Distribution of mutations in recombinant and wild-type MSV genomes. Under the name of each group of mutants (that is, VWMPCPLIRMat, MSV-MatA, MSV-VW, and the VWMPCPMat + MatMPCPVW and VWMPCPLIRMat + MatVMPCPLIRVW-derived recombinant MSV) the distribution of mutations is a composite of all the unique mutations identified in each population of viruses. Whereas the numbers that are written in italics and coloured in grey indicate sites where transversion mutations were detected, those in regular font and in black colour indicate sites where transition mutations were detected. These numbers are connected by vertical lines which refer to the mutated nucleotide of a specific virus listed in Additional file 7, and for simplicity we use the genomic co-ordinates of MSV-MatA to pinpoint the genomic position of each mutation. The lines are predominately drawn in black. However, those lines in red, blue or green indicate genomic positions (among at least a pair of viruses belonging to the different virus population groups) where identical mutations were detected. Those genomic sites where at least two viruses isolated from different plants have a particular convergent mutation are indicated using the symbols *, †, ‡ and §. At the bottom of the panels, MP (movement protein), CP (coat protein), SIR (short intergenic region), C2 + C1 (replication-associated proteins), and LIR (long intergenic region) delineate MSV open-reading frames and intergenic regions.