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In silico Comparison of Simple Sequence Repeats in High Nucleotides-Rich Genomes of Microorganism



Fakher Rahim
 
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ABSTRACT

This study determined the distribution of a specific group of Simple Sequence Repeats (SSRs), in genome sequences of 7 chromosomes (Shigella flexneri 2a str 301 and 2457 T, Shigella sonnei, E. coli K12, M. tuberculosis, M. leprae and S. saprophytycus) have downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs. The data obtained in the present study show that: (i) Tandem repeats are widely distributed throughout the genomes. (ii) SSRs are differentially distributed among coding and non-coding regions in investigated Shigella genomes. (iii) Total frequency of SSRs in non-coding regions is higher than coding regions. (iv) In all investigated chromosomes ratio of Tri-nucleotide SSRs are much higher than randomized genomes and Di nucleotide SSRs are lower. (v) Ratio of total and mono-nucleotide SSRs in real genome is higher than randomized genomes in E. coli K12, Sh. flexneri str 301 and S. saprophyticus, while it is lower in Sh. flexneri str 2457T, Sh. sonnei and M. tuberculosis and it is approximately same in M. leprae. (vi) Frequency of codon repetitions are vary considerably depending on the type of encoded amino acid.

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  How to cite this article:

Fakher Rahim , 2008. In silico Comparison of Simple Sequence Repeats in High Nucleotides-Rich Genomes of Microorganism. Pakistan Journal of Biological Sciences, 11: 2372-2381.

