Dna Analysis

Microsatellite Diversity, Complexity, And Host Range Of Mycobacteriophage Genomes Of The Siphoviridae Family

Microsatellite Diversity, Complexity, And Host Range Of Mycobacteriophage Genomes Of The Siphoviridae Family

Abstract

The incidence, distribution, and variation of simple sequence repeats (SSRs) in viruses is instrumental in understanding the functional and evolutionary aspects of repeat sequences. Full-length genome sequences retrieved from NCBI were used for extraction and analysis of repeat sequences using IMEx software. We have also developed two MATLAB-based tools for extraction of gene locations from GenBank in tabular format and simulation of this data with SSR incidence data. Present study encompassing 147 Mycobacteriophage genomes revealed 25,284 SSRs and 1,127 compound SSRs (cSSRs) through IMEx. Mono- to hexa-nucleotide motifs were present. The SSR count per genome ranged from 78 (M100) to 342 (M58) while cSSRs incidence ranged from 1 (M138) to 17 (M28, M73). Though cSSRs were present in all the genomes, their frequency and SSR to cSSR conversion percentage varied from 1.08 (M138 with 93 SSRs) to 8.33 (M116 with 96 SSRs). In terms of localization, the SSRs were predominantly localized to coding regions (∼78%). Interestingly, genomes of around 50 kb contained a similar number of SSRs/cSSRs to that in a 110 kb genome, suggesting functional relevance for SSRs which was substantiated by variation in motif constitution between species with different host range. The three species with broad host range (M97, M100, M116) have around 90% of their mono-nucleotide repeat motifs composed of G or C and only M16 has both A and T mononucleotide motifs. Around 20% of the di-nucleotide repeat motifs in the genomes exhibiting a broad host range were CT/TC, which were either absent or represented to a much lesser extent in the other genomes.

Authors:

Chaudhary Mashhood Alam
Luke/BI Plant Genome Dynamics Lab, Institute of Biotechnology and Viikki Plant Science Centre, University of Helsinki, Helsinki, Finland.

Ingenious e-Brain Solutions Gurugram, India

Asif Iqbal
PIRO Technologies Private
Limited, New Delhi, India

Anjana Sharma
Department of Biomedical Sciences, SRCASW, University 
of Delhi, New Delhi, India

Alan H. Schulman
Luke/BI Plant Genome Dynamics Lab, Institute of Biotechnology and Viikki Plant Science Helsinki, Centre,University of  Helsinki,Finland

Natural Resources Institute
Finland (Luke), Helsinki, Finland

Safdar Ali
Department of Biomedical 
Sciences, SRCASW, University of Delhi, New Delhi, India

Department of Biological
Sciences, Aliah University, Kolkata, India

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