Fig. 1.—

Clonal phylogeny with large genomic insertions and deletions. (A) Phylogenetic tree constructed by concatenating SNPs identified in the core genome. The colored lines of the tree indicate each of the five clades we identified among the Sulfolobus acidocaldarius genomes isolated in 2012. Leaves are color-coded according to the hot spring from which they were isolated. Circles to the right of leaves indicate the presence or absence of genomic islands. First column; glycosyltransferase island; second column, STIV; third and fourth columns, plasmids 1 and 2, respectively. The colors in the glycosyltransferase island correspond to the deletion patterns shown in part (B). Trees were visualized using the interactive tree of life (ITOL) program (itol.embl.de). (B) Complete open reading frames found in the large genomic island encoding glycosyltransferases. We observed six different deletion patterns in this genomic island; the letters to the left indicate the designated deletion pattern. These correspond to the deletion pattern letters shown in supplementary table S7, Supplementary Material online. The numbers at the top indicate the ORF number of the ORF in S. acidocaldarius DSM639, with “Saci_” preceding the number in the ORF label. These genes are described in supplementary table S6, Supplementary Material online. Purple: glycosyltransferases, yellow: membrane proteins, light blue: methyltransferases, green: cell envelope, surface polysaccharides and lipopolysaccharides, orange: metabolite transport-related protein, gray: hypothetical protein.