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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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Updated: May 2, 2026

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

Multiple reference genomes and transcriptomes for Arabidopsis thaliana.

Xiangchao Gan¹, Oliver Stegle, Jonas Behr

¹Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK.

|August 30, 2011

Summary

This summary is machine-generated.

Genetic variations in Arabidopsis thaliana accessions drive phenotypic diversity. Re-annotating genomes reveals alternative gene models, uncovering significant sequence and expression differences, especially in biotic response genes.

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Area of Science:

Plant genetics
Genomics
Molecular biology

Background:

Arabidopsis thaliana accessions exhibit significant phenotypic variation due to genetic differences.
Previous studies primarily used the Col-0 reference accession for interpretation.
Understanding genetic diversity across natural accessions is crucial for functional genomics.

Purpose of the Study:

To sequence, assemble, and annotate the genomes and transcriptomes of 18 natural Arabidopsis thaliana accessions.
To investigate the impact of genetic variation on gene models and expression.
To identify patterns of sequence and expression variation, particularly in relation to environmental responses.

Main Methods:

Whole-genome sequencing and assembly of 18 Arabidopsis thaliana accessions.
Transcriptome sequencing (RNA-Seq) for gene expression analysis.
Comparative genome annotation and re-annotation to identify gene model variations.

Main Results:

One-third of protein-coding genes appear disrupted based on reference annotation, but re-annotation often restores coding potential.
Nearly half of expressed genes show differences in seedling expression, frequently linked to cis-variants.
Intron retention and alternative splicing events correlate with cis-variants; variation is highest in biotic response genes.

Conclusions:

Re-annotation is essential for accurate interpretation of genetic variation in natural accessions.
Extensive sequence and expression variation exists across Arabidopsis thaliana accessions, impacting gene function.
The generated data and the MAGIC population will advance evolutionary and functional studies in Arabidopsis.