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. 2021 May 6;22:138. doi: 10.1186/s13059-021-02348-5

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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. 1 — Recent TE mobilization at the species level. a Relative proportion of the 11 major TE superfamilies identified in the reference genome (TAIR10) and their respective contribution to TE insertion polymorphisms (TIPs). b Density of TIPs across the genome for each superfamily compared to the distribution of genes or TEs annotated in the reference genome. c Folded frequency spectrum of TIPs and biallelic SNPs. d Proportion of each variant category at frequencies below 5% and above 5%. e Distribution of fitness effects of each variant category as effectively neutral (N_es < 1) and deleterious (1 < N_es). f Frequency distribution of non-private TIPs by local haplotype age. g Pairwise differences in TIPs and SNPs between accessions diverging by < 500 SNPs. Regression line and confidence intervals are indicated in red and gray, respectively. h Pairwise differences in TIPs and SNPs between all accessions. Regression lines between all and closely related accessions are shown in black and red, respectively