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\title{Computational Analysis of Microsatellite Repeats in Chloroplast Genomes By}
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             \author[1]{G. V. Padma  Raju}

             \affil[1]{  SRKR ENGINEERING COLLEGE AFFILIATED TO ANDHRA UNIVERSITY}

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\date{\small \em Received: 13 December 2014 Accepted: 3 January 2015 Published: 15 January 2015}

\maketitle


\begin{abstract}
        


Chloroplasts are the food producers of the cell. These organelles are found only in plant cells and algae. Chloroplasts work to convert light energy of the Sun into sugars that can be used by cells. Microsatellites are a special class of DNA repeats that are found to be helpful to understand evolution, diseases and are widely used in various applications including, DNA Fingerprinting, Paternity Studies, Linkage Analysis etc. These repeats are ubiquitously present in all genomes including chloroplasts and very little is known about their presence in organelle genomes. In this study, we have analyzed more than 370 chloroplast genomes and a brief report on the distribution and frequency of these repeats in chloroplast genomes has been presented.

\end{abstract}


\keywords{chloroplast; microsatellites; bioinformatics; genomes; repeats; distribution; computational analysis;.}

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\let\tabcellsep& 	 	 		 
\section[{Introduction}]{Introduction}\par
hloroplasts, the organelles responsible for photosynthesis, are in many respects similar to mitochondria.\par
Both chloroplasts and mitochondria function to generate metabolic energy, evolved by endosymbiosis, contain their own genetic systems, and replicate by division. However, chloroplasts are larger and more complex than mitochondria, and they perform several critical tasks in addition to the generation of ATP. Most importantly, chloroplasts are responsible for the photosynthetic conversion of Carbon Di-oxide to carbohydrates. In addition, chloroplasts synthesize amino acids, fatty acids, and the lipid components of their own membranes. The reduction of nitrite to ammonia, an essential step in the incorporation of nitrogen into organic compounds, also occurs in chloroplasts. Moreover, chloroplasts are only one of several types of related organelles (plastids) that play a variety of roles in plant cells \hyperref[b0]{[1]}\hyperref[b1]{[2]}\hyperref[b2]{[3]}\hyperref[b3]{[4]}\hyperref[b4]{[5]}\hyperref[b5]{[6]}\hyperref[b6]{[7]}.\par
Microsatellites (sometimes referred to as a variable number of tandem repeats or VNTRs) are short segments of DNA that have a repeated sequence, and they tend to occur in DNA. In some microsatellites, the repeated unit may occur four times, in others it may be seven, or two, or three \hyperref[b7]{[8]}. These repeats are ubiquitous in nature and are responsible for causing several diseases and cancers \hyperref[b8]{[9]} \hyperref[b9]{[10]}.\par
These are used in various applications like DNA Fingerprinting, DNA Forensics, Paternity Studies, and have been considered as potential markers for identifying species, for establishing phylogenetic relationships and also to study evolution \hyperref[b10]{[11]}. Microsatellites are ubiquitously found in both coding and non-coding regions of all organisms and their distribution in coding regions (genes) is known to affect protein formation and gene regulation \hyperref[b11]{[12]}.\par
Next-generation sequencing enabled researchers to study biological systems at a level never before possible. Studying mutations in chloroplast microsatellite repeats can be very helpful to understand various biological questions and their usage in various other diverse applications. Few studies \hyperref[b12]{[13]}\hyperref[b13]{[14]}\hyperref[b14]{[15]}\hyperref[b15]{[16]} earlier analyzed the distribution of microsatellites in chloroplast genomes but they are only confined to single or very low number of genomes. This paper describes the study performed to analyze microsatellite repeats in more than 370 chloroplasts genomes and details have been presented. 
\section[{II.}]{II.} 
