Genetic and epigenetic divergence among Arabidopsis thaliana Col-0 laboratory lineages since the 1950s

The Arabidopsis thaliana Columbia-0 (Col-0) accession is often treated as a standard reference genotype shared by plant researchers worldwide. However, a new study by Tadros et al. shows that decades of independent propagation in different laboratories have left distinct genetic and epigenetic signatures in Col-0 stocks. By sequencing the genomes and DNA methylomes of 78 Col-0 strains obtained from laboratories and stock centers around the world, the authors reconstructed the history of these lineages and tracked the changes that accumulated over time. Their analyses uncovered both DNA sequence mutations and large numbers of DNA methylation changes, revealing that many laboratory stocks have been evolving separately for generations. Interestingly, phylogenies based on DNA methylation closely mirrored those based on genetic variation and often provided finer resolution among closely related lineages. The study also identified candidate epialleles and mutations associated with differences in gene expression, suggesting that some of these changes may have biological consequences. Together, the findings challenge the view of Col-0 as a single uniform genotype and highlight how long-term laboratory propagation can generate divergence that may influence experimental reproducibility across research groups. (Summary by Fatai Ayomide Akande) bioRxiv https://doi.org/10.64898/2026.08.05.743031