Deciphering the dynamics of active autonomous terminal inverted repeat transposons in the plant kingdom

This study is led by Professor Xinyan Zhang (Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen, China). Active autonomous transposons act as both "symbionts" and "parasites," driving genome evolution, yet a systematic understanding of recently active elements remains scarce. To tackle this challenge, the research team developed an efficient data-distillation pipeline that recasts the identification of recently active TIR transposons as a streamlined bioinformatics task centered on detecting clusters of highly similar copies. This approach enabled the construction of a comprehensive atlas of active autonomous TIR transposons across 1,007 plant genomes and allowed in-depth exploration of their lineage differentiation patterns and adaptive mechanisms. The study revealed a strikingly uneven distribution of active autonomous TIR transposons.

Vascular plants harbor significantly more active clusters than non-vascular plants, whereas functional extinction is widespread, with 42.7% of surveyed species lacking any detectable active elements. Amplification is also tightly restrained: 93.3% of active clusters persist at low copy numbers. Lineage specificity is pronounced, particularly in crops, where 63.7% of active clusters are strain-specific, underscoring that single reference genomes substantially underestimate transposon dynamics. Among the identified superfamilies, Mutator-like elements (MULEs) predominate, comprising 57.6% of all active clusters. Using the maize MuDR system as a model, the researchers found that the MURA transposase interacts with the accessory MURB protein through a non-conserved N-terminal domain. This modular interaction likely confers greater adaptability and long-term persistence to MULEs. Together, this atlas provides critical insights into transposon–host coevolution and delivers a rich, species-specific resource for plant biotechnology.

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Deciphering the dynamics of active autonomous terminal inverted repeat transposons in the plant kingdom

https://www.sciencedirect.com/science/article/pii/S2662173825002164