1 Identifying core genes is important to understand evolutionary and
2 functional phylogenies. Therefore, in this work we present methods to
3 build a genes content evolutionary tree. More precisely, we focus on
4 the following questions considering a collection of 99~chloroplasts
5 annotated from NCBI \cite{Sayers01012011} and Dogma \cite{RDogma}: how
6 can we identify the best core genome and what is the evolutionary
7 scenario of these chloroplasts.\\
8 Chloroplast (such as mitochondria) are fondamental key elements in
9 living organisms history. Indeed, chlorplast in Eucaryotes are organites responsible for
10 photosynthesis. Photosynthesis is the main way to produce organic matter
11 from mineral matter, using solar energy. Consequently photosynthetic
12 organisms are at the base of most ecosystems trophic chains and
13 photosynthesis in eucaryotes allowed a great speciation in the lineage
14 (to a great biodiversity). From an ecological point of view,
15 photosynthetic organisms are at the origin of the presence of dioxygen
16 in the atmosphere (allowing extant life) and are the main source of mid-
17 to long term carbon stockage (using atmospheric CO2, important in the
18 context of climate change). Chloroplast found in Eucaryots have an endosymbiotic origin, meaning
19 that they are a fusion of a photosynthetic bacteria (Cyanobacteria) and
20 a eucaryotic cell (enable to produce organic matter = heterotrophic).
21 This fusion or First Endiosymbiosis ended in a Great diversification of
22 a lineage comprising Red Algae, Green Algae and Land Plants (terrestrial).
23 Several Second Enbiosymbioses occurred then: two involving a Red
24 Algae and other heterotrophic eucaryotes and giving birth to both Brown
25 Algae and Dinoflagellates lineages; another involving a Green Algae and
26 a heterotrophic eucaryot and giving birth to Euglens.