DOI: 10.3923/pjbs.2008.2372.2381

URL: https://scialert.net/abstract/?doi=pjbs.2008.2372.2381
 

INTRODUCTION

Repetitive DNA consists of homopolymeric tracts of single nucleotides or of small or large numbers of multimeric classes of repeats. These can either be homogeneous (i.e., built from identical units) or heterogeneous (i.e., built from mixed units) (Van Belkum et al., 1998). A special category of repeats are tandem repeats, which are made up of monomeric sequences of variable length, repeated periodically, with contiguous monomers arranged in a head-to-tail fashion (Yeramian and Buc, 1999). Simple Sequence Repeats (SSRs) refer to the sequences that are one to six-nucleotides (nt) repeated in tandem in a genome. SSRs have many advantageous features for various biological studies: SSRs are ubiquitous and abundant in a genome, highly variable and suitable for high-throughput applications (Ellegren, 2004; Lawson and Zhang, 2006; Selkoe and Toonen, 2006; Choi et al., 2004; Yu et al., 2004a, b; Suwabe et al., 2006; Dettman and Taylor, 2004). In addition to practical usages of SSRs for biological studies, the SSRs have also been under the intense scrutiny of researchers to elucidate the evolution of genomes: (1) why are they ubiquitously present in a genome, (2) how do they arise, (3) why are they are unusually polymorphic and (4) what are their biological or structural functions are (Ellegren, 2004; Buschiazzo and Gemmell, 2006)? The evolutionary dynamics of SSRs have been actively discussed and hypotheses for experimental confirmation have been reviewed in the recent literature (Ellegren, 2004; Buschiazzo and Gemmell, 2006; Li et al., 2002, 2004). The variability in repeat number of these small tandem repeats (also called simple sequence repeats or SSRs) is caused by slipped-strand mispairing, in which the tertiary structure of the repetitive DNA allows mismatching of the neighboring repeats and repeats can then be inserted or deleted during DNA polymerase-mediated DNA duplication (Van Belkum et al., 1998; Levinson and Gutman, 1987; Van Belkum et al., 1999). The genus Shigella an etiological agent of bacillary dysentery, identified in 1890`s, a very important member of the family Enterobacteriaceae is classified into four etiologically important species viz., Shigella flexneri, Shigella dysenteriae, Shigella sonnei and Shigella boydii (Hale, 1991). Simple sequence repeats (SSRs), or microsatellites, are the genetic loci where one or a few bases are tandemly repeated for varying numbers of times (Levinson and Gutman, 1987). Repetitive DNA consists of simple homopolymeric tracts of a single nucleotide type [poly (A), poly (G), poly (T), or poly(C)] or of large or small numbers of several multimeric classes of repeats. These multimeric repeats are built from identical units (homogeneous repeats), mixed units (heterogeneous repeats), or degenerate repeat sequence motifs (Jeffreys et al., 1985). SSRs have been extensively studied in eukaryote genomes and are well-established targets for pedigree analysis (Jeffreys et al., 1986). But little is currently known about microsatellites in simple organisms (Field and Wills, 1998). Bacterial SSR-type DNA can be divided into four main categories. First, dispersed repeat motifs that generally do not occur in tandem have been identified. Although these repeats occur throughout genomes of a multitude of microorganisms, they are sometimes organized in tandem as well. The homopolymeric tracts form a second class. Multimers of one of the four nucleotides are peculiar sequence elements that are frequently encountered in the genome of S. cerevisiae, for instance. These homogeneous stretches can amount to as much as 42 nucleotides. Third, short-motif SSRs are identified. With repeat units differing from 2 to 6 bases, it is this class of repeats that is most liable to unit number variation at a given locus. Particularly, when these short-motif repeats are located within genes and are not 3 or 6 nucleotides long, they can drastically affect the coding potential of a given transcript. Fourth, repeats harboring more than 8 nucleotides per unit form a separate category. (Van Belkum et al., 1998). Some investigators considered SSRs to be selectively neutral sequences randomly or almost randomly distributed over the euchromatic genome (Schlotterer and Wiehe, 1999; Schlotterer, 2000). Initial studies of humans reported a higher mutation rate of tetra-nucleotide repeats (Weber and Wong, 1993), whereas a later study that compared microsatellite variability in different human populations found strong evidence for an inverse correlation of microsatellite repeat unit length and mutation rate (Chakraborty et al., 1997). Prokaryotic and eukaryotic repeat families are clustered to nonhomologous proteins. This may indicate that repeated sequences emerged after these two kingdoms had split. The eukaryotes incorporating more repeats may have an evolutionary advantage of faster adaptation to new environments (Kashi et al., 1997; King and Soller, 1999; Wren et al., 2000). In a variety of organisms, it has been demonstrated that microsatellite mutation rates are positively correlated with repeat number (Wierdl et al., 1997; Schlotterer et al., 1998). In prokaryotes, strong positive selective pressures are associated with highly mutable microsatellite tracts that control pathogenicity (Moxon et al., 1994).

The increasing availability of prokaryotic genome sequences has shown that SSRs are also widespread in prokaryotes and that there is extensive variation in their length, number and distribution (Cox and Mirkin, 1997; Field and Wills, 1998; Gur-Arie et al., 2000; Coenye and Vandamme, 2003; Yang et al., 2003). The present study attempt to analyze distribution and composition of SSRs in the entire genomes of three strain of Shigella and compared with E. coli K12, GC rich (M. tuberculosis and M. leprae) and also AT rich genomes (S. saprophytycus).

MATERIALS AND METHODS

This study was conducted in the physiology research center, Ahwaz Jondishapour University of Medical Sciences, Ahwaz, Iran, from July 2006-July 2007.

DNA sequences: The whole genome sequence of Sh. flexneri 2a str 301 (NC_004337), Sh. flexneri 2a str 2457T (NC_004741), Shigella sonnei Ss046 (NC_007384), Escherichia coli K12 (NC_000913), Mycobacterium tuberculosis CDC1551(NC_002755.2), Mycobacterium leprae TN (NC_002677) and Staphylococcus saprophyticus subsp. saprophyticus ATCC 15305(NC_007350) were downloaded from the GenBank database (Table 1).

