Schematic representation of events occurring in the pathogen during the infection process; A) 15 sai; B) 7 hai, C) 48 hai, and D) 10 dai of a susceptible soybean leaf with Phakopsora pachyrhizi . Drawing in black represents a cross-section of a soybean leaf where zone 1 represents the upper cuticle, zone 2 the upper epidermis cell layer, zone 3 the palisade mesophyll cell layer, zone 4 the spongy mesophyll cell layer, zone 5 the lower epidermis cell layer, and zone 6 the lower cuticle. Drawing in brown represents P. pachyrhizi structures on and inside the soybean leaf showing spore (S), mitochondrion (M), germ tube (GT), appressorium (A), primary hypha (PH), infectious hyphae (IH), haustorium (H), and uredinium (U). Metabolic pathways, proteins, E. C. numbers, products, and substrates colored in blue are activated or expressed; those colored in green are up-regulated compared to the previous time-point; and those colored in red are down-regulated compared to the previous time-point; while boxes colored in yellow represent enzymes encoded by transcripts with varied regulatory status. Metabolic pathways, proteins, E.C. numbers, products, and substrates colored in black were not activated or expressed in the present data set.