Fig. 4

Chromosomised view of a pangenome graph for 42 finished V. cholerae as found on RefSeq. Nodes represent protein clusters, edges represent local neighborhood relations of proteins in the clusters. As the species has two chromosomes, protein clusters from chromosome 1 are colored blue, and protein clusters from chromosome 2 are colored red, protein clusters, where the chromosome cannot be decided as they occur on both chromosomes in the template genomes, are coloured pink and protein clusters which cannot be assigned a chromosome as they do not occur in the templates are colored grey. The size of the nodes is defined by how many strains the respective protein cluster includes, meaning core clusters are larger and protein clusters from the shell and cloud are smaller. We would expect two large circles from the two chromosomes, but they are connected through protein clusters including proteins on either chromosome. Loops represent structural rearrangements and inDel regions in parts of the pangenome. The smaller connected components unconnected to the main chromosomal components represent either rare insertions - potentially horizontal gene transfer - or variants, sequences created by contamination of some of the input genomes or assembly and annotation artefacts. The graph was generated by only allowing edges with a minimal support of 2 to be added, to single out these potentially erroneous protein clusters