update

diff --git a/annotated.tex b/annotated.tex
index ad0f65412276c72dc410b7d2a565acd6e761608f..dd57e11dd760cf0fbef6fcfa783cfa26c7678ebb 100644 (file)
--- a/annotated.tex
+++ b/annotated.tex
@@ -295,11 +295,7 @@ names\_Accession number)}. While an edge is labelled with the number of
 lost  genes from  a leaf  genome or  an intermediate  core  gene. Such
 numbers are  very interesting because  they give an  information about
 the evolution:  how many genes  were lost between two  species whether
 lost  genes from  a leaf  genome or  an intermediate  core  gene. Such
 numbers are  very interesting because  they give an  information about
 the evolution:  how many genes  were lost between two  species whether

-they  belong  to  the  same  family  or not.   By  the  principle  of
-classification, a  small number of genes lost  among species indicates
-that those 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. To depict  the links between
+they  belong  to  the  same  lineage  or not. 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 investivation of photosynthetic plants phylogeny. To depict  the links between

 species   clearly,  we   built   a  phylogenetic   tree  showing   the
 relationships based on the distances among genes sequences. Many tools
 are    available   to    obtain    a   such    tree,   for    example:
 species   clearly,  we   built   a  phylogenetic   tree  showing   the
 relationships based on the distances among genes sequences. Many tools
 are    available   to    obtain    a   such    tree,   for    example:


@@ -336,7 +332,7 @@ We implemented the three algorithms using dell laptop model latitude E6430 with
  & \multicolumn{2}{c}{Annotation} & \multicolumn{2}{c}{Features} & \multicolumn{2}{c}{E. Time} & \multicolumn{2}{c}{C. genes} & \multicolumn{2}{c}{Bad Gen.} \\
 ~ & N & D & Name & Seq & N & D & N & D & N & D \\
 \hline
  & \multicolumn{2}{c}{Annotation} & \multicolumn{2}{c}{Features} & \multicolumn{2}{c}{E. Time} & \multicolumn{2}{c}{C. genes} & \multicolumn{2}{c}{Bad Gen.} \\
 ~ & N & D & Name & Seq & N & D & N & D & N & D \\
 \hline

-Gene prediction & $\surd$ & - & - & $\surd$ & ? & - & ? & - & 0 & -\\[0.5ex]
+Gene prediction & $\surd$ & - & - & $\surd$ & 1.7 & - & ? & - & 0 & -\\[0.5ex]

 Gene Features & $\surd$ & $\surd$ & $\surd$ & - & 4.98 & 1.52 & 28 & 10 & 1 & 0\\[0.5ex]
 Gene Quality & $\surd$ & $\surd$ & $\surd$ & $\surd$ & \multicolumn{2}{c}{$\simeq$3 days + 1.29} & \multicolumn{2}{c}{4} & \multicolumn{2}{c}{1}\\[1ex]
 \hline
 Gene Features & $\surd$ & $\surd$ & $\surd$ & - & 4.98 & 1.52 & 28 & 10 & 1 & 0\\[0.5ex]
 Gene Quality & $\surd$ & $\surd$ & $\surd$ & $\surd$ & \multicolumn{2}{c}{$\simeq$3 days + 1.29} & \multicolumn{2}{c}{4} & \multicolumn{2}{c}{1}\\[1ex]
 \hline


@@ -357,7 +353,7 @@ The second important factor is the amount of memory usage in each methodology. T
 \hline\hline
 Method& & Load Gen. & Conv. gV & Read gV & ICM & Core tree & Core Seq. \\
 \hline
 \hline\hline
 Method& & Load Gen. & Conv. gV & Read gV & ICM & Core tree & Core Seq. \\
 \hline

-Gene prediction & ~ & ~ & ~ & ~ & ~ & ~ & ~\\
+Gene prediction & NCBI & 100 & - & - & - & 108 & -\\

 \multirow{2}{*}{Gene Features} & NCBI & 15.4 & 18.9 & 17.5 & 18 & 18 & 28.1\\
               & DOGMA& 15.3 & 15.3 & 16.8 & 17.8 & 17.9 & 31.2\\
 Gene Quality  & ~ & 15.3 & $\le$3G & 16.1 & 17 & 17.1 & 24.4\\ 
 \multirow{2}{*}{Gene Features} & NCBI & 15.4 & 18.9 & 17.5 & 18 & 18 & 28.1\\
               & DOGMA& 15.3 & 15.3 & 16.8 & 17.8 & 17.9 & 31.2\\
 Gene Quality  & ~ & 15.3 & $\le$3G & 16.1 & 17 & 17.1 & 24.4\\ 

diff --git a/discussion.tex b/discussion.tex
index 7f17a7fc595982cae0d24f7f416cde1269900cda..97fcb3f90f659475a493b8dbdd60f1abf60ee283 100644 (file)
--- a/discussion.tex
+++ b/discussion.tex
@@ -1,3 +1,9 @@
+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.\\

 The interesting 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 
 The interesting 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 


@@ -13,22 +19,25 @@ theories of chloroplasts (and so photosynthetic ability) origins in
 different Eucaryotic lineages.
 Interestingly, The sole organisms included that possesses a 
 chloroplast (and so a chloroplastic genome) but that have lost the 
 different Eucaryotic lineages.
 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 
+photosynthetic ability (being parasitic plants) are found at the base of 

 the tree, and not together with its related species phylogenetically, 
 meaning that functional chloroplast genes are evolutionnary constrained 
 when used in photosynthetic process, but loose rapidly their efficiency 
 when not used. They are Cuscuta-grovonii an Angiosperm (flowering plant) 
 at the base of the DOGMA Angiosperm-Conifers branch, and 
 Epipactis-virginiana also an Angiosperm at the complete base of the tree.
 the tree, and not together with its related species phylogenetically, 
 meaning that functional chloroplast genes are evolutionnary constrained 
 when used in photosynthetic process, but loose rapidly their efficiency 
 when not used. They are Cuscuta-grovonii an Angiosperm (flowering plant) 
 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 
+Another interesting result is that land plants that 

 represent single sublineage originating from the large and diverse 
 represent single sublineage originating from the large and diverse 