Analysis of SSRs: In this study two softwares for identifying SSRs have been used. The first one was developed by Gur-Arie et al. (2000) to screen the entire genome of the organisms included in this study for SSRs with minimal number of three repeats for chromosomes, minimal motif length of one and minimal length of whole SSR array two. This software can be downloaded from ftp://ftp.technion.ac.il/supported/biotech/ssr.exe. The second software was MICAS (microsatellite Analysis Server) an Interactive web-based server to find non-redundant microsatellites in coding and non-coding region of genome sequence. This software also can be downloaded from http://210.212.212.7/MIC/gr-ve.html or (http://www.cdfd.org.in/micas).

Table 1: Whole-genome sequences used in this study

Statistical analysis: To determine difference between the observe and the expected number of tandem repeats in entire genome of the organisms included in this study, distribution of SSRs between coding and non-coding regions of the genome and compare SSRs distributions with random expectations in coding and non coding regions, SPSS 11.0.1, SAS 9.1 and Sequence Shuffling Tool (http://bcf.arl.arizona.edu/resources/online_tools/ shuffle.php) have been used. Statistical significance was tested with χ2 test and two-tailed t-tests.

RESULTS

Distribution of SSRs: By a computer-based screen of genome sequence of three chromosome of Shigella, we found large number of SSRs with motif length 1-9 bp scattered through out genome (Table 2). The number of mono-nucleotide SSRs decreased rapidly with increasing size of the repeat unit and there is an almost perfect and highly significant linear relationship between the logarithm of the number of mono-nucleotide repeats and the repeat size (p<0.0001 for all genomes). Mono-nucleotide SSRs constituted the majority of SSRs in all 3 Shigella genomes, with the majority of mono-nucleotide SSRs being = 6 bp. As mono-nucleotide repeats number became higher, there is more and more representation of SSRs in non-coding regions, but it is no markedly difference in di and tri nucleotide SSRs (Table 4 and Fig. 2). In 2 strain of Shigella flexneri (301 and 2457T), coding regions contain less di-nucleotide and tetra-nucleotide SSRs than tri-nucleotide SSRs. In Sh. sonnei tri-nucleotide and tetra-nucleotide SSRs are more represented in coding regions than di-nucleotide repeats (Table 2).

Frequency of SSRs: In all investigated Shigella chromosomes, total frequency of SSRs in non-coding regions is higher than coding regions. Frequency of total SSRs in whole genome and coding regions of Sh.f 2457T is more than sh.f 301 and Sh.sonnei, however in non-coding region it is more in Sh. sonnei (Table 2). There is significant difference between frequency of total SSRs and also mono-nucleotide SSRs in coding regions and non-coding regions of 3 chromosomes of Shigella by χ2 test (p = 0.0001). Frequency of total, mono-nucleotide and Di-nucleotide SSRs are higher in genome of Staphylococcus saprophyticus (AT-rich) than other genomes, it is 24, 21.68 and 1.2% of total nucleotides of the genome, respectively. Frequency of total and mono-nucleotide SSRs is lower in Mycobacterium tuberculosis (GC-rich) 15.5 and 13.04% and frequency of di-nucleotide SSRs is lower in Sh.f1a str 301. Frequency of triplet SSRs in Mycobacterium tuberculosis is much more than other genomes (Table 3). The distribution of mono-nucleotide SSRs over different length categories are significantly different between investigated genomes by χ2 test (p = 0.0001).

The upper limits: The upper limits for mono-nucleotide SSRs are; 29 nt poly (T) in Sh. sonnei, 22 nt poly (G) in M. leprae, 17 nt poly (G) in Sh.f 301, 14 nt poly (G) in Sh.f 2457T,10 nt poly (G) in E. coli K12, 9 nt poly(G) in M. tuberculosis and 9 nt poly (A/T) in S. saprophyticus. The upper limits for any given SSRs are 108 bp in Sh.f 301, 98 bp in Sh. sonnei, 63 bp in M. tuberculosis, 58 bp in Sh.f 2457T, 48 bp in E. coli K12, 42 bp in M. leprae and 28 bp in S. saprophyticus.

