Por1_6 likely has an integrated plasmid. We surveyed all Por1_6 scaffolds for sequences similar to known P. syringae plasmid genes. Por1_6 scaffolds 34 and 110 showed significant levels of similarity to a known plasmid, pPSR1 (Sundin et al. 2004). Coverage levels within the raw reads were determined for these scaffolds as well as for unique portions of each PtoDC3000 plasmid and unique genomic regions from both Por1_6 and PtoDC3000. (red diamonds). Four single-copy chromosomal genes commonly used in MLST studies (rpoD, fruK, gyrB, gltA) were chosen from PtoDC3000 and Por1_6 as controls for chromosome-level coverage, and two duplicated genes (ilvA2 and PSPTO_0034) were randomly chosen as positive controls for duplicated regions. Coverage levels for sequences from both PtoDC3000 plasmids were consistently higher than those for the single-copy PtoDC3000 chromosomal sequences (A). Hence, there are multiple copies of each plasmid present within a cell relative to the chromosome. In contrast, the coverage levels of Por1_6 scaffolds 43 and 110 were very similar to that of the four control genes (B), implying that these regions are present on a very low copy number plasmid or have been integrated into the Por1_6 chromosome.
