Fig. 1

Structure of a provirus and generation of a solo LTR and their detection from whole genome sequence data. Structure of a typical provirus (a) with its internal region (red line) encoding gag, pol and env genes flanked by two long terminal repeats (LTR). Ectopic recombination occurs between the two LTRs of the provirus (b) leading to the deletion of the internal region along with one LTR, resulting in the formation of a solo LTR (c). Note how the 5′ and 3′ junction sequences between the element and the flanking host DNA (black line), including the target site duplication (not shown), remain the same after recombination. Presence of provirus is identified from whole genome resequencing data aligned to the reference assembly when the reference allele is a solo LTR using the findprovirus pipeline (d). The findprovirus pipeline infer the presence of provirus from the mates of discordant reads with significant homology to the internal region of the respective HERV family. The discordant reads are colored light green and the forward and reverse reads originated from the same fragment are matched by numbers (e.g. F1 and R1). The findsoloLTR pipeline identifies the presence of solo LTR when the reference allele is provirus (e). It infers the presence of solo LTR based on the deviation of read depth across the provirus and across the flank