Figure 2

Neighbour-joining tree depicting clustering of recombinant virus genotypes around that of MSV-MatA. The recombinants arising during MatMPCPVW+VWMPCPMat or MatMPCPLIRVW+VWMPCPLIRMat chimaeric pair mixed infections in a MSV-sensitive maize genotype (panels A and C, respectively), and that either continue to persist or arise de novo following transmission of these viruses into a MSV-resistant maize genotype (panels B and D, respectively). The linearised genome schematics illustrate the recombination mosaics, where regions in orange are derived from MatMPCPVW or MatMPCPLIRVW viruses, and regions in green are derived from VWMPCPMat or VWMPCPLIRMat viruses. The panel on the right of each phylogenetic tree shows both the recombination pattern and number of breakpoints in each recombinant. The diagram above the mosaics shows the position of genomic features: V2 = movement protein gene; V1 = coat protein gene; SIR = short intergenic region; C1/C2 = replication-associated protein gene; C1 = repA gene; LIR = long intergenic region. The viability of viruses highlighted in blue is shown in Figure 4.