The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity

0568619 - BC 2023 RIV GB eng J - Journal Article
Schley, R. J. - Pellicer, J. - Ge, X. - Barrett, C. - Bellot, S. - Guignard, M. S. - Novák, Petr - Suda, Jan - Fraser, D. - Baker, W. J. - Dodsworth, S. - Macas, Jiří - Leitch, A. R. - Leitch, I. J.
The ecology of palm genomes: repeat-associated genome size expansion is constrained by aridity.
New Phytologist. Roč. 236, č. 2 (2022), s. 433-446. ISSN 0028-646X. E-ISSN 1469-8137
R&D Projects: GA MŠMT(CZ) LM2018131
Institutional support: RVO:60077344 ; RVO:67985939
Keywords : adaptation * Arecaceae (palms) * ecology * genome size * phylogenetic regression * plant evolution * trait evolution * transposable elements
OECD category: Genetics and heredity (medical genetics to be 3); Genetics and heredity (medical genetics to be 3) (BU-J)
Impact factor: 9.4, year: 2022
Method of publishing: Open access
https://nph.onlinelibrary.wiley.com/doi/10.1111/nph.18323

Genome size varies 2400-fold across plants, influencing their evolution through changes in cell size and cell division rates which impact plants environmental stress tolerance. Repetitive element expansion explains much genome size diversity, and the processes structuring repeat communities are analogous to those structuring ecological communities. However, which environmental stressors influence repeat community dynamics has not yet been examined from an ecological perspective. We measured genome size and leveraged climatic data for 91% of genera within the ecologically diverse palm family (Arecaceae). We then generated genomic repeat profiles for 141 palm species, and analysed repeats using phylogenetically informed linear models to explore relationships between repeat dynamics and environmental factors. We show that palm genome size and repeat community composition are best explained by aridity. Specifically, Ty3-gypsy and TIR elements were more abundant in palm species from wetter environments, which generally had larger genomes, suggesting amplification. By contrast, Ty1-copia and LINE elements were more abundant in drier environments. Our results suggest that water stress inhibits repeat expansion through selection on upper genome size limits. However, elements that may associate with stress-response genes (e.g. Ty1-copia) have amplified in arid-adapted palm species. Overall, we provide novel evidence of climate influencing the assembly of repeat communities.
Permanent Link: https://hdl.handle.net/11104/0339892