Fig. 3

(a) The maximum likelihood phylogenetic tree based on reference sequences of imopoviruses and isolate SqVYV-IR-BA, rooted by WMV. The bootstrap values < 100 are indicated in the main nodes. (b) Heatmap based on a matrix including the pairwise distance between the nucleotide sequence of reference sequences of ipomoviruses with the sequence of SqVYV-IR-BA calculated by MEGA X. The color intensity indicates the level of distance between the species. Dark red indicates the highest number, while dark green represents the lowest number in the heatmaps. (c) Recombination event in genome of SqVYV-Iraq isolate detected by RDP analysis of a matrix including reference sequences of ipomovirus, available SqVYV isolates, and SqVYV-IR-BA. This event has been detected by RDP, GENECONV, BootScan, MaxChi, SiScan, and 3Seq with a P-value less than 10^− 09. The estimated major and minor parents were SqVYV-IR-BA and SqYV0-SM2008cHe. (d) The schematic presentation of the SqVYV-IR-BA genome. The recombination region is shown in red color in positions 1,178 -1,371 in the SqVYV-IR-BA sequence located in the P1a region