PMC3088116_01
Circos plot mapping of the consensus L2c sequence against L2/434 and D/UW3. The figure highlights candidate recombinant regions of L2c that match to D/UW3 or L2/434. Mapping was performed using 100-nt windows; sequence comparisons used BLAST score ratio (see Materials and Methods). Note that the coordinates of the D/UW3 genome follow the original GenBank accession number and do not start at the origin of replication as for L2/434 and L2b/UCH-1/proctitis. Fragments of L2c that have a stronger match to L2/434 are shown in grey; those in red have a stronger match to D/UW3. The inner track with purple and orange bands represents protein-coding genes on the negative strand (purple) and positive strand (orange). The figure was produced using Circos software, a tool for graphical representation of genome data.
mbo0021111080005.jpg
PMC3088116_01_mbo0021111080005.jpg
f5
Matches with a BLAST score ratio of <0.95 were plotted using Circos software (Fig. 5).
SimPlot representation and maximum chi-square analyses of putative recombinant crossover regions in the tarp gene for clinical strain L2c compared with those of parental strains L2/434, L2b/UCH-1/proctitis, and D/UW3. The outgroup was the collective sequence of the ocular strains A/2497, B/HAR36, and C/TW3, as they were identical for this gene. (A) The number of informative sites shared by the recombinant L2c tarp gene sequence with parental LGV (green) and D/UW3 (red) tarp gene sequences is shown. The ocular outgroup is denoted in blue. Note that L2c is more similar to D in the first ~996 bp and to LGV strains in the middle ~800 bp but similar again to D for the remainder of the gene. (B) The similarity plot is shown using the L2c tarp gene sequence as the query sequence in comparison with those of the LGV (green), ocular group (blue), and D/UW3 (red) strains (similarity score on the y axis). (C) The bootscan analyses are shown, with percent similarity and phylogenetic relatedness (percentage of permuted trees on the y axis), with significance of support for each node in the tree between recombinant and parental sequences as denoted by the colors. (D) The phylogenetic reconstructions are shown for each region bounded by recombination breakpoints supporting each crossover along with the results for 1,000 bootstrap replicates as supported by the analysis represented in panel C. Left tree, base pairs 0 to 996; middle tree, base pairs 997 to 1689; right tree, base pairs 1690 to 3735. See Materials and Methods.
mbo0021111080007.jpg
PMC3088116_01_mbo0021111080007.jpg
f7
The parameters included a window size of 200 base pairs (bp), a step of 20 bp, neighbor-joining trees calculated using the Kimura-2-parameter distance model (60), and 1,000 bootstrap replicates to determine confidence for each branch (Fig. 7).