From 9771923779498f5cbf4e21e9389062ac5d5cbb11 Mon Sep 17 00:00:00 2001 From: bassam al-kindy Date: Mon, 16 Dec 2013 13:32:31 +0100 Subject: [PATCH] update --- annotated.tex | 10 +++------- discussion.tex | 23 ++++++++++++++++------- intro.tex | 14 +++++++------- main.tex | 9 ++++----- population_Table.tex | 10 +++++----- 5 files changed, 35 insertions(+), 31 deletions(-) diff --git a/annotated.tex b/annotated.tex index ad0f654..dd57e11 100644 --- 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 -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: @@ -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 -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 @@ -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 -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\\ diff --git a/discussion.tex b/discussion.tex index 7f17a7f..97fcb3f 100644 --- 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 @@ -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 -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. -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 -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 -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 -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 -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 ddb2fcb..9a70444 100644 --- 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 -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 d411c36..92ec494 100755 --- a/main.tex +++ b/main.tex @@ -21,12 +21,11 @@ \begin{document} -\title{Finding the core-genes of Chloroplast Species} +\title{Finding the core-genes of Plant Species Chloroplast} \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} } diff --git a/population_Table.tex b/population_Table.tex index 6a65f00..7f1536c 100644 --- a/population_Table.tex +++ b/population_Table.tex @@ -1,7 +1,7 @@ \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}|} @@ -66,7 +66,7 @@ & & 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 \\ @@ -154,12 +154,12 @@ \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, - Brypoytes, + Bryophytes, Dinoflagellates, Euglena, - Haptophytes, and Lycopodiophyta respectively. + Haptophytes, and Lycophytes respectively. \normalsize \end{table} \end{center} -- 2.39.5