Search research articles

ABOUT JoVE

Overview Leadership Blog JoVE Help Center

AUTHORS

Publishing Process Editorial Board Scope & Policies Peer Review FAQ Submit

LIBRARIANS

Testimonials Subscriptions Access Resources Library Advisory Board FAQ

RESEARCH

JoVE Journal Methods Collections JoVE Encyclopedia of Experiments Archive

EDUCATION

JoVE Core JoVE Business JoVE Science Education JoVE Lab Manual Faculty Resource Center Faculty Site

Terms & Conditions of Use

Related Concept Videos

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.

RNA-seq

RNA-seq

RNA sequencing, or RNA-Seq, is a high-throughput sequencing technology used to study the transcriptome of a cell. Transcriptomics helps to interpret the functional elements of a genome and identify the molecular constituents of an organism. Additionally, it also helps in understanding the development of an organism and the occurrence of diseases.
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...

Evolutionary Relationships through Genome Comparisons

Evolutionary Relationships through Genome Comparisons

Genome comparison is one of the excellent ways to interpret the evolutionary relationships between organisms. The basic principle of genome comparison is that if two species share a common feature, it is likely encoded by the DNA sequence conserved between both species. The advent of genome sequencing technologies in the late 20th century enabled scientists to understand the concept of conservation of domains between species and helped them to deduce evolutionary relationships across diverse...

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by

Same author

Effects of temperature on the life-history traits of <i>Myzus persicae</i> and its efficiency in transmitting potato virus Y (PVY) in potato crops.

PeerJ·2026

Same author

Particulate matter-bound metals and chlorinated paraffins co-exposure: A population-based study on attention-deficit/hyperactivity disorder in Chinese youth.

Journal of hazardous materials·2026

Same author

An ovary-enriched piRNA controls ovarian development via Gadd45a-JNK-mediated nurse-cell apoptosis in the arbovirus vector Aedes albopictus.

Insect science·2026

Same author

Suppression of transgenerational lipid provisioning inhibits desiccation resistance, but not diapause, in the vector mosquito, Aedes albopictus.

Scientific reports·2026

Same author

GISDD: A comprehensive global integrated sequence and genotyping database platform for dengue virus, facilitating a stratified coordinated surveillance strategy.

iMetaOmics·2026

Same author

Suppression of transgenerational lipid provisioning inhibits desiccation resistance, but not diapause, in the vector mosquito, Aedes albopictus.

Research square·2026

Same journal

Mild oxidative stress and dietary epigenetic modulators direct DNA methylation remodeling toward stress-resilience pathways.

BMC genomics·2026

Same journal

Integrative ATAC-Seq and RNA-Seq analysis identifies key genes for intramuscular fat content in Laiwu pigs.

BMC genomics·2026

Same journal

A comprehensive long RNA landscape of multi-regional porcine lung-derived small extracellular vesicles.

BMC genomics·2026

Same journal

pGWAS-Portal: a comprehensive online platform for integrative post-genome-wide association study analysis.

BMC genomics·2026

Same journal

Physiological and transcriptomic analyses of Rosa persica in response to drought stress and functional validation of the transcription factor RpERF113-like.

BMC genomics·2026

Same journal

Integrated analysis of chromatin accessibility and transcriptome profiles in granulosa cells of sheep with different FecB genotypes.

BMC genomics·2026

See all related articles

Search research articles

Related Experiment Video

Updated: Mar 17, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

Comparative performance of transcriptome assembly methods for non-model organisms.

Xin Huang¹, Xiao-Guang Chen², Peter A Armbruster³

¹Department of Biology, Georgetown University, 37th and O Streets NW, Washington, DC, 20057, USA. xh33@georgetown.edu.

|July 29, 2016

Summary

This summary is machine-generated.

De novo transcriptome assembly is effective, even with fragmented genomes, but can be redundant. Combining assembly methods may improve results, but using related genomes requires caution.

Keywords:

Aedes albopictus De novo assembly Genome-guided assembly Next-generation sequencing Non-model organisms Reference-based re-assembly TransPS Transcriptome assembly

More Related Videos

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

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Published on: February 23, 2024

Related Experiment Videos

Last Updated: Mar 17, 2026

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Leveraging CyVerse Resources for De Novo Comparative Transcriptomics of Underserved Non-model Organisms

Published on: May 9, 2017

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

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Author Spotlight: Cost-Effective Transcriptomic Drug Screening - Unlocking New Targets

Published on: February 23, 2024

Area of Science:

Bioinformatics
Genomics
Transcriptomics

Background:

Next-generation sequencing (NGS) enables genomic and transcriptomic studies.
Transcriptome assembly is crucial for RNA-Sequencing (RNA-Seq) analysis.
Optimal assembly strategies for organisms without a reference genome are still debated.

Purpose of the Study:

To compare four transcriptome assembly methods: de novo, reference-based re-assembly, TransPS, and genome-guided assembly.
To evaluate assembly performance using RNA-Seq data from Aedes albopictus.
To provide guidance on selecting transcriptome assembly strategies.

Main Methods:

Comparative analysis of four transcriptome assembly strategies.
Assessment of assembly quality using contig metrics, read mapping, and gene model representation.
Utilized Aedes albopictus transcriptomic data with a recently completed genome sequence.

Main Results:

De novo assembly produced comparable gene models to genome-guided assembly but with higher redundancy and computational cost.
Reference-guided assembly using a closely related genome introduced sequence bias.
Increased read pairs did not necessarily improve assembly quality, potentially increasing redundancy.

Conclusions:

De novo assembly is an effective strategy, especially for fragmented reference genomes.
Combining de novo and genome-guided assembly can be beneficial with sufficient resources.
Caution is advised when using related reference genomes for transcriptome assembly.