plosone-phylo
Figure 5
Recombination breakpoints occur between key gene regions in a P. ramorum RXLR effector family.Maximum likelihood trees were constructed for different fragments of genes exhibiting recombination among paralogs and show the changing evolutionary relationships among both genes and alleles between gene regions. Approximate recombination breakpoints were inferred using RDP and indels were removed. The sequences between inferred recombination breakpoints used for phylogenetic analysis were A. 5’ flanking sequences (201 bp), B. the targeting region (157 bp), from the start codon to RXLR motif, C. the functional (C-terminal) region (149 bp), and D. 3’ flanking sequences (70 bp). A short region around the DEER motif is not shown. Branch support is given as a percentage of 500 bootstrap samples. The branch lengths are drawn to scale and measured in the number of substitutions per site.
Figure 5
Recombination breakpoints occur between key gene regions in a P. ramorum RXLR effector family.Maximum likelihood trees were constructed for different fragments of genes exhibiting recombination among paralogs and show the changing evolutionary relationships among both genes and alleles between gene regions. Approximate recombination breakpoints were inferred using RDP and indels were removed. The sequences between inferred recombination breakpoints used for phylogenetic analysis were A. 5’ flanking sequences (201 bp), B. the targeting region (157 bp), from the start codon to RXLR motif, C. the functional (C-terminal) region (149 bp), and D. 3’ flanking sequences (70 bp). A short region around the DEER motif is not shown. Branch support is given as a percentage of 500 bootstrap samples. The branch lengths are drawn to scale and measured in the number of substitutions per site.