Abstract—Due to the recent evolution of sequencing techniques, the number of available genomes is rising steadily, leading to the possibility to make large scale genomic comparison among sets of close species. An interesting question to answer is: what are the common functionality genes of a collection of species, or conversely, to determine what is specific to a given species when compared to other ones belonging in the same genus, family, etc. Investigating such problem means to find both core and pan genomes of a collection of species, i.e. genes in common to all the species vs. the set of all genes in all species under consideration. However, obtaining trustworthy core and pan genomes is not an easy task, leading to a large amount of computation, and requiring a rigorous methodology. Surprisingly, as far as we know, this methodology in finding core and pan genomes has not really been deeply investigated. This research work tries to fill this gap by focusing only on chloroplastic genomes, whose reasonable sizes allow a deep study. To achieve this goal, a collection of 99 chloroplasts are considered in this article. Two methodologies have been investigated, respectively based on sequence similarities and genes names taken from annotation tools. The obtained results will finally be evaluated in terms of biological relevance.

Index Terms—Chloroplasts, coding sequences, clustering, genes prediction, methodology, pan genome, core genome.

Bassam Alkindy, Christophe Guyeux, and Jacques M. Bahi are with the FEMTO-ST Institute, UMR 6174 CNRS, DISC Computer Science Department, University of Franche-Comté, France (e-mail: bassam.al-kindy@univ-fcomte.fr, christophe.guyeux@univ-fcomte.fr, jacques.bahi@univ-fcomte.fr).
Jean-Francois Couchot and Michel Salomon are with the FEMTO-ST Institute, UMR 6174 CNRS, IUT-Belfort, University of Franche-Comté, France (e-mail: jean-francois.couchot@univ-fcomte.fr, michel.salomon@univ-fcomte.fr).
Arnaud Mouly is with the Chrono-Environnement Lab., UMR 6249 CNRS, University of Franche-Comté, France (e-mail: arnaud.mouly@univ-fcomte.fr).

Cite: Bassam ALkindy, Jean-François Couchot, Christophe Guyeux, Arnaud Mouly, Michel Salomon, and Jacques M. Bahi, "Finding the Core-Genes of Chloroplasts," International Journal of Bioscience, Biochemistry and Bioinformatics vol. 4, no. 5, pp. 361-368, 2014.