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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.

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...

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Updated: Jun 24, 2025

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Annotation of Plant Gene Function via Combined Genomics, Metabolomics and Informatics

Published on: June 17, 2012

A data-driven genome annotation approach for cassava.

Swetha Chenna¹, Maxim Ivanov¹, Tue Kjærgaard Nielsen¹

¹Department of Plant and Environmental Sciences, Copenhagen Plant Science Centre, University of Copenhagen, Thorvaldsensvej 40, Frederiskberg C, 1871, Denmark.

The Plant Journal : for Cell and Molecular Biology

|June 4, 2024

Summary

This summary is machine-generated.

Improving genome annotations with TranscriptomeReconstructoR (TR) identified twice as many cold-induced genes in cassava. This enhances the discovery of environmentally responsive genes for plant science.

Keywords:

Quant‐seq RNA STRIPE‐seq gene expression genome annotation trancription

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Published on: July 27, 2018

Area of Science:

Genomics
Plant Biology
Molecular Biology

Background:

Genome annotation files are crucial for accurate DNA sequence analysis and gene function prediction.
Existing genome annotations may lack comprehensive gene models, potentially missing environmentally responsive genes.

Purpose of the Study:

To generate improved cassava genome annotations using experimental RNA data.
To assess the impact of enhanced genome annotations on identifying cold-responsive genes in cassava.

Main Methods:

Generated experimental RNA 5'/3' ends and full-length RNA data for cassava under varying temperatures.
Utilized TranscriptomeReconstructoR (TR) to create new genome annotation files.
Merged TR-generated annotations with existing cassava genome annotations.
Compared gene expression analysis using standard versus enhanced annotations.

Main Results:

TR-generated annotations identified additional genes and improved transcript boundary accuracy.
The merged annotation revealed approximately twice as many cold-induced genes compared to standard annotations.
Environmentally induced genes might be absent in commonly used genome annotation files.

Conclusions:

TranscriptomeReconstructoR (TR) effectively enhances crop genome annotations.
Improved annotations are vital for discovering differentially expressed genes in plant-environment interactions.
This approach has significant implications for plant breeding and stress response research.