Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.The study of the interactions between LTR-RTs and the host genome relies on h...Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.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 analyzed 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 preallopolyploidization 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.展开更多
基金supported by the National Key R&D Program of China(Grant No.2022YFC3400300 to Kai Ye and Xiaofei Yang)the National Natural Science Foundation of China(Grant Nos.32125009 to Kai Ye,32070663 to Kai Ye,62172325 to Xiaofei Yang,and 32422019 to Xiaofei Yang)+2 种基金the Natural Science Foundation of Shaanxi Province(Grant No.2024JC-JCQN-28 to Xiaofei Yang)the Fundamental Research Funds for the Central Universities(Grant No.xzy012024088 to Xiaofei Yang)Funding for open access charge:National Key R&D Program of China.
文摘Long terminal repeat retrotransposons(LTR-RTs),a major type of class I transposable elements,are the most abundant repeat element in plants.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 analyzed 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 preallopolyploidization 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.
