Related Experiment Video

Updated: May 13, 2026

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
08:56

Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes

Published on: July 27, 2018

Occurrence and analysis of imperfect microsatellites in diverse potyvirus genomes

Ch Mashhood Alam1, B George, Ch Sharfuddin

  • 1Molecular Virology Laboratory, School of Life Sciences, Jawaharlal Nehru University, New Delhi, India.

Gene
|March 26, 2013
PubMed

Insights

Compound microsatellites, or simple sequence repeats (SSRs), are common in plant viruses like Potyviruses. These viral SSRs primarily feature variant motifs, unlike those in prokaryotes, impacting virus biology.

Area of Science:

  • Virology
  • Genomics
  • Bioinformatics

Background:

  • Simple sequence repeats (SSRs) are widespread in all life forms, including viruses.
  • Previous studies analyzed SSR imperfections in human, E. coli, and HIV genomes.
  • Compound microsatellites in plant viral genomes remain understudied.

Purpose of the Study:

  • To investigate the nature and distribution of compound microsatellites in 45 Potyvirus species.
  • To compare compound microsatellite characteristics in Potyviruses with those in prokaryotic genomes.
  • To correlate SSR patterns with Potyvirus biology.

Main Methods:

  • Bioinformatic analysis of complete genomes from 45 Potyvirus species.
  • Identification and classification of compound microsatellites.
  • Comparative analysis of SSR complexity and motif types.

Main Results:

  • Compound microsatellites constitute 0% to 15.15% of all SSRs in Potyviruses, exhibiting lower complexity than prokaryotic SSRs.
  • 14% of compound microsatellites showed similar motif duplications (e.g., CA, TA, AG).
  • The SSR couple (AG)-x-(AC) was the most abundant; Potyviral compound SSRs predominantly featured variant motifs, contrasting with eukaryotes.

Conclusions:

  • Potyviral compound microsatellites are characterized by variant motifs, differing from eukaryotic SSRs.
  • The distribution and types of these SSRs offer insights into Potyvirus biology.
  • Further research on these variations is crucial for understanding SSR origins, mutation, and structure.

More Related Videos

MicroRNA-based Regulation of Picornavirus Tropism09:05

MicroRNA-based Regulation of Picornavirus Tropism

Published on: February 6, 2017

Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones05:56

Direct Agroinoculation of Maize Seedlings by Injection with Recombinant Foxtail Mosaic Virus and Sugarcane Mosaic Virus Infectious Clones

Published on: February 27, 2021

Related Concept Videos

Subviral Agents01:29

Subviral Agents

Subviral agents are infectious entities that resemble viruses but lack one or more viral components, such as a capsid or essential replication machinery. These agents include viroids, prions, and satellites, each possessing distinct structural and functional characteristics that influence their mode of infection and replication.Viroids are the simplest subviral agents, consisting of circular, single-stranded RNA molecules without a protein coat. They exclusively infect plants, relying entirely...
Retroviruses02:33

Retroviruses

Retroviruses and retrotransposons both insert copies of their genetic elements into the genome of the host cell. Thus, the viral genes are passed on when the host genome is replicated or translated. A typical retroviral DNA sequence contains 3-4 genes that encode the different proteins required for its structural assembly and function as a molecular parasite. This DNA is transcribed into a single mRNA, which is very similar in structure to conventional mRNAs, i.e., it is capped at the 5’...
Size and Structure of Viral Genomes01:26

Size and Structure of Viral Genomes

Viral genomes exhibit remarkable diversity in size, structure, and composition, influencing their replication strategies and interactions with host cells. These genomes consist of either DNA or RNA and may be linear or circular. Additionally, they can be single-stranded or double-stranded, with each configuration affecting how the virus propagates within a host. RNA viruses, for instance, generally have smaller genomes than DNA viruses, a factor that contributes to their high mutation rates and...
Viruses with RNA Genomes01:29

Viruses with RNA Genomes

RNA viruses are categorized into positive-strand, negative-strand, or double-stranded groups based on their genomic structure and replication mechanisms. This classification dictates how they exploit host cellular machinery for protein synthesis and replication. Some RNA viruses also utilize reverse transcription as part of their life cycle, further diversifying their replication strategies.Positive-Strand RNA VirusesPositive-strand RNA viruses have genomes that function directly as messenger...
Viruses of Archaea01:29

Viruses of Archaea

Archaeal viruses play a crucial role in the ecosystems of extremophilic archaea, particularly those belonging to the phyla Euryarchaeota and Crenarchaeota. By shaping host evolution and facilitating gene transfer, these viruses influence microbial communities and contribute to genetic diversity in extreme environments. The archaea they infect thrive in acidic hot springs and hydrothermal vents characterized by high temperatures and low pH. Archaeal viruses exhibit remarkable structural...