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. 2024 Nov 7;25(12):5780–5809. doi: 10.1038/s44319-024-00304-5

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. Creative Commons Public Domain Dedication waiver http://creativecommons.org/publicdomain/zero/1.0/ applies to the data associated with this article, unless otherwise stated in a credit line to the data, but does not extend to the graphical or creative elements of illustrations, charts, or figures. This waiver removes legal barriers to the re-use and mining of research data. According to standard scholarly practice, it is recommended to provide appropriate citation and attribution whenever technically possible.

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(A) Schematic representation of the strategy used to quantify and map new EVD insertions from EM-seq data. EVD copy number was estimated using: (i) the increased EVD coverage of concordant paired read mates in EM-seq data, consequence of EVD transposition or, (ii) mapping new EVD insertions through discordant read pairs mapping to EVD and elsewhere in the genome. New insertions had to be supported by at least three discordant read pairs from each border to be considered. (B) Inferred EVD copy number using either relative coverage or discordant reads in WT Col-0, rdr6 and in RDR6- and rdr6-EVD F6 individuals with active and silenced EVD (marked with empty green and filled red arrowheads, respectively, numbers indicate same individuals as in Figs. 2 and 3). (C) Number and relative proportion (in %) of mapped new EVD insertions in pericentromeric or chromosomic arm locations in each indicated sample. Numbers of new EVD insertions at each location are indicated in brackets. (D) Histogram of the size (in bp) distribution of target site duplications at all new EVD insertions. Source data are available online for this figure.