Figure 1.
The reference pan-genome approach.
Conceptual pipeline showing the approach to generate a list of unique genes from more than one reference strain. Step 1: Compiling a gene list from reference genomes reflecting strain diversity from public repositories such as NCBI, or after automatic annotation on assembled contiguous segments (for example using RAST). Step 2: Comparative list analysis to remove duplicate genes that show ≥70% sequence identity over ≥50% of the sequence of another gene in the list. Step 3: Creating a final reference pan-genome list.
Table 1.
Publicly-available genomes used to produce a Campylobacter reference pan-genome.
Figure 2.
Phylogenetic tree of 192 Campylobacter genomes and novel epidemiological markers.
Maximum-likelihood tree of 130 C. jejuni and 62 C. coli genomes. Isolates belonging to C. jejuni are shown in blue, and those belonging to C. coli clade 1 are indicated in red, clade 2 in yellow, and clade 3 in green. The scale bar indicates the estimated number of substitutions per site. Example genomes from C. coli clades 1-3 and C. jejuni ST-21, ST-45, ST-353 and ST-61 clonal complexes were used to define the 7 isolate reference pan-genome gene list. The number of epidemiological markers from this list is indicated for each lineage. The asterisk indicates that markers were not found to be absolutely specific to that lineage, but were also present at low frequency in other lineages. Details about the markers are shown in Table 2 and Table 3.
Figure 3.
Rarefaction and accumulation curve estimates of C. jejuni and C. coli core and pan-genomes.
The number of shared genes (A), and the total number of genes (B and C), were determined as genome sampling increased. Comparisons were made based on matrices of gene presence/absence, derived from the reference pan-genome list, for C. coli (62 genomes), C. jejuni (130 genomes) and the two species combined (192 genomes). Randomized genome sampling was carried out 100 times to obtain the average number of genes for each sample comparison number (plain lines) and standard deviations (dotted lines). Pan-genome size estimates were calculated using the reference pan-genome (B) or the NCTC11168 annotation (C).
Table 2.
Functional categories of genes present in the reference pan-genome and in the reference genome of C. jejuni NCTC11168.
Table 3.
Prevalence of C. coli and C. jejuni associated genes from a comparison of 192 genomes.
Table 4.
Lineage associated genes in C. coli and C. jejuni from a comparison of 192 genomes.