Figure 5
Observed (A) expression values (mean fpkm) for Foc Fus2 genes expressed during infection of onion seedlings at 72 hpi and predicted expression values from generalized linear modelling (B). Differences in gene expression are observed between effector-type, genomic region and presence of a mimp within 2 Kb of the gene. Number of genes in each category is shown above observed values. Pairwise significances (P < 0.05) are shown above predicted values, as determined by a Tukey test of terms from a negative binomial GLM. Effector categories include genes encoding non-effectors, secreted proteins, secreted carbohydrate active enzymes (CAZY) and secreted proteins with an effector-like structure (EffectorP). Genomic regions shown are core chromosomes 1–10 (Core), effector-enriched core chromosomes 11–13 (effector-enriched core), non-PS LS contigs, and PS contigs. Expression is shown for genes within 2 Kb of a mimp sequence (mimp).
