FIG. 4.

Identification of recombination sites in the M, HE, and N genes of torovirus field variants. (A) Recombination sites were identified with the program PhylPro (58). This phylogenetic profile method introduces the phylogenetic correlation measure, i.e., the principle that phylogenetic relationships in different regions of an aligned sequence will be similar when no recombination has occurred. An alignment of the coding regions of the M, HE, and N genes of P-MAR, P4, P9, P10, BRV, B6, B145, B150, and B155 was generated. For each individual sequence in the alignment, the phylogenetic correlations were computed at every position with a sliding-window technique, with window limits fixed at 15 differences. Shown are the phylogenetic profiles of B6 and B145, with x and y axes indicating the nucleotide positions and the phylogenetic correlation, respectively; as a reference, the genes for M, HE, and N, drawn to scale, are depicted as boxes (top). For clarity, profiles of P4, B150, and B155 were hidden in the graph. (B) Phylogenetic profiles of B150 and B155; for clarity, profiles of P4, B6, and B145 were hidden. Window limits were fixed at 10 differences. (C) Alignments of HE sequences surrounding the recombination sites; arrows and numbers correspond to those in panels A and B. Nucleotide differences with respect to the B145 sequences are shown. Nucleotide positions given are numbered from A¹ of the B145 HE gene.