Figure 4.

Recombinant regions (a, b and c) detected within the African isolates of CLCuGV sequences using RDP3. Four genetic groups (G1 to G4) have been defined on the presence or absence of recombination events. The genome at the top of the figure corresponds to the schematic representation of sequences below. Region coordinates are nucleotide positions of detected recombination breakpoints in the multiple sequence alignment used to detect recombination. Wherever possible, parental sequences are identified. "Major" and "Minor" parents are sequences that were used, along with the indicated recombinant sequence, to identify recombination. Whereas for each identified event the minor parent is apparently the contributor of the sequence within the indicated region, the major parent is the apparent contributor of the rest of the sequence. Note that the identified "parental sequences" are not the actual parents but are simply those sequences most similar to the actual parents in the analysed dataset. Recombinant regions and parental viruses were identified using the RDP (R), GENECONV (G), BOOTSCAN (B), MAXIMUM CHI SQUARE (M), CHIMAERA (C), SISTER SCAN (S) and 3Seq (T) methods. Whereas upper case letters imply a method detected recombination with a multiple comparison corrected P-value < 0.01, lower case letters imply the method detected recombination with a multiple comparison corrected P-value <0.05 but > = 0.01.