\section[{Materials \& Methods}]{Materials \& Methods}\par
Imperfect microsatellites have been extracted from Chloro Mito SSRDB \hyperref[b16]{[17]} version 2.0, an opensource microsatellite repository of sequenced organelle genomes. For this study, a total of 370 chloroplast genome sequences have been used that belong to various classes as shown in Table \hyperref[tab_0]{1}.  
\section[{Discussion a) Genome Size Analysis}]{Discussion a) Genome Size Analysis}\par
We did a preliminary study to analyze the genome sizes of all chloroplasts. The chloroplast genome sizes vary from few kbs to a maximum of 1 Mb. The smallest chloroplast genome reported is of size 29529bp that belongs to plant named Plasmodium falciparum HB3 apicoplast (ID: NC\textunderscore 017928) belongs to Non-Viridiplantae category. The largest chloroplast genome spans about 1021616 bp of length that belongs to Paulinella chromatophora chromatophore (ID: NC\textunderscore 011087) belongs to Rhizaria.\par
In Viridiplantae, the smallest chloroplast genome is Helicosporidium sp. ex Simulium jonesii plastid(ID: NC\textunderscore 008100) of length 37454 bp where as the largest chloroplast genome is Floydiella terrestris(ID: NC\textunderscore 014346) chloroplast of length 521168 bp.\par
In Non-Viridiplantae, the smallest chloroplast genome is found as Plasmodium falciparum HB3 apicoplast (ID: of length 29529 bp where as the largest chloroplast genome is Paulinella chromatophora chromatophore (ID: NC\textunderscore 011087) chloroplast of length 1021616 bp. It is observed that this non-Virdiplantae category genome size is greater than the Viridiplantae genomes.\par
When the average genome sizes of chloroplast are considered category wise, it has been observed that the average lengths of Viridiplantae chloroplast genomes are little bit higher when compared to those of other non Virdiplantae(Refer Fig \hyperref[fig_0]{1)}.  \hyperref[tab_1]{2} gives a summary of the total number of genomes categorized based on genome sizes of the two classes of chloroplast. It has been observed that majority of the genome sizes lie between 10kb to 500kb, only two genomes namely Floydiella terrestris chloroplast (NC\textunderscore 014346) and Paulinella chromatophora chromatophore (NC\textunderscore 011087) are found to be greater than 500kb. On the other hand, 311 plants of Viridiplantae show genome sizes between 100kb and 500kb.  
\section[{b) Distribution of Microsatellites}]{b) Distribution of Microsatellites}\par
Microsatellites in or near genes (coding regions) are found to impact protein formation and gene regulation. When the distribution of microsatellites has been analyzed overall, it is found that around 57\% of microsatellite repeats fall in coding regions of all chloroplast genomes. Out of the total 78536 chloroplast microsatellites, 45518 microsatellites fall in gene regions where as the rest 33018 repeats fall in non-coding regions. However, it is surprising to see that the distribution differs when the two classes have been compared separately (Refer Fig. \hyperref[fig_1]{2}). Genomes of Non-Viridiplantae are found to be having majority of its microsatellites in coding regions (64\%). On the other hand, green plants (Viridiplantae) show that around 57\% of their microsatellites to be distributed in coding regions. When two chloroplast categories are compared (Refer Fig. \hyperref[fig_2]{3}), these two categories exhibit a similar distribution of its microsatellites in coding and non coding regions. It would be interesting to study the reason behind the major number of microsatellite repeats in Viridiplantae. 
\section[{c) Motif-size wise Analysis}]{c) Motif-size wise Analysis}\par
