Convergence and divergence of DNA methylation and gene expression patterns in neopolyploid Arabidopsis kamchatica

Polyploidization is a key evolutionary force in plants, but the reasons behind its prevalence remain unclear. While the potential ecological benefits of established polyploids are well studied, little is known about the short-term genomic and epigenetic responses immediately after polyploidization, which are crucial for successful speciation. In this study, we assemble the genomes of the two progenitors of Arabidopsis kamchatica (A. halleri and A. lyrata) and examine the epigenome of synthetic and natural tetraploids of A. kamchatica to investigate the combined effect of allopolyploidization and environment on DNA methylation changes. We find the most significant methylation changes at allopolyploidization, followed by smaller changes in subsequent generations. Offspring grown under different conditions show divergent patterns, suggesting environmental effects, while their methylation patterns converge toward those of natural tetraploids over generations. Our findings highlight two key epigenetic changes post-polyploidization: convergence toward established polyploids and divergence driven by environmental factors.