Figure 4

Intrinsic markers of reticulate evolution. A) In a previous paper [16] we described a network between diverse Ty3/Gypsy-Retroviridae lineages based on similarity, host distributions, and variability of three evolutionary markers. These are the CCHC array in NC (network in red); the sequence motif (namely, pattern 3) defining the structural flap of PR (in black); and the GPY/F motif in the C-terminus of INT (in blue). In view of this network, we performed a deep characterization of these and other markers found not only in the Ty3/Gypsy and Retroviridae families but also in the Bel/Pao, Caulimoviridae and Ty1/Copia families. As shown in the figure we considered: B) the number of CCHC arrays in NC; C) all possible variants of pattern 3 in PR; D) the variants of the ILG motif in PR; E) the presence-absence and ORF position of int; F) all possible variants of the GPY/F motif in INT; G) the presence-absence of the chromodomain in INT; H) the presence-absence of env; I) the presence-absence of additional genes. The figure includes an idealized retroelement genomic reference noting the usual position of each marker.