We have further analyzed the distribution of chloroplast microsatellites based on their motif sizes. Table \hyperref[tab_2]{3} lists the proportionate distribution of chloroplast microsatellites motif-size wise. It has been observed that chloroplast genomes are rich in tri and tetra nucleotide repeats which tohether account for more than 77\% in Non-virdiplantae, and around 62\% in Virdiplantae. Mono, Penta and Hexa-nucleotide repeats are found to be very low in number. When the microsatellite tract lengths have been analyzed, the genomes reported few interesting tract lengths for almost all motif sizes. The average microsatellite tract lengths are usually observed to be not more than 19 bp. But, it is surprising to note that some of the tetra and tri repeats have shown exceptional tract lengths as large as 276bp have been observed. Based on the results in Table \hyperref[tab_3]{4}, we have further tried to find repeats in chloroplast genomes that have exceptional tract lengths. Interestingly, we found 10 repeats in chloroplast with tract lengths 100bp or more; out of those, two repeats have tract lengths 200bp or more. Two significant tract lengths of 276 and 203 have been reported for genomes with IDs NC\textunderscore 020321, NC\textunderscore 008117 respectively.\par
IV. 
\section[{Conclusion}]{Conclusion}\par
In this paper, we have presented a brief description about the distribution of microsatellite repeats in all sequenced chloroplast genomes of Plants. This study forms the first comprehensive analysis of microsatellite repeats in chloroplast genomes and the statistics of this study can be a useful resource for biologists.\begin{figure}[htbp]
\noindent\textbf{1}\includegraphics[]{image-2.png}
\caption{\label{fig_0}Figure 1 :}\end{figure}
 \begin{figure}[htbp]
\noindent\textbf{2}\includegraphics[]{image-3.png}
\caption{\label{fig_1}Figure 2 :}\end{figure}
 \begin{figure}[htbp]
\noindent\textbf{3}\includegraphics[]{image-4.png}
\caption{\label{fig_2}Figure 3 :}\end{figure}
 \begin{figure}[htbp]
\noindent\textbf{1} \par 
\begin{longtable}{P{0.5977272727272728\textwidth}P{0.125\textwidth}P{0.12045454545454547\textwidth}P{0.006818181818181819\textwidth}}
\tabcellsep Category\tabcellsep Total No.\tabcellsep \\
\tabcellsep Alveolata\tabcellsep 9\tabcellsep \\
\multicolumn{2}{l}{Cryptophyta}\tabcellsep 3\tabcellsep \\
\tabcellsep Euglenozoa\tabcellsep 5\tabcellsep \\
\multicolumn{2}{l}{Glaucocystophyceae}\tabcellsep 1\tabcellsep \\
\multicolumn{2}{l}{Haptophyceae}\tabcellsep 4\tabcellsep \\
\tabcellsep Rhizaria\tabcellsep 2\tabcellsep \\
\multicolumn{2}{l}{Rhodophyta}\tabcellsep 9\tabcellsep \\
\multicolumn{2}{l}{Stramenopiles}\tabcellsep 14\tabcellsep \\
\multicolumn{2}{l}{Viridiplantae}\tabcellsep 323\tabcellsep \\
\multicolumn{2}{l}{Total Genomes}\tabcellsep 370\tabcellsep \\
\multicolumn{4}{l}{Among the 370 genomes, 323 genomes belong}\\
\multicolumn{4}{l}{to Viridiplantae (Green Plants), 47 genomes belongs to}\\
\multicolumn{4}{l}{Non-Viridiplantae which include genomes of Alveolata,}\\
Cryptophyta,\tabcellsep Euglenozoa,\tabcellsep \multicolumn{2}{l}{Glaucocystophyceae,}\\
Haptophyceae,\tabcellsep Rhizaria,\tabcellsep Rhodophyta\tabcellsep and\end{longtable} \par
  {\small\itshape [Note: C © 2015 Global Journals Inc. (US) Global Journal of C omp uter S cience and T echnology Volume XV Issue III Version I Year ( ) C Stramenopiles (]} 
\caption{\label{tab_0}Table 1 :}\end{figure}
 \begin{figure}[htbp]
\noindent\textbf{2} \par 
\begin{longtable}{P{0.03213058419243986\textwidth}P{0.08762886597938144\textwidth}P{0.5958762886597938\textwidth}P{0.11391752577319587\textwidth}P{0.020446735395189004\textwidth}}
\tabcellsep \tabcellsep \multicolumn{2}{l}{Average genome sizes of chloroplast}\\
\tabcellsep 150000\tabcellsep 148178.28\\
\tabcellsep 145000\tabcellsep \\
Genome size\tabcellsep 140000\tabcellsep \tabcellsep 136551.53\\
\tabcellsep 135000\tabcellsep \\
\tabcellsep 130000\tabcellsep \\
\tabcellsep \tabcellsep Viridiplantae\tabcellsep Non-Viridiplantae\\
\tabcellsep \tabcellsep Size Range\tabcellsep No. of plants\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{>= 10 Kb and <50 Kb}\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{Non-Viridiplantae}\tabcellsep 5\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{Viridiplantae}\tabcellsep 2\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{>= 50 Kb and <100 Kb}\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{Non-Viridiplantae}\tabcellsep 10\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{Viridiplantae}\tabcellsep 9\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{>= 100 Kb and <500 Kb}\\
\tabcellsep \tabcellsep \multicolumn{2}{l}{Non-Viridiplantae}\tabcellsep 31\end{longtable} \par
 
