Abstract
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.
Data availability
The data used in this study is available with bioproject accession numbers PRJEB100521 at Eu-ropean Nucleotide Archive (ENA, EMBL-EBI) and PRJNA898910, PRJNA242989 at Nation-al Center for Biotechnology Information (NCBI).
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Acknowledgements
The authors thank the French National Research Agency (ANR, Bridges_Coffea project, Grant Number ANR-23-CE20-0047-01) and FAPESP (Grant Number #2023/03353-3) for financial support. We would also like to thank the Rufford Foundation (Small Grant 39692-1) and the following HPC bioinformatics platform for its support: the French Bioinformatics Institute (IFB, funded by ANR, ANR-11-INBS-0013).
Funding
ANR, Bridges_Coffea project, Grant Number ANR-23-CE20-0047-01. Fapesp Grant Number # 2023/03353-3.
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MD, LGG and SOA conducted the main analyses; RB, NR, LFPP, DC, PDB, CF, LB, PD, PH participated to data acquisition (sample and sequencing); DSD and RG designed and conceived the study and wrote the draft manuscript. All authors participated to revise the manuscript.
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41598_2026_40031_MOESM1_ESM.csv
Sup. Data 1. GPS positions, genome size and bioclimatic data (Worlclim) for the species used in this study. Lat: latitude, long: longitude, group: phylogeographic group, bio1 to bio19 (worldclim data), All to Satellite columns: RepeatExplorer results (number of reads per elements).
Sup. Data 2. Phylogenetic tree of species used in this study with bootstraps.
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Sup. Data 5. Correlation between genome size (Mb) and all repeated reads.
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Dupeyron, M., Gonzalez-Garcia, L., Orozco-Arias, S. et al. Evolutionary history and climate-driven dynamics of transposable elements has shaped genome evolution in the Coffea genus.
Sci Rep (2026). https://doi.org/10.1038/s41598-026-40031-6
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DOI: https://doi.org/10.1038/s41598-026-40031-6
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