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The study of the interactions between LTR-RTs and the host genome relies on high-resolution characterization of LTR-RTs. However, for non-model species, this remains a challenge. To address this, we developed LTR_Stream for sublineage clustering of LTR-RTs in specific or closely related species, providing higher precision than current database-based lineage-level clustering. Using LTR_Stream, we\u00a0analyzed Retand LTR-RTs in three Papaver species. Our findings show that high-resolution clustering reveals complex interactions between LTR-RTs and the host genome. For instance, we found that autonomous Retand elements could spread among the ancestors of different subgenomes, like retroviral pandemics, enriching genetic diversity. Additionally, we identified that specific truncated fragments containing transcription factor motifs such as TCP and bZIP may contribute to the generation of novel topologically associating domain-like (TAD-like) boundaries. Notably, our pre-allopolyploidization and post-allopolyploidization comparisons show that these effects diminished after allopolyploidization, suggesting that allopolyploidization may be one of the mechanisms by which Papaver species cope with LTR-RTs. We demonstrated the potential application of LTR_Stream and provided a reference case for studying the interactions between LTR-RTs and the host genome in non-model plant species.<\/jats:p>","DOI":"10.1093\/gpbjnl\/qzaf061","type":"journal-article","created":{"date-parts":[[2025,7,21]],"date-time":"2025-07-21T05:26:21Z","timestamp":1753075581000},"source":"Crossref","is-referenced-by-count":0,"title":["Deciphering Complex Interactions Between LTR Retrotransposons and Three\n                    <i>Papaver<\/i>\n                    Species Using LTR_Stream"],"prefix":"10.1093","volume":"23","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-3194-1834","authenticated-orcid":false,"given":"Tun","family":"Xu","sequence":"first","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9341-2562","authenticated-orcid":false,"given":"Stephen J","family":"Bush","sequence":"additional","affiliation":[{"name":"School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi\u2019an Jiaotong University , Xi\u2019an 710049,","place":["China"]}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4483-6582","authenticated-orcid":false,"given":"Yizhuo","family":"Che","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0009-0003-8641-6487","authenticated-orcid":false,"given":"Huanhuan","family":"Zhao","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9238-0968","authenticated-orcid":false,"given":"Tingjie","family":"Wang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3429-919X","authenticated-orcid":false,"given":"Peng","family":"Jia","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4482-8128","authenticated-orcid":false,"given":"Songbo","family":"Wang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0796-2133","authenticated-orcid":false,"given":"Peisen","family":"Sun","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8696-4983","authenticated-orcid":false,"given":"Pengyu","family":"Zhang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3810-6527","authenticated-orcid":false,"given":"Shenghan","family":"Gao","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3386-1379","authenticated-orcid":false,"given":"Yu","family":"Xu","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0362-4498","authenticated-orcid":false,"given":"Chengyao","family":"Wang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-2473-1142","authenticated-orcid":false,"given":"Ningxin","family":"Dang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3770-2383","authenticated-orcid":false,"given":"Yong E","family":"Zhang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5118-7755","authenticated-orcid":false,"given":"Xiaofei","family":"Yang","sequence":"additional","affiliation":[]},{"ORCID":"https:\/\/orcid.org\/0000-0002-2851-6741","authenticated-orcid":false,"given":"Kai","family":"Ye","sequence":"additional","affiliation":[]}],"member":"286","published-online":{"date-parts":[[2025,7,8]]},"reference":[{"key":"2025121705430095900_qzaf061-B1","doi-asserted-by":"crossref","first-page":"2","DOI":"10.1186\/s13100-017-0107-y","article-title":"Human transposable elements in Repbase: genomic footprints from fish to humans","volume":"9","author":"Kojima","year":"2018","journal-title":"Mob DNA"},{"key":"2025121705430095900_qzaf061-B2","doi-asserted-by":"crossref","first-page":"2245","DOI":"10.1101\/gr.2693004","article-title":"Whole-genome analysis of Alu repeat elements reveals complex evolutionary 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