\caption{\label{tab_1}Table 2 :}\end{figure}
 \begin{figure}[htbp]
\noindent\textbf{3} \par 
\begin{longtable}{P{0.14484304932735426\textwidth}P{0.33923766816143497\textwidth}P{0.36591928251121075\textwidth}}
Motif Size\tabcellsep Non-Viridiplantae\tabcellsep Viridiplantae\\
Mono\tabcellsep 159(1.80\%)\tabcellsep 8602(12.33\%)\\
Di\tabcellsep 840(9.55\%)\tabcellsep 7909(11.34\%)\\
Tri\tabcellsep 3506(39.87\%)\tabcellsep 17055(24.45\%)\\
Tetra\tabcellsep 3300(37.52)\tabcellsep 26796(38.42\%)\\
Penta\tabcellsep 623(7.08\%)\tabcellsep 5680(8.14\%)\\
Hexa\tabcellsep 365(4.15\%)\tabcellsep 3701(5.31\%)\\
Total\tabcellsep 8793\tabcellsep 69743\end{longtable} \par
 
\caption{\label{tab_2}Table 3 :}\end{figure}
 \begin{figure}[htbp]
\noindent\textbf{4} \par 
\begin{longtable}{P{0.14384615384615385\textwidth}P{0.14384615384615385\textwidth}P{0.06538461538461539\textwidth}P{0.14384615384615385\textwidth}P{0.08717948717948718\textwidth}P{0.12205128205128205\textwidth}P{0.14384615384615385\textwidth}}
\tabcellsep \multicolumn{3}{l}{Non-Viridiplantae}\tabcellsep \tabcellsep Viridiplantae\tabcellsep \\
Motif Size\tabcellsep High\tabcellsep Low\tabcellsep Avg\tabcellsep High\tabcellsep Low\tabcellsep Avg\\
MONO\tabcellsep 25\tabcellsep 12\tabcellsep 13.93\tabcellsep 46\tabcellsep 12\tabcellsep 14.49\\
DI\tabcellsep 54\tabcellsep 11\tabcellsep 12.90\tabcellsep 83\tabcellsep 11\tabcellsep 13.24\\
TRI\tabcellsep 51\tabcellsep 11\tabcellsep 12.19\tabcellsep 276\tabcellsep 11\tabcellsep 12.38\\
TETRA\tabcellsep 29\tabcellsep 11\tabcellsep 11.91\tabcellsep 203\tabcellsep 11\tabcellsep 12.13\\
PENTA\tabcellsep 65\tabcellsep 14\tabcellsep 15.27\tabcellsep 100\tabcellsep 14\tabcellsep 15.41\\
HEXA\tabcellsep 42\tabcellsep 17\tabcellsep 18.74\tabcellsep 145\tabcellsep 17\tabcellsep 19.70\end{longtable} \par
 
\caption{\label{tab_3}Table 4 :}\end{figure}
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