-lineage of Green Algae in Eucaryots history are present in two different 
+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 lineage 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 

 terrestrial way of life necessitates more functional genes for an 
 optimal photosynthesis than marine way of life. But a more detailed 
 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.
+analysis of selected genes is necessary to better understad the reasons why?
+
+
+

diff --git a/intro.tex b/intro.tex
index ddb2fcb6e91ff0a8e98e658dddfe76d0292d031a..9a70444bd0874aaa646f07e56a77cd3ff23d55fd 100644 (file)
--- a/intro.tex
+++ b/intro.tex
@@ -17,10 +17,10 @@ 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 
 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.
\ No newline at end of file
+a eucaryotic cell (enable to produce organic matter from solar energy = heterotrophic). \\
+
+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.

diff --git a/main.tex b/main.tex
index d411c361bc58dff26f11066ded1b8750e6be1145..92ec4949f8e8b58afb0f8bbdcb2544fa105e7979 100755 (executable)
--- a/main.tex
+++ b/main.tex
@@ -21,12 +21,11 @@
  
 \begin{document}
 
  
 \begin{document}
 

-\title{Finding the core-genes of Chloroplast Species}
+\title{Finding the core-genes of Plant Species Chloroplast}

 \author{
 \author{

-Bassam AlKindy\footnote{email: bassam.al-kindy@univ-fcomt\'{e}.fr} \and Jean-Fran\c{c}ois Couchot 
-\and Christophe Guyeux \and Arnaud Mouly \and Michel Salomon \and\\
-FEMTO-ST Institute, UMR 6174 CNRS, \\
-Computer Science Department DISC, \\
+Bassam AlKindy\footnote{email: bassam.al-kindy@univ-fcomt\'{e}.fr} \and Jean-Fran\c{c}ois Couchot \and Christophe Guyeux \and Arnaud Mouly \and Michel Salomon \and Jacques Bahi \\
+FEMTO-ST Institute, UMR 6174 CNRS,\\
+Computer Science Department DISC, \and Lab. Chrono-Environnement, UMR 6174 CNRS,\\

 Universit\'{e} de Franche-Comt\'{e}, France \\
 {\small \it Authors in alphabetic order}
 }
 Universit\'{e} de Franche-Comt\'{e}, France \\
 {\small \it Authors in alphabetic order}
 }

diff --git a/population_Table.tex b/population_Table.tex
index 6a65f007e17de906f9198be3192acecfbb20b99f..7f1536cf6cd62d134e737bb5ccc0f9e472048290 100644 (file)
--- a/population_Table.tex
+++ b/population_Table.tex
@@ -1,7 +1,7 @@
 \begin{center}  
   \begin{table}
     \tiny
 \begin{center}  
   \begin{table}
     \tiny

-    \caption[NCBI Genomes Families]{List of family groups of Chloroplast Genomes from NCBI\label{Tab2}}
+    \caption[NCBI Genomes Families]{List of chloroplast genomes of photosynthetic Eucaryotes lineages from NCBI\label{Tab2}}

     \begin{minipage}{0.50\textwidth}
       \setlength{\tabcolsep}{4pt}
       \begin{tabular}{|p{0.1cm}|p{0.1cm}|p{1.3cm}|p{3cm}|}
     \begin{minipage}{0.50\textwidth}
       \setlength{\tabcolsep}{4pt}
       \begin{tabular}{|p{0.1cm}|p{0.1cm}|p{1.3cm}|p{3cm}|}


@@ -66,7 +66,7 @@
       &  & NC\_020018.1 & Monomorphina aenigmatica \\ 
        \hline
        % Entering seventh group
       &  & NC\_020018.1 & Monomorphina aenigmatica \\ 
        \hline
        % Entering seventh group

-       \parbox[t]{1mm}{\multirow{5}{*}{\rotatebox[origin=c]{90}{Fern}}}     &       \multirow{5}{*}{5}
+       \parbox[t]{1mm}{\multirow{5}{*}{\rotatebox[origin=c]{90}{Ferns}}}     &       \multirow{5}{*}{5}

        & NC\_003386.1 & Psilotum nudum \\ 
       & & NC\_008829.1 & Angiopteris evecta \\
       &  & NC\_014348.1 & Pteridium aquilinum \\ 
        & NC\_003386.1 & Psilotum nudum \\ 
       & & NC\_008829.1 & Angiopteris evecta \\
       &  & NC\_014348.1 & Pteridium aquilinum \\ 


@@ -154,12 +154,12 @@
   \end{minipage}
  
   \scriptsize 
   \end{minipage}
  
   \scriptsize 

-  \noindent where families F1, F2, F3, F4, F5, and F6 are 
+  \noindent where lineages F1, F2, F3, F4, F5, and F6 are 

   Red Algae,
   Red Algae,

-  Brypoytes, 
+  Bryophytes, 

   Dinoflagellates,
   Euglena,
   Dinoflagellates,
   Euglena,

-  Haptophytes, and Lycopodiophyta respectively.
+  Haptophytes, and Lycophytes respectively.

   \normalsize
   \end{table}
 \end{center}  
   \normalsize
   \end{table}
 \end{center}