41 Genomic islands that are identified from genomes of Salmonella HC20_373

Pan-genome construction. A pan-genome of genes of over 300 bp in length was calculated s from all HC20_373 genomes using PEPPAN [39] with the parameters ‘—min_cds 300’. Genes of Assignments of genes to genomic islands. We reconstructed the presence or absence of all genes in the pan genome for each internal node of a core genome maximum-likelihood phylogeny that had been constructed with TreeTime [40]. The most recent common ancestor (MRCA) of HC20_373 contained 4107 genes which were interpreted as “ancestral”. Deletions of at least five continuous genes in any internal node were scored as large deletions of genomic islands. 496 genes were acquired at internal nodes, and these assigned as the acquisition of genomic islands as previously described [41]. In brief, a directed graph of all orthologous genes was drawn for pairs of orthologous genes that were co-located on a single contig or on pairs of contigs that were linked by read-pairs that straddled both of them. The most likely gene order of the pan genome was identified with Concorde [42] as consisting of the shortest possible path that visited all the genes in the graph, and subsequently manually revised to break and re-join links to duplicated genes and collapsed repeats. All genomic islands are listed in Supplementary Table S4D, summarized in Supplementary Table S5, and illustrated in Supplementary Figure S1.