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. 2020 Jul 3;11:23. doi: 10.1186/s13100-020-00213-z

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© The Author(s) 2020

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 2 — TE contents in D. melanogaster, D. simulans and D. virilis (from left to right). Barplots represent TE copy numbers for the top 20 TE superfamilies. Piecharts illustrate genomic sequence occupancy of each TE order (in percentages of the assemblies). These results were obtained using the D. melanogaster reference genome assembly (r6.29), and recently produced long-reads assemblies of D. simulans and D. virilis [99]. RepeatMasker was used to recover TE fragments and TE genomic sequence occupancy (RepeatMasker v1.332, -nolow, -norna, -species drosophila; Repbase-derived RepeatMasker libraries 20181026 [100],). TE fragments were assembled into TE copies using OneCodeToFindThemAll [101].