The LxLYLAR K motif is closely related to the F LxLY LALK motif found in Aphanomyces euteiches.

Con sistent with results obtained in other oomycete genomes, we found that the LxLYLAR K motif Inhibitors,Modulators,Libraries was located between 46 and 64 amino acids after the methionine, fol lowed by a variable domain that ended with a conserved motif at the proposed recombination site, reflecting the modular design of CRN proteins in the oomycetes. This recombi nation site, which is characteristic for the DWL domain, was found highly conserved Inhibitors,Modulators,Libraries in 11 of the putative P. ulti mum CRN genes, consisting of an aliphatic amino acid followed by a conserved histidine, another three aliphatic amino acids, two variable amino acids and a conserved proline. In a phylogenetic analysis, these 11 genes were predominantly placed basal to the validated CRNs from Phytophthora. Although the CRN like genes in Pythium are more divergent than the validated CRNs of Phytophthora, both the recombination site and the LxLY LAR K motif, which is a modification of the prominent LxLFLAK motif present in most Phytophthora CRNs, show a significant degree of conservation, highlighting that the CRN family, greatly expanded in Phytophthora, had already evolved in the last common ancestor of P.

ultimum and Phytophthora. A novel family of candidate effectors In the absence of obvious proteins with an amino term inal RXLR motif, we used other known features of effec tors to identify candidate effector families in P. ultimum. Ph. Inhibitors,Modulators,Libraries infestans RXLR effectors are not only characterized by a conserved amino terminal transloca tion domain but also by their occurrence in gene sparse regions that are enriched in repetitive DNA. Based on the length of the flanking non coding regions, the distribution of P. ultimum genes is not multimodal as was observed in Ph. infestans.

However, relative to the rest of the genes, P. ulti mum secretome genes more frequently have long flank ing non coding regions. In addition, the secretome genes show selleck chemicals llc a higher propor tion of closely related paralogs, suggesting recent dupli cations in P. ultimum and indicating that the secretome genes may have distinct genome organization and evolution as noted in Phytophthora spp. Using genome organization properties to identify families of secreted proteins in P.