adding the directory of paper2

[chloroplast13.git] / discussion.tex

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-The interesting with the tree produced (especially from DOGMA) is 
+The first endiosymbiosis ended in a great diversification of 
+a lineage comprising \textit{Red Algae, Green Algae} and \textit{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\cite{mcfadden2001primary}.\\
+The interesting point with the tree produced (especially from DOGMA) is 

 that organisms resulting from the first endosymbiosis are distributed in 
 every of the lineage found in the chloroplast genome structure 
 evolution: with Red Algae chloroplasts together in one lineage, and 
 that organisms resulting from the first endosymbiosis are distributed in 
 every of the lineage found in the chloroplast genome structure 
 evolution: with Red Algae chloroplasts together in one lineage, and 

-Green Algae and Land Plants chloroplasts together in antoher lineage; 
-while oranisms resulting from secondary endosymbioses are localized in 
+Green Algae and Land Plants chloroplasts together in another lineage; 
+while organisms resulting from secondary endosymbioses are more localized in 

 the tree: both the chloroplasts of Brown Algae and Dinoflagellates 
 representatives are found exclusively in the lineage also comprising the 
 Red Algae chloroplasts from which they evolved, while the Euglens 
 chloroplasts are related to the Green Algae chloroplasts from which they 
 the tree: both the chloroplasts of Brown Algae and Dinoflagellates 
 representatives are found exclusively in the lineage also comprising the 
 Red Algae chloroplasts from which they evolved, while the Euglens 
 chloroplasts are related to the Green Algae chloroplasts from which they 

-evolved. This make sense in term of biology and history of lineages and 
+evolved. This makes sense in terms of biology, history of lineages, and 

 theories of chloroplasts (and so photosynthetic ability) origins in 
 theories of chloroplasts (and so photosynthetic ability) origins in 

-different Eucaryotic lineages.
+different Eucaryotic lineages\cite{mcfadden2001primary}.

 Interestingly, The sole organisms included that possesses a 
 chloroplast (and so a chloroplastic genome) but that have lost the 
 Interestingly, The sole organisms included that possesses a 
 chloroplast (and so a chloroplastic genome) but that have lost the 

-photosynthetic ability (being parasitic plant) are found at the base of 
-the tree, and not together with its related species phylogenetically, 
-meaning that functional chloroplast genes are evolutionnary constrained 
+photosynthetic ability (being parasitic plants) are found at the base of 
+the tree, and not together with their phylogenetically related species. This means that functional chloroplast genes are evolutionnary constrained 

 when used in photosynthetic process, but loose rapidly their efficiency 
 when used in photosynthetic process, but loose rapidly their efficiency 

-when not used. They are Cuscuta-grovonii an Angiosperm (flowering plant) 
+when not used, as recently observed for a species of Angiosperms\cite{li2013complete}. These species are \textit{Cuscuta-grovonii} an Angiosperm (flowering plant) 

 at the base of the DOGMA Angiosperm-Conifers branch, and 
 at the base of the DOGMA Angiosperm-Conifers branch, and 

-Epipactis-virginiana also an Angiosperm at the complete base of the tree.
-Another interesting result in your work is that Land Plants that 
-represent single sublineage originating from the large and diverse 
-lineage of Green Algae in Eucaryots history are present in two different 
+\textit{Epipactis-virginiana} also an Angiosperm at the complete base of the tree.
+Another interesting result is that land plants that 
+represent a single sublineage originating from the large and diverse 
+lineage of green algae in Eucaryots history are present in two different 

 branches of the DOGMA tree, associated with Green Algae, one branch 
 branches of the DOGMA tree, associated with Green Algae, one branch 

-comprising the "inferior" Land Plants (mosses and ferns) and the second 
-comprising the "superior" Land Plants (Conifers and flowering plants). 
+comprising the basal grade of land plants (mosses and ferns) and the second 
+comprising the most internal lineages of land plants (Conifers and flowering plants). 

 But independently of their split in two distinct branches of the DOGMA 
 tree, the Land Plants always show a higher number of functional genes in 
 But independently of their split in two distinct branches of the DOGMA 
 tree, the Land Plants always show a higher number of functional genes in 

-their chloroplasts than their related Green Algae, probably meaning that 
+their chloroplasts than the green algae from which they emerged, probably meaning that the

 terrestrial way of life necessitates more functional genes for an 
 terrestrial way of life necessitates more functional genes for an 

-optimal photosynthesis than marine way of life. But a more detailed 
-analysis of selected genes is necessary to better understad the reasons why.
+optimal photosynthesis than the marine way of life. However, a more detailed 
+analysis of selected genes is necessary to better understand the reasons why?
+
+
+