alexa In Silico Mining of Simple Sequence Repeats in Whole Genome of Xanthomonas sp.
ISSN: 0974-7230

Journal of Computer Science & Systems Biology
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Research Article

In Silico Mining of Simple Sequence Repeats in Whole Genome of Xanthomonas sp.

Mukti Jaiswal and Anjana Pandey*

Nanotechnology and Molecular Biology laboratory, Department of Biotechnology, University of Allahabad, Allahabad-211002, Uttar Pradesh, India

*Corresponding Author:
Anjana Pandey
Department of Biotechnology
University of Allahabad, Allahabad -211002
Uttar Pradesh, India
Tel: +91-9453029719
E-mail: [email protected]

Received Date: July 14, 2014; Accepted Date: August 18, 2014; Published Date: August 20, 2014

Citation: Jaiswal M, Pandey A (2014) In Silico Mining of Simple Sequence Repeats in Whole Genome of Xanthomonas sp. J Comput Sci Syst Biol 7:203-208. doi: 10.4172/jcsb.1000157

Copyright: © 2014 Jaiswal M, et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

 

Abstract

In current scenario, microsatellites are a large source of genetic markers. In this study, we mined simple sequence repeats in whole genome of Xanthomonas species (Xanthomonas axonopodis pv. citri, Xanthomonas oryzae pv. oryzae, Xanthomonas campestris pv. Campestris) by in silico methods. A total of 640 SSRs, 377 SSRs and 541 SSRs were detected in whole genome having density of 1SSR/8.08 kb, 1SSR/13.10 kb and 1SSR/9.510 kb for 5175.554 kb, 4941.439 kb and 5148.708 kb sequences length respectively. The results elucidated, only 32 types (0.618%), 39 types (0.789%) and 96 types (1.864%) of SSR sequences were present in Xanthomonas axonopodis pv. citri, Xanthomonas oryzae pv.oryzae and Xanthomonas campestris pv. campestis respectively. Depending on the repeat units, the length of SSRs ranged from 10 to 18 bp for di-, 12 to 27 bp for tri-, 12 to 24 bp for tetra-, 20 to 35 bp for penta-, 24 to 72 for hexa-, 21 to 133 bp for hepta-, 24 to 40 bp for octa- and 27 to 36 bp for nano nucleotide repeats. Di-nucleotide repeats were the most frequent repeat type (70.97%) followed by tri-nucleotide (22.23%), hepta–nucleotide (2.86%), hexa-nucleotide (1.91%) and tetra-nucleotide (1.392%) in all three species of Xanthomonas. Annotation of sequences containing SSRs were also carried out to assign function to each of the sequences. SSR containing sequences of Xanthomonas species could not assign any specific class of protein (77.56%) due to the absence of homologs in the protein sequence database and these could be treated as an ideal molecular marker.

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