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. 2021 Aug 20;22:237. doi: 10.1186/s13059-021-02448-2

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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. 2 — RegionA is enriched with Tripsacum-specific LTR retrotransposons. a Venn diagram of different types of LTR-RTs in RegionA. The intersection (blue dotted frame) of low abundance LTR-RTs in B73 and high abundance LTR-RT in Tripsacum represent Tripsacum-specific enriched LTR-RTs (Tse-LTR-RTs). b–g FISH analysis of the distribution of three Tripsacum-specific enriched LTR retrotransposons (Tse-LTR-RTs) cloned from RegionA, all three Tse-LTR-RTs showed genome-wide distribution in Tripsacum dactyloides (2n = 36) (b–d), while they had no obvious signal in Zea mays (e–g). Scale bars = 10 μm. h Gene flow detected between Tripsacum and Zea in RegionA. One migration event was set for analysis (m = 1), direction of gene flow was indicated by an arrow. i Schematic Structure of LTRs and genes in RegionA. Rows from top to bottom indicate location of Tse-LTR-RTs; read coverage of Tripsacum and B73; location of Tripsacum consistent genes and B73 annotation genes, respectively