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. 2021 Mar 12;33(6):1888–1906. doi: 10.1093/plcell/koab077

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© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.

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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Distribution of sequence gaps and sequence differences in BARE1 elements between Morex V1 and V3. The graph is a compilation of results from sequence alignments of 3,305 v1 and v3 full-length BARE1 retrotransposons. As individual retrotransposon copies can differ in length, the length was normalized to 1,000 bins. The plot shows numbers of SNPs and numbers of N’s in 10-bin windows. The LTRs correspond to approximately the first and last 20% of the retrotransposon. These regions are highly enriched in SNPs and sequence gaps because of the inability of short-read assemblies to resolve highly similar regions longer than a few hundred base pair.