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Genome Annotation and Assembly

Genome Annotation and Assembly

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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Related Experiment Video

Updated: Jun 6, 2025

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

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

Orthopoxvirus Genome Sequencing, Assembly, and Analysis.

Crystal M Gigante¹, Michael R Weigand², Yu Li³

¹National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA. CGigante@cdc.gov.

Methods in Molecular Biology (Clifton, N.J.)

|December 2, 2024

Summary

A new protocol enables rapid metagenomic sequencing and orthopoxvirus genome assembly from patient samples. This cost-effective method bypasses traditional challenges posed by large viral genomes.

Keywords:

Genome assembly Genomic surveillance Orthopoxvirus sequencing Phylogenetic analysis Resistance

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An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Published on: November 30, 2014

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Last Updated: Jun 6, 2025

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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Published on: July 27, 2018

Phage Phenomics: Physiological Approaches to Characterize Novel Viral Proteins

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Published on: June 11, 2015

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

An Experimental and Bioinformatics Protocol for RNA-seq Analyses of Photoperiodic Diapause in the Asian Tiger Mosquito, Aedes albopictus

Published on: November 30, 2014

Area of Science:

Virology
Bioinformatics
Genomics

Background:

Poxviruses possess large, complex genomes, posing significant sequencing and assembly challenges.
The 2022 mpox outbreak necessitated rapid sequencing of numerous samples, overwhelming traditional methods.
Existing next-generation sequencing (NGS) protocols needed adaptation for efficient poxvirus genome analysis.

Purpose of the Study:

To present a streamlined protocol for metagenomic sequencing and orthopoxvirus genome assembly.
To enable direct genome assembly from patient lesion swabs without viral enrichment or host depletion.
To provide a cost-effective and efficient approach for poxvirus genome analysis.

Main Methods:

Metagenomic sequencing of DNA extracted directly from patient lesion swabs.
Utilizing high-throughput sequencing instruments for cost-effectiveness.
Employing two publicly available bioinformatic pipelines for assembly, quality control, and annotation.

Main Results:

Successful direct genome assembly of orthopoxviruses from clinical samples.
The protocol effectively handles complex genomic features like repeat elements and low-complexity sequences.
Demonstrated capability to detect genomic insertions, deletions, and large rearrangements with high confidence.

Conclusions:

The developed protocol offers a feasible and efficient solution for rapid poxvirus genome sequencing and assembly.
This approach is valuable for public health surveillance and research during viral outbreaks.
Facilitates timely submission of high-quality viral genomes to public repositories.