Abstract
Chloroplast and mitochondria are specialized structure located in the cytoplasm of plant cells which possess their own genomes and are usually transmitted by one parent only. Organelle DNA markers have been widely used for phylogeny and population genetics studies because theirlow evolutionary rates allow to look further back in the past than nuclear data. This low evolutionary rate, however, was also a drawback because the diversity revealed by traditional methods (Sanger sequencing, microsatellites, RFLP, etc.) was low and was not necessarily discriminatoryenough to study genetic structure and genetic relationships. Nowadays, the fast development of next-generation sequencing methods has changed the way organelle genomes sequences are obtained. It is now easy to get whole organelle genome sequences, even for an orphan species.Because the quantity of data and the amount of diversity generated by these new methods have strongly increased, the way organelle genetic data can be used has also changed. This chapter provides a review on how to retrieve organelle genomic polymorphism from next-generationsequencing technology, with an emphasis on the specificity of organelles compared to nuclear data: how to efficiently sequence this highly repeated DNA resulting from multiple copies of the organelle genome within a cell, how to deal with the intra-individual diversity generated,and how to reconstruct a whole organelle genome sequence. This chapter will then review how next-generation sequencing technology has changed the main fields of organelle population genomics, i.e. population genetics, phylogeny, phylogeography and DNA barcoding.These new possibilities will be analysed in the light of the new drawbacks going along with the ?big data?.