  The aim of this study is to investigate the relation that can be found
between the phylogeny of a large set of complete chloroplast genomes, and the
evolution of gene content inside these sequences. Core and pan genomes have
been computed on \textit{de novo} annotation of these 845 genomes, the former
being used for producing well-supported phylogenetic tree while the latter
provides information regarding the evolution of gene contents over time. It
details too the specificity of some branches of the tree, when specificity is
obtained on accessory genes. After having detailed the material and methods, we
emphasize some remarkable relation between well-known events of the chloroplast
history, like endosymbiosis, and the evolution of gene contents over the
phylogenetic tree.
