Figure 2

Delimitation and effector content of Phytophthora infestans gene sparse regions (GSRs). A) Simulation of core ortholog gene segregation. Genes with both flanking intergenic regions (FIRs) longer than a value 'L' were considered as gene-sparse region (GSR) genes, whereas genes with both FIRs below L were considered as gene-dense region (GDR) genes. To quantitatively define GSRs, the % core orthologs among total genes falling in GDRs (blue) and GSRs (red) was calculated for values of L ranging from 100 bp to 5 kb. Core ortholog segregation rate was defined as the difference between the core ortholog content of the GDRs vs. GSRs (green). The percentage of core orthologs assigned to GDRs is shown as a black line. The highest core ortholog genes segregation rate was obtained for L = 1.5 kb. B) Distribution of P. infestans genes according to the length of their FIRs. All P. infestans predicted genes were sorted into 2-variable bins according to their 3'FIR (Y-axis) and 5'FIR (X-axis). The number of genes in bins is shown as a contour graph with a color code. The 1.5 kb limit for GSRs genes (dotted lines) delimits three groups of genes: genes in GDRs, GSRs, and in between (corresponding genes features and numbers are indicated in labels). C) A sample window from the P. infestans genome browser illustrating typical examples of GDRs and GSR (red background). In this 80 kb region, core ortholog genes are exclusively found in GDRs, secretome genes (yellow) and genes excluded from orthologous segments (OS, red box) are excluded from GDRs. D) Distribution of gene groups into the GDRs and GSRs of P. infestans. The proportion of non-secreted, secretome, known effectors, RXLR effector genes and CRN effector genes that occur in GSRs (red, with % indicated), GDRs (blue with % indicated) and in between (yellow) is shown.