Table 2: Frequency of SSRs > 3 bp in 3 chromosomes of Shigella

Table 3: The ratio of SSRs in real genome/randomized genome in different chromosomes

Fig. 1: Distribution of SSRs in the genomes of selected microorganisms, (A) Sh.f 2457T, (B) Sh.f 301, (C) Sh.sonnei, (D) E. coli K12, (E) M. tuberculosis, (F) M. leprae and (G) S. saprophyticus

Table 4: Comparison of No. of SSRs in 3 Shigella genome, E. coli K12, GC and AT rich genomes

Frequency of SSRs in real genome/randomized genome in different chromosomes: Total number of SSRs observed in 7 computer generated randomized genomes (with the same overall nucleotide frequency as the original genome) were higher than expected by chance alone in E. coli K12, sh.f 301 and Staphylococcus saprophyticus but it is lower in Sh.f 2457T, Sh. sonnei and specially Mycobacterium tuberculosis and it is approximately same in Mycobacterium leprae (Table 2). There is significant difference between frequency of total SSRs in real genome and randomized genome of investigated chromosomes by χ2 test (p<0.0001). Ratio of mono-nucleotide composition in real genome/randomized genome show that there is overrepresentation of A/T mono-nucleotide SSRs in Shigella species and E. coli K12 (with 50-51 GC%), however in M. tuberculosis (with 65% GC) A/T mono-nucleotide SSRs in real genome is approximately same as randomized genome (Table 2).

With increasing size of mono-nucleotide motif length from 3-8 nt, in 3 investigated chromosomes of Shigella and E. coli K12 ratio of A/T mono-nucleotide in real genome/randomized genome are increased and G/C mono-nucleotide are decreased, except in motif length of 7 and 8 in Shigella sonnei (Fig. 3). There is significant difference between frequency of mono-nucleotide repeats of Shigella genomes and E. coli K12 with GC-rich and AT-rich genomes by χ2 test (p<0.0001). In all investigated chromosomes ratio of real genome to randomized genome for Tri-nucleotide SSRs are much higher than 1 and Di nucleotide SSRs are lower and also tetra-nucleotide SSRs are lower than 1.

Fig. 2: Nucleotide composition of the mono-nucleotide SSRs≥6 bp in the genomes of investigated microorganisms

Average of ratio of real genome to randomized genomes in 7 chromosomes for Di, Tri and tetra-nucleotide SSRs is 0.71, 2.9 and 0.8, respectively (Table 2). There is significant difference between ratio of real genome to randomized genomes in 7 chromosome for Di, Tri and tetra-nucleotide SSRs by χ2 test (p<0.0001).

Composition of mono-nucleotide SSRS: The A/T composition of mono-nucleotide repeats in Shigella genomes is significantly higher than the overall composition (and, consequently, an under representation of G and C mono-nucleotide SSRs), however this difference can exclusively be attributed to non-coding regions, difference is significant with χ2 test (p<0.0001).

Fig. 3:

AT% of mono-nucleotide SSRs

Frequency of C mono-nucleotide SSRs in coding and non-coding regions of Sh. sonnei is more than Sh. flexneri 301 and 2457T and frequency of T mono-nucleotide SSRs in coding regions of Sh. flexneri 2457T is more than Sh. flexneri 301 and Sh. sonnei. In the genome of Sh.f 301, Sh.f 2457T, Sh. Sonnei, E. coli K12 and S. saprophyticus as repeat number became higher, frequency of A and T became more and more represented and difference is significant with χ2 test (p<0.001). But no such trend is observable for M. tuberculosis and M. leprae (Table 2).

Frequency of di-nucleotide SSRs: In all 3 genome of Shigella, frequency of GC/CG in coding region is higher and frequency of AT/TA is lower. But frequency of GC/CG in Sh. sonnei is higher than 2 strain of Shigella flexneri. Difference is significant with two-tailed t-test (p<0.01). Frequency of AC/CA in non-coding region is higher but in Shigella sonnei difference is more. Frequency of CT/TC in non-coding region is higher than coding regions in all chromosomes (Table 2).

