Figure 4

Phylogenetic relationships and recombination patterns among the AfSV species on Reunion Island. The maximum-likelihood phylogenetic tree contains 47 known complete genomes of monocot-infecting mastreviruses from Reunion Island and eight complete genomes determined in this study (indicated in bold font). The tree was rooted on chickpea chorosis virus (JN989413) as an outgroup (not shown). Open and closed circles on nodes indicate bootstrap support for the branches to their left of 70–89% and > = 90% respectively. The schematic representation of recombination events detected by RDP4 using seven different methods: RDP, GENCONV, BOOTSCAN, MAXCHI, CHIMERA, SISCAN and 3SEQ. Arrows and blocks at the bottom correspond respectively to open reading frames (ORFs) and intergenic regions: movement protein (MP), coat protein (CP), replication-associated proteins (Rep and Rep A), long intergenic region (LIR) and small intergenic region (SIR)The colours of blocks represent the different AfSV species and strains. More details on each event (lettered A to F) are available in Supplementary Table S3.