adding the directory of paper2

[chloroplast13.git] / intro.tex

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@@ -6,21 +6,22 @@ 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 
 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 
+living organisms history. Indeed, chloroplast 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. 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 
+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 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 from solar energy = heterotrophic). \\
+to long term carbon stockage (using atmospheric CO2) an important feature in the 
+context of climate change. Chloroplasts found in Eucaryotes have an endosymbiotic origin, meaning 
+that they from the incorporation of a photosynthetic bacteria (Cyanobacteria) within an eucaryotic cell. \\

 
 

-By  the  principle  of
-classification, a  small number of genes lost  among species indicates
-that these species are close to  each other and belong to same family,
-while a  large lost  means that we  have an  evolutionary relationship
-between species  from different families.
+By  the  principle  of phylogenetic classification, a mutation in the DNA shared by two to several taxa has a higher probability to be inherited from common ancestor than to have evolved independently. In such a process, shared changes in the genomes allow to build relationships between species. In the case of chloroplasts, an important category of changes in the genome is the loss of functional genes, when inoperant or when transferred to the nucleus. Thereby, we hypothesize that small number of gene losses  among species indicates
+that these species are close to  each other and belong to same lineage,
+while a  large loss  means that we  have an  evolutionary relationship
+between species  from much more distant lineages. Phylogenetic relationships are mainly built by comparison of sets of coding and non-coding sequences. Phylogenies of photosynthetic plants are important to assess the origin of chloroplasts (REF) and the modalities of gene loss among lineages. These phylogenies are usually done using less than ten chloroplastic genes (REF), and some of them may not be conserved by evolution process for every taxa. As phylogenetic relationships inferred from data matrices complete for each species included and with the same evolution history are better assumptions, we selected core genomes for a new investigation of photosynthetic plants phylogeny. To depict the links between species clearly, we here intend to built a phylogenetic tree showing the relationships based on the distances among gene sequences of a core genome. The circumscription of the core chloroplast genomes for a given set of photosynthetic organisms needs bioinformatic tools for sequence annotation and comparison that we describe here.
+
+Other possible scientific questions to consider for introduction improvement:
+Which bioinformatic tools are necessary for genes comparison in selected complete chloroplast genomes? Which bioinformatic tools are necessary to build a phylogeny of numerous genes and species, etc?
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