Organization, alignment, and phylogenetic comparison of 8 vinyl chloride reductase genomic islands (vcr-GIs). (A) To scale summary plot (0 - 100% ID. 14 bp window) of a multiple alignment of all 8 vcr-GIs. Horizontal axis numbers indicate the distance downstream of ssrA, in nucleotides. Bar heights are shaded darker grey when their value is 100%. Position and orientation of genes are annotated above the plot, shaded according to Figure 1. Regions of categorically different similarity correspond to the integration and vcrABC cargo modules, with region-wide average % IDs of 75.0 and 99.4, respectively. (B) Enlarged view of the multiple alignment at key positions. (Left) The presumed boundary between integration and cargo modules. (Right) The region of atypically high substitutions occurring in the leader sequence of vcrA. Identical sequence is shaded light-grey, nucleotides that disagree with the consensus are indicated with tick marks shaded red, green, yellow or blue representing nucleotides A, T, G, C, respectively. (C) Phylogenetic discontinuity between integration modules (left) and their attached vcrABC cargo (right), represented by separately calculated Maximum Likelihood trees. Middle cartoon summarizes the major phylogenetic separations of the trees, with curves connecting modules if one of the 8 vcr-GIs contains the corresponding combination of module types. vcr-GIs sequences are from Dehalococcoides strain VS [GenBank:CP001827], strain GT [GenBank:NC_013890]) and two metagenomes (KB-1 [JGI:4083612], ANAS [JGI:4085297]), as well as targeted sequencing (this study) from the vinyl chloride-respiring Dehalococcoides enrichment cultures WBC-2, PM, EV, and WL [GenBank:JN034252-JN034255].
McMurdie et al. BMC Genomics 2011 12:287 doi:10.1186/1471-2164-12-287