\begin{abstract}
DNA analysis techniques have received  a lot of attention  these last 
years,  because they play an  important role  in understanding 
genomes evolution over time, and in phylogenetic and genetic analyses. Various models 
of genomes evolution  are based on the analysis  of DNA sequences, SNPs, 
mutations, and so on. We have recently investigated the use of
core (\emph{i.e.}, common  genes) and pan genomes  to infer evolutionary information 
on a collection of 107 chloroplasts. In particular,
we have regarded methods to  build a genes content evolutionary tree  using  
distances to core  genome. However,  
the production of reliable core and pan genomes is not an easy task,
due to error annotations of the NCBI. The presentation will then
consist in various compared approaches to construct such a tree using
fully annotated genomes by NCBI and Dogma, followed by a gene quality 
control among the  common genes. We will finally explain how, by comparing 
sequences from Dogma with NCBI contents, we achieved to identify the 
genes that play a key role in the dynamics of genomes evolution. \\

\textbf{Keywords:} genome evolution, phylogenetic tree, core genes, evolution tree, genome annotation  
\end{abstract}