Figure 8.

Phylogenetic relationships among coronavirus PLpros.A, expected, and B,reconstructed and unrooted trees for coronavirus PLpros. The genetic groups recognized in coronaviruses are uniquely colored. A,the topology of this tree of PLpros was approximated on the basis of sequence comparisons of other coronavirus replicative enzymes³ that result in a tree topology identical to the one shown here for the PL1pro and PL2pro subgroups. This representation is called the “expected” tree. The two lineages that were reshuffled in B, MHVA/BCoVL_PL2 and TGEV/HCoV_PL1, are shown with a gray background. B, the “reconstructed” tree was generated using an alignment of PLpros (Fig. 3; see also Fig. 2A in (32)) and the NJ algorithm with the Kimura correction as implemented in the ClustalX program. The alignment included the following sequences: HCoV_PL1pro (1043–1227), HCoV_PL2pro (1690–1885), TGEV_PL1pro (1082–1266), TGEV_PL2pro (1577–1763), MHVA_PL1 (1110–1292), MHVA_PL2 (1705–1896), BCoVL_PL1 (1063–1245), BCoVL_PL2 (1660–1851) and IBV_PL2 (1263–1457). BCoVL is from Footnote 3; for the sources of the other sequences see Fig. 3. The number of trees, in which a particular bifurcation was sustained in the course of 1000 bootstrap simulations, is given at each node.