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Genome wide identification and analysis of microsatellite repeats in the largest DNA viruses (Poxviridae Family): An in silico approach

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Title Genome wide identification and analysis of microsatellite repeats in the largest DNA viruses (Poxviridae Family): An in silico approach
Not Available
 
Creator Burranboina K K
Abraham S
Murugan K K
Manjunatha Reddy G B
Yogisharadhya R
Gajendragad MR
 
Subject Poxviridae
SSR
cSSR
relative density
relative abundance
compound
 
Description Not Available
Background: Microsatellites also known as simple sequence repeats (SSRs), which is also called
as junk DNA, mainly used as a neutral genetic marker, presented across coding and non-coding
regions of prokaryotes, eukaryotes, and viruses. They are subjects of different fields, such as gene
mapping, population genetics, DNA fingerprinting, forensic studies and evolution.Aim: The presented study is focused on the evolutionary relationship between poxviruses for the
identification and systematic analysis of the nature and distribution of complex microsatellites,
presenting in large DNA viral genomes of poxviruses (Poxviridae family) in vertebrates and
invertebrates.
Materials and Methods: Genome sequences of seventeen species from the Poxviridae family
were assessed by the National Center for Biotechnology (NCBI). The microsatellite was extracted
using IMEx software, and statistical analysis was performed using Microsoft office Excel 2007.
Furthermore, the molecular evolutionary analyses of poxviruses were conducted using MEGA6.
Results: In the current study, we screened 17 vertebrate and invertebrates of pox viral genomes
and a total of 8539 SSRs which revealed a total of 2387 cSSRs distributed across all the genomes.
From the sequences, poly A or poly T mononucleotide prevailed over a poly G or poly C. Among
the identified motifs dinucleotides 51.73% which were the most common types of repeats followed
by mononucleotides 36.12%, trinucleotides 11.28%, tetranucleotides 0.56%, pentanucleotides
0.10%, and hexanucleotides 0.21%. Polymorphism increases with genome length and decreasing
GC content of repeat motifs for dinucleotides, trinucleotides, and tetranucleotides. This result may
help genome-wide evolutionary and quantitative analysis like genome size or GC content which
has an influence on the number, simple and compound microsatellite of relative abundance and
relative densities.
Conclusion: We conclude that largest DNA virus of invertebrates show a higher percentage of
microsatellites and repeat motif than the vertebrate poxviruses. The genome size and GC content
is an important factor in affecting the occurrence of repeat motif as well microsatellites, in
vertebrate and invertebrate poxviruses. The analysis on the phylogenetic relationships and
microsatellites in vertebrates and invertebrates, as well the pattern of their evolution, may help to
understand (the understanding) of poxviruses in the course of natural evolution.
Not Available
 
Date 2018-11-12T05:13:37Z
2018-11-12T05:13:37Z
2018-01-01
 
Type Research Paper
 
Identifier Not Available
2347-565X
http://krishi.icar.gov.in/jspui/handle/123456789/10270
 
Language English
 
Relation Not Available;
 
Publisher Annual Research & Review in Biology