Abstract—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 de novo annotations 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.

Index Terms—Chloroplasts, phylogeny, taxonomy, core and pan genomes, gene content.

Bashar Al-Nuaimi is with FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, University of Bourgogne Franche-Comté, France. He is also with the Department of Computer Science, University of Diyala, Diyala, Iraq.
Christophe Guyeux, Bassam AlKindy, Michel Salomon, Jean-Francois Couchot are with Department of Computer Science, University of Diyala, Diyala, Iraq (email: christophe.guyeux@univ-fcomte.fr).
Bassam AlKindy is with Department of Computer Science, University of Mustansiriyah, Baghdad, Iraq.

Cite: Bashar Al-Nuaimi, Christophe Guyeux, Bassam AlKindy, Michel Salomon, Jean-Francois Couchot, "Relation between Gene Content and Taxonomy in Chloroplasts," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 7, no. 1, pp. 41-50, 2017.