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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.

Next-generation Sequencing

Next-generation Sequencing

The first human genome sequencing project cost $2.7 billion and was declared complete in 2003, after 15 years of international cooperation and collaboration between several research teams and funding agencies. Today, with the advent of next-generation sequencing technologies, the cost and time of sequencing a human genome have dropped over 100 fold.
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RNA-seq

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Maxam-Gilbert Sequencing

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Related Experiment Video

Updated: May 8, 2026

Novel Sequence Discovery by Subtractive Genomics

Novel Sequence Discovery by Subtractive Genomics

Published on: January 25, 2019

Anchoring and ordering NGS contig assemblies by population sequencing (POPSEQ).

Martin Mascher¹, Gary J Muehlbauer, Daniel S Rokhsar

¹Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), D-06466 Seeland OT, Gatersleben, Germany.

The Plant Journal : for Cell and Molecular Biology

|September 4, 2013

Summary

We developed a new method to create a linear, chromosome-level genome assembly using progeny sequencing. This approach successfully maps the gene space of complex genomes like barley without prior sequence data.

Keywords:

Hordeum vulgare barley genetic mapping genome assembly next-generation sequencing population sequencing technical advance

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Last Updated: May 8, 2026

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Area of Science:

Genomics
Bioinformatics
Plant Genetics

Background:

Next-generation whole-genome shotgun sequencing provides valuable data but struggles to link sequence contigs linearly within chromosomes for complex genomes.
Establishing a chromosome-level assembly is crucial for understanding genome organization and gene function in large, repetitive genomes.

Purpose of the Study:

To introduce a novel strategy for de novo, genetically anchored, linear genome assembly.
To demonstrate the application of this method for reconstructing the chromosomal organization of a complex plant genome.

Main Methods:

Sequencing progeny from a segregating population to generate genetic linkage information.
Utilizing this genetic data to order and orient sequence contigs into a linear, chromosome-level assembly.
Validating the assembly against existing physical and genetic frameworks.

Main Results:

Successfully reconstructed the chromosomal organization of the barley (Hordeum vulgare) gene space, a 5.1 Gb complex genome.
Demonstrated the robustness of the new assembly through comparison with independent barley genome datasets.
The method proved effective for a large, highly repetitive genome.

Conclusions:

The developed strategy enables the de novo production of genetically anchored linear genome assemblies.
This approach is independent of pre-existing sequence resources, offering a rapid and cost-efficient solution for genome sequencing.
The method has broad applicability for generating high-quality genomic information across diverse species.