Figure 2

Phylogeny of the six LGR proteins encoding genes (lgr) of P. amoebophila. A: Neighbor-Joining tree of the nucleotide sequences of the lgr s without the sequence corresponding to the LRR domain, using the Kimura 2-parameter distance and the complete deletion parameter with a bootstrap analysis of 1'000 samples. Bootstrap values are shown in percent. B: Bayesian tree performed on the same non-LRR sequences was drawn after 100'000 generations, sampling 100 generations and 5 chains, respectively. The general-time reversible model was used with gamma rates of among-site variation. C: UPGMA tree based on the comparison of the amino acids composition of the LRRs: same data as those used for Figure 6 to calculate the center of gravity. In all three analyses, lgrA and lgrE are very close. Except in A, in which all other lgr s seem to emerge from the same nod, the relationships between the four others is strikingly conserved in the dendrograms B and C.