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. 2021 Nov 9;19:241. doi: 10.1186/s12915-021-01158-2

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© The Author(s) 2021

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. 6. — TE landscape across Sitophilus species. A Proportion of TE per species estimated from short reads with dnaPipeTE and a custom TE library including Repbase (release 2017) and annotated TE consensus discovered in S. oryzae. S. oryzae, S. zeamais, and S. granarius harbor similar TE content, while S. granarius presents a smaller TE load, and S. linearis harbors the smallest TE content and the higher proportion of unknown repeats. The proportion of unknown repeats only found by dnaPipeTE (black) increases from S. oryzae to S. linearis with the phylogenetic distance. B Distribution of divergence values between raw reads and repeats contig assembled with dnaPipeTE (blastn) across four Sitophilus species. S. oryzae appears to share its TE landscape with S. zeamais and S. granarius, but the three species display a distinct repeatome than S. linearis, in spite of their phylogenetic proximity. SO2: S. oryzae’s TE library produced in this analysis, DPTE: DNApipeTE TE annotation (repeats only found by dnaPipeTE)