Frequency of tri-nucleotide SSRs: The tri-nucleotide SSRs are predominant in coding regions of Sh. flexneri str 301 and 2457T and Sh. sonnei. The tri-nucleotide SSRs can be grouped into 10 motif subclasses, each representing six overlapping and complementary unit patterns. Analysis of present data also indicates that (i) there is a tremendous overrepresentation of A and T in mononucleotide SSRs = 6 bp (and, consequently, an underrepresentation of G and C) (Fig. 1). The tri-nucleotide SSRs Groups number 9 and 10 in coding and non-coding regions of chromosomes, are over represented and group`s number 5 and 6 are under represented in coding and non-coding regions of all Shigella chromosomes (Table 2). Between distribution of tri-nucleotide SSRs in coding region and non-coding region in both strain of Shigella flexneri is significant difference by two-tailed t-test (p<0.001).

Codon repetitions in complete genome sequences: In Sh.f 2a.str 2457T and 301, Sh. sonnei and E. coli K12 repetitions of Alanine (271, 237, 298, 318 time, respectively) are predominant, followed by Arginine (236, 220, 273, 246 times, respectively), Glutamine (174,173,161,163 time, respectively), Leucine and Valine. In Mycobacterium tuberculosis Arginine repetitions (1310 times) are predominant, followed by Alanine (958 times), Valine (287 time) and Serine (235 times). In Mycobacterium leprae Arginine repetitions (276 times) are predominant, followed by Alanine (268 times), Valine (177 times), Tereonin (117 times) and Serine (104 times). In Staphylococcus saprophyticus Isoleucine repetitions (267 times) a re predominant, followed by Tyrosine (133 times), Serine (96 times) and Leucine (66 times).

Frequency of tetra-nucleotide SSRs: In Sh.f 2a st 301 most frequency of tetra nucleotide SSRs are GCTG (6 times), CAGC (5 times), TGCC (5 times), CCAG (4 times) and CTGG (4 times). But in sh.f 2a str 2457T most frequency of tetra nucleotide SSRs is GCTG (6 time), TGGC (6 times), CTGG (5 times) and CCGA (4 times) and most of them are in coding region. The tetra-nucleotide SSRs are predominant in coding regions of Sh. sonnei and sh.f 2a str 2457T and non-coding regions of Sh.f 2a str. 301.

Frequency of longer unit SSRs: Frequency of Penta-nucleotide repeats was 7 in M. tuberculosis and M. leprae and 2 in Sh.f 2a str 2457T and 301 and S. saprophyticus. Frequency of hexa-nucleotide repeats was 17 in M. tuberculosis, 10 in Sh.f 2a str 2457T, 9 in Sh.f 2a str 301, 8 in Sh. sonnei, 4 in M. leprae and 3 in S. saprophyticus. Frequency of hepta-nucleotide repeats was 3 in Sh. sonnei, 1 in M. leprae and S. saprophyticus. Frequency of octa-nucleotide repeats was 1 in Sh. sonnei and S. saprophyticus. Frequency of nonanucleotide repeats was 36 in M. tuberculosis. There are no penta-nucleotide repeats in Sh. sonnei and E. coli K12, heptanucleotide repeats in Sh.f 2a str 2457T and 301, E. coli K12 and M. tuberculosis, octa-nucleotide repeats in all investigated genomes except Sh. sonnei and nona-nucleotide repeats in all investigated genomes except M. tuberculosis. In Sh.f str 301 and 2457 T the hexa-nucleotide SSRs are predominant in coding regions but in Sh. sonnei it is predominant in non-coding regions.

