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

## TL;DR

This paper introduces LTR_Stream, a new tool for analyzing LTR retrotransposons in plants, revealing their complex interactions with the host genome in three Papaver species.

## Contribution

The novel contribution is the development of LTR_Stream, which enables high-resolution clustering of LTR-RTs in non-model species.

## Key findings

- Autonomous Retand elements spread among ancestors of different subgenomes, increasing genetic diversity.
- Truncated LTR-RT fragments with transcription factor motifs may create new TAD-like boundaries.
- Allopolyploidization reduced the impact of LTR-RTs, suggesting it helps Papaver species manage these elements.

## 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.