The genetic control of rapid genome content divergence in Arabidopsis thaliana
Authors: Christopher Fiscus; Daniel Koenig
Affiliation: University of California, Riverside
Keywords: Comparative genomics & genome evolution
Repetitive sequences compose the majority of eukaryotic genomes and vary widely in both copy number and sequence content. Attempts to understand the evolution of repetitive sequences and their role in shaping genome content variation have been hindered by the lack of high-quality genome assemblies with resolved repeats. Here, we employ a novel K-mer based approach to study variation in genome content in 1,142 resequenced Arabidopsis thaliana genomes. We use our approach to study repeat evolution in this species and identify hundreds of repetitive sequences with copy number variation. We then map the genetic basis of this variation to both cis and trans-acting loci using genome wide association (GWAS). Furthermore, we use a meta-GWAS approach to identify loci associated with copy number variation of different types of repeats, suggesting that these loci are involved in modulating the rate of genome content evolution. Finally, we show that loci associated with repeat copy number change are under strong purifying selection with minor alleles largely associated with copy number decrease. Overall, our work provides insight into the genetic basis of genome content variation in plant genomes.