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. 2021 Jun 29;11(10):jkab238. doi: 10.1093/g3journal/jkab238

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© The Author(s) 2021. Published by Oxford University Press on behalf of Genetics Society of America.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

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Relationship between TE frequency and relative position to the nearest gene. Helitrons (A), TIRs (B), and LTRs (C) were categorized using the following hierarchy: gene completely within the TE, TE completely within the 5’ UTR, completely within the 3’ UTR, completely within an exon, completely within an intron, completely encompassed by a gene, 0–1 kb upstream of a gene, 1–5 kb upstream of a gene, 5–10 kb upstream of a gene, 0–1 kb downstream of a gene, 1–5 kb downstream of a gene, 5–10 kb downstream of a gene, intergenic (not shown in figure). Full colored bars (left bars) contain frequencies for TEs in each genomic region and transparent bars (right bars) contain frequencies for genome-wide background rates based on 100 bootstrap iterations. (D) Proportion of LTRs with low LTR similarity (LTR similarity <95%), moderate LTR similarity (LTR similarity between 95 and 99%), and high LTR similarity (LTR similarity >99%) in each gene proximity category.