\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  99~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. We will  first compare different  approaches to
construct such a tree using fully annoted genomes provided by NCBI and
Dogma, followed by a gene quality control among the common genes. Then
we  will 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}
