Figure 5

Schematic illustration of recombination events in complete PiCV genome sequences detected after the start of joint housing of experimental birds. The methods used to detect recombination events are RDP (R), GENCONV (G), BOOTSCAN (B), MAXCHI (M), CHIMERA (C), SISCAN (S) and 3SEQ (T). For each recombination event, the method with the lowest p-value is underlined. The color of the recombinant sequence names indicates the maternal loft of the pigeon from which the recombinant sequence has been obtained, whereas the color of the bars indicates the maternal lofts of the pigeons from which the parental sequences have been obtained: green—loft I, blue—loft II, purple—loft III, pink—loft IV and orange—loft V. The color coding was made according to Fig. 1. All sequence names are encoded with the following formula: B (blood)/S (swab), loft number (I–V), _pigeon number (1–3), sampling date (a–h), _clone number (C1–C10).