The evolutionary dynamics of organellar pan-genomes in Arabidopsis thaliana

In plants, comparative analyses of organellar genomes often depend on draft assemblies, with large-scale investigations into the complex structural rearrangements of mitochondrial genomes remaining scarce. Here, we conducted a comprehensive analysis of the dominant conformations and dynamic heteroplasmic variants of organellar genomes in the model plant Arabidopsis thaliana, utilizing high-quality long-read assemblies validated at read-level resolution from 149 samples. We found that mitochondrial and plastid genomes share common types of structural and small-scale variants driven by similar DNA sequence features. However, rearrangements mediated by repetitive sequences in mitochondrial genomes evolved so rapidly that they often became decoupled from other types of variants. Rare complex events involving elongation and fusion were also observed, contributing to the unalignable regions commonly found at the interspecies level. Additionally, we demonstrated that disrupting and rescuing organellar DNA maintenance could drive the rapid evolution of dominant mitochondrial genome conformations. Our study provides an unprecedentedly detailed view of the dynamics of organellar genomes at pan-genome scale in A. thaliana, paving the way to unlock the full potential of organellar genetic resources. SignificancePlant mitochondrial genomes exhibit rapid rearrangements within species. Large-scale analyses using high-quality assemblies offer detailed insights into their evolutionary dynamics, paving the way for organellar genome engineering and functional research in the future.