De novo assembly using low-coverage short read sequence data from the rice pathogen Pseudomonas syringae pv. oryzae

Por_{1_6} genome redefines the P. syringae pan-genome and type III effectorome. (A) The Por_{1_6} genome adds 97 unique genes to the pan-(distributed) genome of P. syringae (red boxes) and reduces the core (overlapping) genome by 161 genes (blue diamonds). (B) Por_{1_6} shares about 4000 of its 4450 predicted ORFs with each of the other three fully sequenced P. syringae strains. Shown are predictions based on a BLAST homology (E < 10⁻⁶). (C) Por_{1_6} contains a unique combination of type III effector proteins compared with the three previously sequenced strains. Type III effector proteins in Por_{1_6} were predicted using both homology with the known type III effectors in the other three fully sequenced P. syringae strains and gene prediction software (Methods). Note that the presence of a given type III effector gene, or homolog, does not necessarily imply that it is translocated (Chang et al. 2005; Schechter et al. 2006).