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. 2019 Nov 22;48(1):290–303. doi: 10.1093/nar/gkz1080

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© The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com

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Figure 8. — De novo and epigenetically controlled piRNA production. Panel A shows a 10.3 kb region that contains a solo-LTR from the burdock retrotransposon that is present only in DGRP379. Abundant piRNAs are being produced from the LTR itself as well as several kilobases of the region flanking the LTR insertion, whereas very few piRNAs align to this region in the DGRP732 genome. Panel B shows a 20 kb region within the intron of the transcriptional corepressor gene known as Smr. The two DGRP strains are 98% identical across this region and there are no TE insertions present in either strain, but DGRP379 piRNAs are much more abundant compared to those from DGRP732. See Supplementary Figure S13 for an expanded view which includes the Smr gene model. piRNA coverage values for both panels were obtained from alignments based on the unique-weighting mode in ShortStack to probabilistically assign alignments of multi-mapping reads based on the number of nearby uniquely mapping reads.