Study Uncovers How Polyploid Plants Harness Transposons for Evolutionary Innovation

Polyploidization, the combination and duplication of genomes, is a major driver of plant evolution and diversification. Yet this process causes "genome shock," leading to rapid activation of transposable elements (TEs). While TEs can threaten genome stability, they also serve as sources of genetic novelty by altering gene regulation and chromosomal structure. Among plant TEs, Helitron elements are known for their ability to capture gene fragments through a unique rolling-circle replication mechanism, potentially facilitating new gene functions. However, the biological significance and regulatory consequences of such gene capture during allopolyploid formation remain poorly understood. Due to these challenges, there is a need to investigate how epigenetic mechanisms influence gene capture during polyploid evolution.

Researchers from Wuhan University have uncovered how epigenetic modifications guide gene capture by Helitron TEs in the allopolyploid crop Brassica napus. The study, published (DOI: 10.1093/hr/uhaf028) on May 1, 2025, in Horticulture Research, analyzed natural and resynthesized B. napus lines to reveal how captured gene fragments are redistributed across the genome, shaped by changes in DNA methylation and small RNA pathways. The findings highlight a previously underexplored mechanism by which polyploid plants balance genome stability with evolutionary innovation.

The team identified 3,156 gene capture events involving 1,793 Helitron elements in the B. napus genome. These Helitrons acquired fragments from 326 donor genes, many of which contained long untranslated regions (UTRs), suggesting capture favors regulatory sequences rather than protein-coding domains. Once captured, the gene fragments were dispersed throughout the genome, frequently contributing to pseudogene formation, expanding the pool of latent genetic material available for evolutionary modification.

Epigenetic analysis showed that donor genes exhibited reduced small RNA abundance but elevated DNA methylation relative to non-captured genes. This suggests that siRNA-mediated "crosstalk" between TEs and donor genes increases methylation and decreases expression of donor loci. Moreover, during early stages of polyploid formation, methylation levels of both donor genes and gene-capturing TEs were temporarily reduced-indicating a relaxed repression period that may enable capture activity to occur. As the genome stabilized over evolutionary time, methylation increased again, reestablishing TE silencing.

Together, these findings indicate that epigenetic mechanisms not only suppress potentially harmful TE mobilization but also facilitate controlled genomic diversification through gene capture.

Gene capture by TEs has often been viewed as a disruptive event, but our results show it can also be an engine of evolutionary creativity. Epigenetic regulation allows the genome to temporarily relax constraints during polyploidization, enabling gene fragments to be redistributed and stored without immediately altering essential functions. Over time, these sequences may evolve into new regulatory modules or coding genes. This balance between control and flexibility is key to understanding how polyploid crops adapt and diversify."

Jianbo Wang, study's corresponding author

​​​​This work provides a new framework for understanding how polyploid crops generate adaptive variation. By showing that TEs can store gene fragments as evolutionary "reserve material" while epigenetic modifications modulate their effects, the study suggests new strategies for plant breeding and genomic innovation. Controlled manipulation of TE activity or DNA methylation could accelerate the development of traits such as stress tolerance, growth performance, and metabolic diversity. More broadly, the findings highlight gene capture as a natural mechanism by which genomes explore new functional possibilities, potentially guiding future crop improvement and synthetic genome engineering.