Fig. 4

Pacific Biosciences (a) and Oxford Nanopore MinION (b) long read verification of L1-mediated transduction insertions. a Left panel: alignment dotplot – surrounding reference genome sequence for the human chr4:104210671-104214687 region shown on the x-axis; PacBio read on the y-axis: ~1000 bp shift shows presence of insertion. Right panel: Inspection of the inserted sequence verified the presence of the L1 element (in blue) and the transduced sequence including the new polyA tail (in red; based on the consensus sequence created from all PacBio reads); the new polyadenylation signal is underlined. b Dotplot – with reference genome sequence on the x-axis and MinION read on the y-axis: ~1200 bp shift shows presence of an insertion. The inserted sequence verified both the presence of an L1 element (in blue) and additional transduced sequence including the new polyA tail (in red; based on the consensus sequence created from subset of MinION reads). c Alignment of the inserted L1 sequence to the ~6 kb long L1 consensus sequence shows that the integrated L1 is 5′-truncated (pairwise-alignment performed with BLAST)