DISCUSSION

Present data show that the investigated Shigella chromosomes contain numerous SSRs, with a motif length between 1- 9 nt, which are distributed almost evenly over the genome. This confirms similar findings reported in earlier studies for other organisms and Shigella flexneri 301 (Field and Wills, 1998; Gur-Arie et al., 2000; Coenye and Vandamme, 2003; Yang et al., 2003). As mono-nucleotide repeat number became higher, there is more and more representation of SSRs in non-coding regions in 3 investigated Shigella genome, which can be due to the fact that longer mono-nucleotide SSRs has more opportunity to undergo slipped-strand mispairing and there will be more mutability in their length than in shorter mono-nucleotide SSRs. This could help to explain why these are overrepresented in non-coding regions of the genome as selection has ample opportunity to operate against these larger repeats that would cause frame shift and non-sense mutations in coding regions (Coenye and Vandamme, 2005). The observation that in some genomes (including the genomes of the e-Proteobacteria Campylobacter jejuni, Helicobacter pylori, Helicobacter hepaticus, Wolinella succinogenes and those of Haemophilus ducreyi, Neisseria meningitidis and Synechocystis sp.) larger mono-nucleotide SSRs are not (or to a lesser extent) excluded from coding regions, suggest they may play an important role in phase variation as this process has been observed in these organisms (Henderson et al., 1999; Linton et al., 2001; Saunders et al., 1998). DNA strand slippage can occur during transient dissociation and reannealing in the repeat region and this could be a deceptive event for DNA processing machinery leading to expansions or deletions in the repeat tracks. It has been suggested that if the nucleotides on the single strand are self-complementary, they can base pair to form loops or hairpins and stabilize strand slippage (Gacy et al., 1995; Moore et al., 1999). The upper limits for length of any given SSRs was higher in sh.f 301 (108 bp) and for mono-nucleotide SSRs was higher in Sh. sonnei (29 bp). The upper limits for length of any given SSRs and mono-nucleotide SSRs in Staphylococcus saprophyticus was lower (28 and 9, respectively). It has been proposed that these limits to repeat lengths are evidence for the fact that the increase of repeat length by mutations is counteracted by selection (through a mechanism acting on the length of the SSR sequence itself and/or through a mechanism acting on gene expression as affected by the SSR) (Gur-Arie et al., 2000). If this is true, present data suggest that, these mechanisms are less active in Shigella genomes than Staphylococcus saprophyticus.

The over representation of poly (A) and poly (T) mono-nucleotide repeats in all Shigella sp. can be explained by the fact that strand separation for these poly (A) and poly (T) tracts is considerably easier than for poly (G) or poly (C) tracts, increasing the possibility of slipped strand mispairing. In this study in 3 investigated Shigella genomes, E. coli K12, M. tuberculosis and M. leprae CG/GC Di-nucleotide SSRs are more frequent compared with other diucleotide repeats followed by GT/TG Di-nucleotide repeats and AT/TA Di-nucleotide repeats are extremely rare. In S. Saprophyticus AT/TA are predominant followed by AC/CA and GT/TG Di-nucleotide repeats (AT reach genome). It is evident that in human and Drosophila chromosomes, AC Di-nucleotide repeats are more frequent, followed by AT and AG repeats. In contrast, Arabidopsis chromosomes contain more AT repeats, followed by AG repeats. However, in the yeast genome, AT repeats seems to be predominant compared with other Di-nucleotide repeats. Interestingly, GC Di-nucleotide repeats are extremely rare in all of the eukaryotic genomes studied. Lower frequencies of CpG di-nucleotides in vertebrate genomes have been attributed to methylation of cytosine, which, in turn, increases its chances of mutation to thymine by deamination (Schorderet and Gartler, 1992). However, CpG suppression by this mechanism cannot explain the rarity of (CG)n Di-nucleotide repeats in yeast, C. elegans and Drosophila, since they do not show cytosine methylation. However, it has been observed that similar to present study: TA is underrepresented in almost all prokaryotic genomes; which could be due to the fact that (i) TA forms the thermodynamically least stable DNA (allowing unwinding of the helix), (ii) RNases preferentially degrade UA Din-ucleotides in mRNA and/or (iii) TA is part of many regulatory sequences. This may explain why TA/AT in di-nucleotide SSRs is lower than GC/CG. Tri-nucleotide SSRs in coding regions of three investigated Shigella genome are overrepresented, whereas Di-nucleotide and tetra-nucleotide repeats are underrepresented. It has been reported that triplet repeats show approximately twofold greater frequency in exonic regions than in intronic and intergenic regions in all human chromosomes except the Y chromosome (Subramanian et al., 2003). Such dominance of triplets over other repeats in coding regions may be explained on the basis of the suppression of nontrimeric SSRs in coding regions, possibly caused by frame shift mutations (Metzgar et al., 2000).

