Deciphering Complex Interactions Between LTR Retrotransposons and Three Papaver Species Using LTR_Stream

Genomics Proteomics & Bioinformatics, vol. 23

Abstract

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 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.

Authors 13

1. Tun Xu

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   Xi’an Jiaotong University MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, , Xi’an 710049,

   Xi’an Jiaotong University School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, , Xi’an 710049,

2. Stephen J. Bush

   Xi'an Jiaotong University

   Affiliation as printed

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi’an Jiaotong University , Xi’an 710049,

   Xi’an Jiaotong University School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, , Xi’an 710049,

3. Yizhuo Che

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   Xi’an Jiaotong University MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, , Xi’an 710049,

   Xi’an Jiaotong University School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, , Xi’an 710049,

4. Huanhuan Zhao

   First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

   The First Affiliated Hospital of Xi’an Jiaotong University Center for Mathematical Medical, , Xi’an 710061,

5. Tingjie Wang

   First Affiliated Hospital of Xi'an Jiaotong University

   Affiliation as printed

   Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

   The First Affiliated Hospital of Xi’an Jiaotong University Center for Mathematical Medical, , Xi’an 710061,

6. Peng Jia

   First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

   Affiliation as printed

   Department of Gynecology and Obstetrics, Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

   The First Affiliated Hospital of Xi’an Jiaotong University Department of Gynecology and Obstetrics, Center for Mathematical Medical, , Xi’an 710061,

7. Songbo Wang

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   Xi’an Jiaotong University MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, , Xi’an 710049,

   Xi’an Jiaotong University School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, , Xi’an 710049,

8. Peisen Sun

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   Xi’an Jiaotong University MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, , Xi’an 710049,

   Xi’an Jiaotong University School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, , Xi’an 710049,

9. Pengyu Zhang

   Xi'an Jiaotong University

   Affiliation as printed

   MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

   Xi’an Jiaotong University MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, , Xi’an 710049,

   Xi’an Jiaotong University School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, , Xi’an 710049,

10. Chengyao Wang

    First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

    Affiliation as printed

    Department of Endocrinology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

    Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

    Genome Institute, The First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

    The First Affiliated Hospital of Xi’an Jiaotong University Department of Endocrinology, , Xi’an 710061,

11. Ningxin Dang

    First Affiliated Hospital of Xi'an Jiaotong University

    Affiliation as printed

    Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

    Genome Institute, The First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

12. Yong E. Zhang

    Chinese Academy of Sciences · Institute of Zoology · Key Laboratory of Zoological Systematics and Evolution

    Affiliation as printed

    Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China

    Chinese Academy of Sciences Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, , Beijing 100101,

13. Kai Ye corresponding Aachen Faculty of Science, Leiden University

    Leiden University · First Affiliated Hospital of Xi'an Jiaotong University · Xi'an Jiaotong University

    Affiliation as printed

    Center for Mathematical Medical, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

    Faculty of Science, Leiden University, 2311 EZ, Leiden, The Netherlands

    Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an 710061, China

    MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

    School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, Xi'an 710049, China

    School of Life Science and Technology, Xi'an Jiaotong University, Xi'an 710049, China

    Genome Institute, The First Affiliated Hospital of Xi’an Jiaotong University , Xi’an 710061,

    Leiden University Faculty of Science, , Leiden 2311EZ, The

    The First Affiliated Hospital of Xi’an Jiaotong University Center for Mathematical Medical, , Xi’an 710061,

    Xi’an Jiaotong University MOE Key Lab for Intelligent Networks & Networks Security, Faculty of Electronic and Information Engineering, , Xi’an 710049,

    Xi’an Jiaotong University School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, , Xi’an 710049,

    Xi’an Jiaotong University School of Life Science and Technology, , Xi’an 710049,