Next generation organellar genomics: potentials and pitfalls of high-throughput technologies for molecular evolutionary studies and plant systematics

Plastid and mitochondrial genomes (plastomes and chondromes, respectively) are rewarding objects for molecular evolutionary studies and useful tools in plant phylogenetics and phylogenomics. The broad availability of NGS technologies has boosted the rate with which plastome and chondrome sequences can be generated from essentially any plant group of interest. Here, we evaluate methodological approaches for complete sequencing, paying attention to common challenges and pitfalls. We review the current knowledge of organellar genome evolution in plants with respect to genome structure, including causes and consequences of microstructural changes and of large-scale reconfigurations, and to the evolution of substitution rates. Finally, we provide an overview of the role of organellar DNA in plant systematics. Although in the future the use of plastid and mitochondrial DNAs for systematic studies likely will decrease in favor of nuclear markers, the collection of complete organellar genomes will continue to provide exciting possibilities to study mechanisms of molecular evolution.