Intra-host evolution of the ssDNA virus tomato severe rugose virus (ToSRV)

•The nucleotide substitution rate of the ssDNA virus ToSRV is equivalent to that of RNA viruses.•The substitution rates for the DNA-B were one order of magnitude lower than for the DNA-A.•The number of substitutions decreased over time, suggestive of bottlenecks during systemic infection.•The patterns of variation were different for the DNA-A and DNA-B components. To evaluate and quantify the evolutionary dynamics of the bipartite begomovirus tomato severe rugose virus (ToSRV) in a cultivated and a non-cultivated host, plants of tomato and Nicandra physaloides were biolistically inoculated with an infectious clone and systemically infected leaves were sampled at 30, 75 and 120 days after inoculation. Total DNA was extracted and sequenced in the Illumina HiSeq 2000 platform. The datasets were trimmed with the quality score limit set to 0.01, and the assembly was performed using the infectious clone sequence as reference. SNPs were filtered using a minimum p-value of 0.001 and the sum frequencies were used to calculate the deviation from the original clone sequence. Nucleotide substitution rates were calculated for the two DNA components in both hosts: 1.73 × 10−3 and 3.07 × 10−4 sub/site/year for the DNA-A and DNA-B, respectively, in N. physaloides, and 8.05 × 10−4 and 7.02 × 10−5 sub/site/year the for DNA-A and DNA-B, respectively, in tomato. These values are in the same range of those estimated for viruses with single-stranded RNA genomes and for other begomoviruses. Strikingly, the number of substitutions decreased over time, suggesting the presence of bottlenecks during systemic infection. Determination of Shannon's entropy indicated different patterns of variation in the DNA-A and the DNA-B, suggesting distinct evolutionary forces acting upon each component.