Phylogenetic analysis of re-sequenced organelle genomes: the case of the Brachypodium distachyon complex chloroplasts.

Chloroplast genomes of grasses contain two single copy regions separated by two nearly identical inverted repeats, harboring in total over a hundred genes. These sequences have great value for the reconstruction of the evolutionary history of plants due to their limited size and constrained rate of change. Here we report that high throughput sequencing experiments of grasses of the Brachypodium distachyion complex ( B.stacei, B.distachyon and B.hybridum ) yield as a by-product sufficient reads to allow the assembly of their plastids. The chloroplasts of a total 54 ecotypes were reconstructed by first filterin g chloroplast Illumina pair-end reads based on their k- mer composition, followed by genome assembly, usin g as reference a collection of sequenced plastids of monocot plant species. Despite the challenge of resolving both inverted repeats, we find that these plastids contain genetic polymorphisms that can help infer their evolutionary history. For instance, a 1Kb insert found in polyploid B.hybridum ABR113, also seen in B.stacei ABR114, contributes to the understanding of its hybrid origin.Peer Reviewe