plosone-phylo
pone.0028850.g002.png
Recombination analyses of Streptococcus pneumoniae genomes. Schematic based on Mauve alignments of the whole genome sequences of four PMEN1 S. pneumoniae isolates. Colored blocks correspond to: pink, regions that are homologous in all four genomes and free from genomic rearrangement; green, regions that differ in strain SV36-T3; blue, regions that differ in strain SV35-T23; purple, regions that differ in strains SV35-T23 and SV36-T3; white, unique to one sequence. White dots highlight polymorphic regions. Asterisks denote the position of contig gaps. Horizontal black lines correspond to gaps within sequenced regions. This schematic does not indicate sequence gaps that are positioned at contig breaks (and thus likely to be the result of incomplete sequencing) or differences within ribosomal RNA encoding sequences (since these are often misassembled). Arrows at the top denote the position of the 18 NGs identified based on SNP strain differences. The tree on the left side corresponds to a neighbor joining phylogenetic tree expressing the relationship among the four PMEN1 isolates.
pone.0028850.g002.png
Recombination analyses of Streptococcus pneumoniae genomes. Schematic based on Mauve alignments of the whole genome sequences of four PMEN1 S. pneumoniae isolates. Colored blocks correspond to: pink, regions that are homologous in all four genomes and free from genomic rearrangement; green, regions that differ in strain SV36-T3; blue, regions that differ in strain SV35-T23; purple, regions that differ in strains SV35-T23 and SV36-T3; white, unique to one sequence. White dots highlight polymorphic regions. Asterisks denote the position of contig gaps. Horizontal black lines correspond to gaps within sequenced regions. This schematic does not indicate sequence gaps that are positioned at contig breaks (and thus likely to be the result of incomplete sequencing) or differences within ribosomal RNA encoding sequences (since these are often misassembled). Arrows at the top denote the position of the 18 NGs identified based on SNP strain differences. The tree on the left side corresponds to a neighbor joining phylogenetic tree expressing the relationship among the four PMEN1 isolates.