Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes

Paulsen, J.; Sharrett, S. T.; Mumey, D.; Larsen, E. M.; Nguyen, N. K.; Lendemer, J.; Calabria, L. M.; Hoffman, J. R.; Magori, K.; Allen, J. L.

doi:10.1101/2025.07.11.664412

bioRxiv · 10.1101/2025.07.11.664412

Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes

Paulsen, J.·Sharrett, S. T.·Mumey, D.·Larsen, E. M.·Nguyen, N. K.·Lendemer, J.·Calabria, L. M.·Hoffman, J. R.·Magori, K.·Allen, J. L.

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Abstract

Mobile genetic elements (MGEs) have the potential to drive genome evolution by introducing mutations and causing structural instability and chromosomal rearrangements, particularly under conditions like environmental or genetic stress. In this study, we generated 18 new long-read based reference genomes for lichenized fungi, which form obligate mutualistic symbioses with algae or cyanobacteria. We used the new genomes and 10 publically available genomes to investigate the relationships between species traits (i.e., dominant reproductive mode, distribution size, and generation length) and the abundance and spatial distribution of MGEs using a phylogenetic comparative framework. We found that species with smaller distribution sizes and longer generation lengths had a higher genomic DNA transposon load. Specifically, their genomes were enriched with Rolling Circle transposons, which contradicts previous research that has identified high proportions of retrotransposons in rare species. Disproportionate distributions of MGEs in rare and range-restricted species may disrupt genomic stability, decrease fitness, and be reflective of species experiencing a greater degree of stress. Conversely, greater MGE activity may be an important source of novel genetic diversity in isolated populations with limited gene flow. Further research is needed to understand the potential mechanisms driving MGE proliferation in rare species genomes, and if MGE content is predictive of increased extinction risk.

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Paulsen, J., Sharrett, S. T., Mumey, D., Larsen, E. M., Nguyen, N. K., Lendemer, J., Calabria, L. M., Hoffman, J. R., Magori, K., Allen, J. L.. 2025-07-16. Helitrons are enriched in lichenized fungi with long generation lengths and small distribution sizes. https://doi.org/10.1101/2025.07.11.664412

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