Frequency of codon repetitions in complete genome sequences of Sh.f 2a .str 2457T and 301, Sh. sonnei and E. coli K12 are approximately same. Codon repetitions are comparatively more numerous in Mycobacterium tuberculosis (Arginine 1310 time) than in other investigated genomes, (even Mycobacterium leprae with Arginine repetition 276 time) since the comparatively frequency of microsatellites is very low. Frequencies of codon repetitions are low in Staphylococcus saprophyticus since the microsatellites are more frequent. While in all investigated genome except Staphylococcus saprophyticus Arginine and Alanine are predominant in Staphylococcus saprophyticus Isoleucine and Tyrosine are predominant and Arginine and Alanine are very low abundant. Within a Tri-nucleotide repeat class, frequencies of different codon repeats vary considerably depending on the type of encoded amino acid. More frequency of small/hydrophilic basic amino acids repetitions than hydrophobic amino acids in investigated genomes (except Staphylococcus saprophyticus) and hydrophobic than small/hydrophilic amino acids in Staphylococcus saprophyticus might play an important role in the structure and function of the encoded proteins in these genomes.

In Drosophila chromosomes, AGC repeats are predominant, followed by AAC repeats. The Arabidopsis and C. elegans chromosomes have comparatively higher frequencies of AAG tri-nucleotide repeats. In contrast, the yeast genome contains more AAT, AAG, AAC, ATG and AGC repeats. Present data indicate that when the GC content of mono-nucleotide SSRs is high and pathogenicity is more, the average and standard deviation of repeat density is lowest. This is confirmed by the observation of Coenye and Vandamme (2005), who have shown that the GC content of mono-nucleotide SSRs is highest when the repeat density is lowest and repeat density is significantly higher in organisms with an intracellular or strictly parasitic lifestyle. These observations suggest that the higher energy cost of G and C over A and T/U could be the reason for the high variation seen in genomic C+G content and it might be responsible for the marked differences observed in G+C content of these mono-nucleotide SSRs, as it would be too costly to have many poly (G) and/or poly(C) SSRs in genomes with a high density of mono-nucleotide SSRs (Coenye and Vandamme, 2005). While density of SSR in E. coli is more than Sh. flexneri str 301 and 2457T and Sh. sonnei and it is very low in M. tuberculosis, there is similarity between distributions of SSR during the genome of these organisms in most of positions.

This observation indicates that, like Staphylococcus aureus, e-Proteobacteria, E. coli and R. solanacearum, the Shigella sp. contains a large number of SSRs. The observed similarities such as distribution of SSRs in the genome and representation of various types of SSRs indicate that investigated Shigella genomes and E. coli K12 have shared a similar evolutionary history. Although there are some differences between investigated Shigella genomes and E. coli K12 such as frequency of total SSRs in whole genome, coding regions and non-coding regions. The upper limits for mono-nucleotide SSRs and any given SSRs, average of SSR density, composition of mono-nucleotide SSRs and frequency of di-nucleotide SSRs. These variations be attributable to differences in gene expression and regulation of gene expression. This study also suggest that, genomic distribution of SSR is nonrandom across coding and non-coding regions and differential distributions of various repeats observed in different genome sequences suggest that apart from the nucleotide composition of repeats, the characteristic DNA replication/repair/recombination machinery might have an important role in the evolution of SSRs.

ACKNOWLEDGMENTS

This study (Grant No. BIM 255) was supported by Bioinformatics Center of University of Pune and Physiology Research Center of Ahwaz Jondishapour University of Medical Sciences. We would like to thanks the Ahwaz Jondishapour University of Medical Sciences to give us opportunity to do this research.

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