aab12074-sup-0001-FigureS1.tifTIFF image78KFig. S1. Schematic representation of the genomic organisation of pepper leafroll virus (PepLRV) showing the two single stranded circular DNA genomic components (DNA-A and DNA-B) of ˜2.6 kb in length. Arrows indicate the open reading frames encoding the coat protein (CP), the replication-associated protein (Rep), protein C4, the transcriptional activator protein (TrAP), and the replication enhancer protein (REn) in DNA-A and the nuclear shuttle protein (NSP) and the movement protein (MP) in DNA-B; in both DNAs, the intergenic region (IR) containing the stem-loop structure, and the common region (CR) between the two components (grey box) are shown. Also, the 992-nt fragment of the DNA-A component considered for the genetic diversity study of PepLRV isolates is shown (black box).
aab12074-sup-0002-FigureS2.tifTIFF image94KFig. S2. A. Colour representation of the pairwise nucleotide sequence identity percentages calculated between a 992-nt fragment [nt 1807 to 230 of the DNA-A component (numbers based on the sequence of the PepLRV isolate PE:P107:pep:2009, GenBank accession number KC769819)] of pepper leafroll virus (PepLRV) isolates collected in a surveys conducted in Peru during 2009 and 2010. The equivalent sequence for the DNA component of the begomovirus tomato leaf deformation virus ToLDeV (GenBank accession number GQ334472) was also included in the comparison. MEGA 5.0 programme (Tamura et al., 2011) was used to calculate the percentages of nucleotide sequence identity by the Kimura 2-parameter distance model. The lowest identity percentage value is underlined. The corresponding phylogenetic tree constructed using the Maximum Likelihood method is included (B). Bootstrap (1000 replicates) values are expressed in percentages, and only the nodes with values greater than 50% are labelled. Scale bar indicates 0.05 nucleotide substitutions per site.

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