Example subgraphs of two LMEMs. (A) A 16 417nt LMEM between a C. coli plasmid (CP013035, positions 23 541–39 957) and C. jejuni chromosome (CP107256: 1 208 016–1 224 432). The parameter c specifies the fraction of LMEM nodes that a path has to traverse in order to be included in the subgraph visualization and n reflects the number of flanking nodes to display (see online methods). The left panel in A shows the subgraph of the LMEM (n = 1.0) with two genomes, 11 045 nodes and 11 057 edges. The right panel shows a relaxed subgraph of the LMEM with paths sharing ≥90% (n = 0.9) of the LMEM nodes. This relaxed subgraph contained 23 051 nodes and 23 665 edges, with paths from 18 genomes. In the left panel we zoom in on the bubbles that prevent further LMEM extension and for example, see that C. coli had aminoglycoside resistance gene (APH(3′)) flanking the LMEM which was absent in C. jejuni at this position. The gray-colored genes were annotated as hypothetical by BV-BRC and the light-colored genes encoded VirB proteins but their annotations were omitted for clearer visualization. (B) A subgraph with 4103 nodes and 4102 edges for a 2068nt LMEM encoding a transposon was found in two genomes from C. jejuni (CP047082: 58 822–60 889) and C. hyointestinalis subsp. hyointestinalis (CP015575: 1 258 714–1 260 781) abbreviated as C. hyo. For the latter species, the transposon disrupted the pycB gene encoding a pyruvate carboxylase according to the NCBI annotation (light green). When we slightly relaxed the subgraph threshold to n = 0.9 we obtained a subgraph with 20 255 nodes and 20 270 edges, with paths from 20 genomes. The extensive branching of paths outside the LMEM indicates the diverse genomic context of this transposon in different C. jejuni and C. hyointestinalis subsp. hyointestinalis genomes.