FIRs were computed using predicted gene coordinates on scaffolds. Binning according to 5 FIRs and 3 FIRs was performed along the x aixs and y axis, respectively, using condi tional counting functions. Logarithmic size was chosen for the bins in order Paclitaxel mw to allow a maximum dispersion of the values. A color code was used to represent the num ber of genes or average values in bins. Average values were computed for bins containing a minimum of three genes. Motif searches were done using the MEME pre diction server with default parameters except the follow ing min width 4. max width 12. min sites 10. Sequences with homology to Inhibitors,Modulators,Libraries gene models in oomycetes genomes were identified by BLAST analysis against the NR database and aligned using MUSCLE. For phy logenetic inference of the CRN genes, alignments were done using RevTrans with the dialign T algorithm.

Molecular phylogenetic reconstructions were done using RAxML version 7. 0. Sequence logos were con structed on the basis of the RevTrans alignment using WebLogo. Comparative genomics analyses In order to find Inhibitors,Modulators,Libraries substantial expansions and contractions of gene families observed in other eukaryotes, we used the PANTHER Classification System. We first scored all predicted proteins from the P. ultimum genome against the PANTHER HMMs, and created a tab delimited file with two columns the P. ultimum pro tein identifier and the PANTHER HMM identifier from the top scoring HMM. We created similar files for three Phytophthora genomes, and a diatom genome for comparison. We removed protein families of probable viral origin or transposons.

This left 7,762 P. ultimum proteins in PANTHER families, 8,169 from Ph. infestans, 7,667 from Ph. ramorum and 7,701 from Ph. sojae. We then uploaded the tab delimited files to the PANTHER Inhibitors,Modulators,Libraries Gene List Comparison Tool and analyzed the list for under and over representation of genes with respect to molecular functions, biological processes, and pathways. For each class that was significantly different between P. ultimum and all of the Phytophthora genomes, we determined the protein family expansions or contractions that made the biggest contributions to these differences. Finally, we determined likely gene duplication and loss events that generated the observed protein family expansions and contractions by building phylogenetic trees Inhibitors,Modulators,Libraries of each of these families using the 48 genomes included in the trees on the PANTHER website, in addition to the five stramenopile genomes above.

Phylogenetic trees were constructed using the GIGA algorithm, which infers the timing of likely gene duplication events relative to speciation events, allowing the reconstruction Inhibitors,Modulators,Libraries of ancestral genome content selleck screening library and lineage specific duplica tions and losses. Using v3 of the annotation, P. ultimum genes orthologous to genes in Ph. infestans, Ph. sojae and Ph.