Fragmented landscapes of mobile transposable element families bolster the diversity of large-effect alleles in Arabidopsis

Petit, A.; Caillieux, E.; Reignier, M.; Gueye, N. A.; De Oliveira, L.; Xu, C.; Cordier, C.; Sezginmert, D.; Colot, V.; Baduel, P.

doi:10.64898/2026.10.12.758581

bioRxiv · 10.64898/2026.10.12.758581

Fragmented landscapes of mobile transposable element families bolster the diversity of large-effect alleles in Arabidopsis

Petit, A.·Caillieux, E.·Reignier, M.·Gueye, N. A.·De Oliveira, L.·Xu, C.·Cordier, C.·Sezginmert, D.·Colot, V.·Baduel, P.

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Abstract

Transposable elements (TEs) are powerful endogenous mutagens, but our understanding of the 'mobilome' - the set of mobile TEs at the species level - has largely been shaped by the study of a single reference genome. To overcome this reference-centric view, we produced long-read genome assemblies for 91 Arabidopsis thaliana strains and performed a reference-free pangenomic graph analysis of structural variants. Our analysis revealed the presence of twice as many TE families with recent mobilization activity as previously described. These >200 newly identified TE families are ancestral, with a third experimentally shown to be mobile and although they are often characterized by the presence of full-length copies in only a few rather than in most strains, they nonetheless contribute significantly to the generation of large-effect alleles. These findings uncover a much more fragmented and impactful mobilome than previously documented and highlight how pangenome approaches dramatically improve the study of genetic diversity.

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Petit, A., Caillieux, E., Reignier, M., Gueye, N. A., De Oliveira, L., Xu, C., Cordier, C., Sezginmert, D., Colot, V., Baduel, P.. 2026-10-16. Fragmented landscapes of mobile transposable element families bolster the diversity of large-effect alleles in Arabidopsis. https://doi.org/10.64898/2026.10.12.758581

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