The genetic control of rapid genome content divergence in <i>Arabidopsis thaliana</i>

Genome evolution within eukaryotes is largely influenced by repetitive sequences, which exhibit significant variation in both copy number and sequence composition. The rate at which these repeats evolve can vary between species and even within the same species, and this variability may be influenced by genetic factors and environmental conditions.

To investigate the underlying factors that determine the rate of genome content variation, researchers analyzed 1,043 resequenced Arabidopsis thaliana genomes using a novel K-mer-based method to identify genome content variation and pinpoint hypervariable regions responsible for differences in repeat abundance. They further treated repeat abundance as a quantitative trait and conducted genome-wide association analyses across over 400 repeat families to uncover the genetic basis of copy number variation.

By combining these results through a meta-GWAS approach, the study identified both cis-acting variants and more than 50 candidate trans-acting loci associated with repeat abundance across the entire genome. Cis-acting variation was predominantly found in pericentromeric and centromeric regions, while trans-acting loci were enriched with candidate genes involved in DNA replication, DNA repair, and DNA methylation regulation.

The findings suggest that purifying selection acts against mutations that accelerate genome content divergence, favoring alleles that curb repeat expansion. These results offer new insights into the genetic architecture and evolutionary forces driving genome evolution in Arabidopsis thaliana and establish a framework for further investigation of these processes in other plant species.