These high-coverage contigs indicate that this strain harbors one or more multi-copy plasmids. Table 1 Genome statistics for strains sequenced in this study Strain Cluster # 1 Contig # Contig N50 Scaffold # Scaffold N50 Genome size ORFs PavBP631 43 M2 38 bp PE 1,613 6,420 297 79,231 6,628,588 4816 38 M 38 bp MP PavVe013 59 M 82 bp PE 389 30,917 66 297,710 6,165,792 5136 43 M 40 bp MP PavVe037 35 M 82 bp PE 220 61,365 61 263,756 6,050,967 5078 45 M 40 bp MP 1. PE: paired-end (ca. 200 bp insert). MP: mate-pair
(3–5 kb insert). KU-57788 ic50 2. Millions of reads. Figure 1 Coverage plots for contigs generated for each Pav strain. Read coverage vs. contig length, plotted on log scales. Box and whisker boxes indicate median, quartiles, and range for each strain, with values more than 2.5 times the interquartile range above or below the median plotted as points. Data were plotted using the car package in R [18, 19]. When the contigs were scaffolded using 38–45
million mate-pairs, the N50 improved to 79 kb for Pav BP631 and to 264–298 kb for the other strains (Table 1). The total genome sizes were 6.6 megabases (Mb) for Pav BP631 and 6.1 to 6.2 Mb for the other two strains, consistent with the presence of extra-chromosomal plasmids in Pav BP631. Pav Ve013 find protocol and Pav Ve037 are largely colinear with the phylogroup 2 reference strain Psy B728a, while Pav BP631 displays substantially more rearrangement relative to Pto DC3000,
the reference strain for phylogroup 1 (Figure 2). There is a 95 kb scaffold in Pav BP631 that is made up of high-coverage contigs and is colinear with plasmid A from Pto DC3000 over about half of its length. Figure 2 Whole-genome alignments of Pav scaffolds to the most closely related reference sequences. A. PavBP631 contigs aligned to Pto DC3000 reference sequence. Inset: Alignment of scaffold 88 to plasmid A from Pto DC3000 (this was done as a separate analysis). B. Pav Ve013 and Pav Ve037 contigs aligned to Psy B728a reference sequence. Each colored block represents a local colinearity block that can be aligned O-methylated flavonoid between strains without any rearrangements. White spaces within blocks indicate regions of low sequence conservation. Vertical red lines indicate scaffold breaks for Pav sequences or boundaries between chromosomes/plasmids in the case of the Pto DC3000 reference sequence. Alignments were generated using progressiveMauve . Ortholog analysis The RAST annotation sever predicted between 4816 and 5136 open reading frames (ORFs) per strain (Table 1) which were grouped into between 4710 and 4951 ortholog groups by orthoMCL (Figure 3a). There were 3967 ortholog GDC-0994 nmr families shared among the three Pav strains, all of which were also found in other strains. Of these, 1856 were found in all 29 P. syringae strains, comprising the operational P. syringae core genome.