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:
Method & \multicolumn{2}{c}{Annotation} & \multicolumn{2}{c}{Features} & \multicolumn{2}{c}{Exec. time (min.)} & \multicolumn{2}{c}{Core genes} & \multicolumn{2}{c}{Bad genomes} \\
~ & N & D & Name & Seq & N & D & N & D & N & D \\
\hline
-Gene prediction & $\surd$ & - & - & $\surd$ & ? & - & ? & - & 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]
+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
\end{tabular}
}
\hline\hline
Method& & Load Gen. & Conv. gV & Read gV & ICM & Core tree & Core Seq. \\
\hline
-Gene prediction & ~ & ~ & ~ & ~ & ~ & ~ & ~\\
+Gene prediction & NCBI & 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\\
+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
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?
+
+
+
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.
\usepackage{algorithm}
\usepackage{algorithmic}
\usepackage{pdflscape}
+\usepackage{authblk}
+\usepackage[T1]{fontenc}
\usepackage{multirow,longtable}
\usepackage{amsmath,mathtools}
\usepackage{amssymb}
% correct bad hyphenation here
\hyphenation{op-tical net-works semi-conduc-tor}
-
-\begin{document}
-\title{Finding the core-genes of Chloroplast Species}
-\author{
-Bassam AlKindy\footnote{email: bassam.al-kindy@univ-fcomt\'{e}.fr} \and Jacques Bahi
-\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, \\
-Universit\'{e} de Franche-Comt\'{e}, France \\
-{\small \it Authors in alphabetic order}
-}
+
+\title{Finding the Core-Genes of Plant Species Chloroplast}
+\author[1]{Bassam AlKindy} %\footnote{email: bassam.al-kindy@univ-fcomt\'{e}.fr}
+\author[1]{Jacques Bahi}
+\author[1]{Jean-Fran\c{c}ois Couchot}
+\author[1]{Christophe Guyeux}
+\author[2]{Arnaud Mouly}
+\author[1]{Michel Salomon}
+\affil[1]{FEMTO-ST Institute, UMR 6174 CNRS, Computer Science Department DISC, Universit\'{e} de Franche-Comt\'{e}, France}
+\affil[2]{Lab. Chrono-Environnement, UMR 6174 CNRS, Universit\'{e} de Franche-Comt\'{e}, France}
+%{\small \it Authors in alphabetic order}
+
+\renewcommand\Authands{ and }
+\begin{document}
\newcommand{\JFC}[1]{\begin{color}{green}\textit{}\end{color}}
\newcommand{\CG}[1]{\begin{color}{blue}\textit{}\end{color}}
% make the title area
+
\maketitle
%IEEEtran, journal, \LaTeX, paper, template.
\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}|}
& & 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 \\
\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}
