Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 in Alternanthera yellow vein virus (AYVV); a betasatellite independent begomovirus infecting Sonchus palustris in Pakistan

Figure 3. Phylogenetic relationships and intra specific recombination patterns among different AlYVV molecules. The maximumlikelihood phylogenetic tree contains 27 known complete genomes of AlYVV from databank and two complete genomes determined in this study (indicated in black boxes). The tree was rooted on ToLCNDV (AB613826) as an out-group. The schematic representation of recombination events detected by RDP4. Arrows and blocks at the bottom correspond respectively to open reading frames (ORFs) and intergenic regions: pre-coat protein (AV2), coat protein (CP), replication-associated proteins (Rep and REn), transcriptional protein (TrAP), and AC4 region. AlYVV from different countries were colored differently. The colors of blocks represent the different ALYVV species and strains. Numbers at nodes indicate bootstrap confidence scores (1000 replicates).