Table 1.
Summary data for the 4 complete sequenced isolates and genomes.
Fig 1.
Alignment showing the genome organization of the four C. jejuni isolates used in this study.
The figure was prepared using Progressive Mauve (Mauve 20150226 build 10 [44]).
Fig 2.
Comparison of C. jejuni isolate pangenome comparison.
The BLAST atlas was obtained using GView Server [43] and further annotated using Adobe Illustrator.
Table 2.
Distribution in genomes and expression of unique chromosomal genes of the 4 isolates.
Fig 3.
Detection of proteins from each of the four isolates.
A. Heat map comparing relative log2 fold change values of proteins for each isolate using 00–0949 as the reference. Only exclusive peptides were used for analysis in Scaffold. The scale bar shows the relationship of color to log2 fold change values. Labels to the right of each lane identify the isolate and experimental replicate associated with that lane. B. PCA comparing the first two components when only exclusive peptides were used for analysis in Scaffold. C. Heat map comparing relative log2 fold change values of proteins for each isolate using 00–0949 as the reference when non-exclusive peptides were included in the Scaffold analysis. D. PCA comparing the first two components when non-exclusive peptides were included in the Scaffold analysis.
Fig 4.
UpSet plots summarizing differential protein expression analysis for the four isolates.
The horizontal bar graph at the bottom left of each figure shows the total number of proteins with differences in log2 fold change expression for each pair of isolates. Joined black circles to the right of these bar graphs indicate that the same differentially expressed proteins were common to the pairwise isolate comparisons shown at left. The vertical bar graph at the top quantitates the number of proteins with similar log2 fold change expression differences in the isolate comparisons. A. Results obtained using only exclusive peptides in the Scaffold pair-wise differential expression analyses. B. Results obtained when non-exclusive peptides were included in the Scaffold pair-wise differential expression analyses. Note the difference in scale between the two bar graphs.
Table 3.
The most highly enriched and depleted GO categories in comparisons between isolates when analysis includes only exclusive peptides.
Table 4.
Total enriched and depleted GO categories in comparisons between isolates when analysis includes non-exclusive peptides.