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Related Concept Videos

Genome Annotation and Assembly03:36

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The genome refers to all of the genetic material in an organism. It can range from a few million base pairs in microbial cells to several billion base pairs in many eukaryotic organisms. Genome assembly refers to the process of taking the DNA sequencing data and putting it all back together in a correct order to create a close representation of the original genome. This is followed by the identification of functional elements on the newly assembled genome, a process called genome annotation.
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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...
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Combining Analysis of DNA in a Crude Virion Extraction with the Analysis of RNA from Infected Leaves to Discover New Virus Genomes
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V-GAP: Viral genome assembly pipeline.

Yoji Nakamura1, Motoshige Yasuike1, Issei Nishiki1

  • 1Research Center for Aquatic Genomics, National Research Institute of Fisheries Science, Fisheries Research Agency, 2-12-4 Fukuura, Kanazawa, Yokohama 236-8648, Kanagawa, Japan.

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|October 18, 2015
PubMed
Summary

Shotgun reads from phage genomes can be assembled into a single contig using a novel resampling method. The Viral Genome Assembly Pipeline (V-GAP) enables reliable de novo assembly of small viral genomes for comparative metagenomics.

Keywords:
De novo assemblyNext-generation sequencingShotgun sequencesVirus genomes

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Area of Science:

  • Genomics
  • Bioinformatics
  • Virology

Background:

  • Next-generation sequencing (NGS) enables rapid genome determination.
  • Assembling large genomes into complete chromosomes remains challenging.
  • Small genomes, like those of viruses, are more amenable to assembly.

Purpose of the Study:

  • To develop a reliable method for assembling small viral genomes from shotgun sequencing data.
  • To demonstrate that phage genomes can be reconstructed into a single contig.
  • To provide a tool for rapid viral genome typing and comparison in metagenomics.

Main Methods:

  • Utilized shotgun sequencing reads from phage genomes.
  • Developed a de novo assembly pipeline named V-GAP (Viral Genome Assembly Pipeline).
  • Implemented a resampling method to control read counts for optimal assembly.

Main Results:

  • Successfully reconstructed phage genomes into a single contig.
  • Achieved reliable assembly of small viral genomes.
  • Demonstrated the effectiveness of the V-GAP pipeline.

Conclusions:

  • The V-GAP pipeline offers a reliable approach for assembling small viral genomes.
  • This method facilitates rapid genome typing of diverse viruses.
  • The pipeline addresses the growing need for viral genome comparisons in metagenomic studies.