Simple sequence repeats in different genome sequences of Shigella and comparison with high GC and AT-rich genomes

Abstract

Simple sequence repeats (SSRs) are omnipresent in prokaryotes and eukaryotes, and are found anywhere in the genome in both protein encoding and noncoding regions. In present study the whole genome sequences of seven chromosomes (Shigella flexneri 2a str301 and 2457T, Shigella sonnei, Escherichia coli k12, Mycobacterium tuberculosis, Mycobacterium leprae and Staphylococcus saprophyticus) have downloaded from the GenBank database for identifying abundance, distribution and composition of SSRs and also to determine difference between the tandem repeats in real genome and randomness genome (using sequence shuffling tool) of the organisms included in this study.

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 noncoding regions in investigated Shigella genomes; (iii) total frequency of SSRs in noncoding regions are higher than coding regions; (iv) in all investigated chromosomes ratio of Trinucleotide SSRs in real genomes are much higher than randomness genomes and Di nucleotide SSRs are lower; (v) Ratio of total and mononucleotide SSRs in real genome is higher than randomness genomes in E. coli K12, S. flexneri str 301 and S. saprophyticus, while it is lower in S. flexneri str 2457T, S.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 acids.

• SSR
• microsatellite
• Shigella
• comparison

Acknowledgements

The authors wish to express deep grateful to Prof. A.S. Kolaskar for contribution criticism and carefully reading of manuscript. One of the authors “Ashraf Hosseini” would sincerely thanks to Kulkarni–Kale Urmila and Fakher Rahim of Bioinformatics centre for training and making available the facility at Bioinformatics Centre, and Prof. Dilip Deobagker for his helpful discussion and comments. The work was supported by grant of Institute of Bioinformatics and Biotechnology, University of Pune.