Evolutionary history and climate-driven dynamics of transposable elements has shaped genome evolution in the Coffea genus

Genome size variation is a fundamental feature of plant genomes and plays an important role in phenotypic diversity, ecological adaptation, and plant evolution across angiosperms. In the Coffea genus (Rubiaceae, 141 species/taxa), significant genome size variations have been observed. There has been nearly a twofold increase between species from East and West Africa and a notable increase from northwest to southeast Madagascar, resulting in geographic gradients. Previous studies suggest a role of Long Terminal Repeat (LTR) retrotransposons in these variations; however, the low resolution of the data to support this hypothesis did not allow for a clear understanding of LTR retrotransposons dynamics within the genus. Here, we present an analysis of the genomes of 22 Coffea species mainly from Africa and Madagascar and their genome size variations within a robust phylogenetic framework. Our results show that genome size and Transposable Elements (TE) landscape are first structured by phylogenetic relationships, reflecting shared evolutionary history and lineage-specific LTR retrotransposon dynamics particularly involving the Tekay/Del, TAT, and SIRE lineages. These lineages contribute to the differentiation of phylogeographic groups, reflecting specific patterns of genomic divergence linked to species adaptation and speciation. We also detected significant association between specific TE families and environmental variables (such as isothermality and annual precipitation). These correlations suggest that environmental factors modulate repeatome evolution and a potential adaptive role of these TEs. These findings highlight the importance of TEs in genome dynamics at the intersection of evolutionary processes and environmental adaptations and open new perspectives on their adaptive role within the Coffea genus.