Genome sequence of the chlorinated compound−respiring bacterium Dehalococcoides species strain CBDB1

Michael Kube, Alfred Beck, Stephen H Zinder, Heiner Kuhl, Richard Reinhardt & Lorenz Adrian

Supplementary Fig. 1 (pdf 140K)
Circular representation of the genome of Dehalococcoides strain CBDB1.

Supplementary Fig. 2 (pdf 20K)
Comparison of the positions of all identified ortholog pairs in thegenomes of strain CBDB1 and strain 195.

Supplementary Fig. 3 (pdf 36K)
Trinucleotide differences of the genomes of Dehalococcoides strain CBDB1 (a) and Dehalococcoides strain 195 (b).

Supplementary Fig. 4 (pdf 224K)
Physical map of the genome of strain CBDB1. rdhAB genes are highlighted in red, rdh-accociated genes in yellow, tRNA in green, and rRNA in black.

Supplementary Fig. 5 (pdf 40K)
Phylogenetic tree of Dehalococcoides rdhA genes. Included are rdhA genes of strain CBDB1 (red, 32 genes), strain 195 (blue, 18 genes), strain FL2 (green, 12 genes), strain BAV1 (7 genes), a vinyl chloride reductive dehalogenase from Dehalococcoides strain VS (Müller et al. 2004), and three trichloroethene reductive dehalogenase from Dehalococcoides strains in mixed culture. Numbers on branches give bootstrap values of 1000 repetitions. Brackets with numbers identify the 12 orthologous gene pairs in strains CBDB1 and strain 195. DET0162, marked with an asterix, contains an internal stop codon and might not be functional. The length of the bar represents 10% sequence diversity.

Supplementary Fig. 6 (pdf 36K)
Phylogenetic tree of the rdhB-genes from strain CBDB1 (red, 32 genes), strain 195 (blue, 18 genes) and four tceB-genes from other Dehalococcoides species. Numbers indicate bootstrap values of 1000 replicas. The numbered brackets correspond to the brackets in Supplementary Figure 5. The length of the bar represents 20% sequence diversity.

Supplementary Fig. 7 (pdf 36K)
Radial phylogenetic tree of MarR-type genes (rdhR) in strain CBDB1 (red, 16 genes), strain 195 (blue, 7 genes) and other bacteria. The length of the bar represents 20% sequence diversity.

Supplementary Table 1 (pdf 44K)
Regions in the genome of strain CBDB1 that are differently organized in strain 195a. rdhAB-genes are highlighted. Regions 1-8 are displayed in Figure 1 of the paper, regions without numbers below the horizontal line are regions smaller than 4 kb and not shown in Figure 1.

Supplementary Table 2 (pdf 40K)
Regions in the genome of strain 195 that are differently organized in strain CBDB1a. rdhAB-genes are highlighted. Regions I-IX4 and X-XII are shown in Figure 1 of the paper, regions without numbers are regions smaller than 5 kb and not indicated in Figure 1.

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