Fig. 2

Circular representation of non-linear pan genome from 58 Xanthomonas fragariae genomes used in this study. The complete genome of strain PD 885^T was used as reference. A total of 10,189 CDS were included in the pan genome and compared to all 58 strains. Each circle corresponds to a single X. fragariae strain. The colors used for the circles correspond to the X. fragariae CRISPR (sub) groups (Gétaz et al. 2018b); Xf-CGr-II: blue, Xf-CGr-IA: red, Xf-CGr-IB: orange, and Xf-CGr-IC: green. Strong colors correspond to a 100% identity, lighter colors correspond to 90% identity, and grey regions correspond to 70% identity. Numbers from 1 to 30 correspond to variable sites between assemblies. The sites 1 and 21 in the red squares correspond to the plasmid regions pXf29 and pXf21, respectively. The site 6 corresponds to CRISPR associated proteins Cas3, Csy1 and Csy2. Site 25 is composed of a phage-related cluster of proteins. Site 30 comprised a cluster of 10 VirB proteins, TrbM and hypothetical proteins and is present only in four strains ICMP 20572 to ICMP 20575. Finally, sites 2, 7, 8, 10, 14, 15, 17, 19, 20, 22, 26, 28 and 29 include mainly hypothetical genes