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