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Genome Annotation and Assembly

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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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Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

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Related Experiment Video

Updated: May 22, 2026

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform

Transcriptome Profiling of In-Vivo Produced Bovine Pre-implantation Embryos Using Two-color Microarray Platform

Published on: January 30, 2017

Enchytraeus albidus microarray: enrichment, design, annotation and database (EnchyBASE).

Sara C Novais¹, Joel Arrais, Pedro Lopes

¹Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal.

|May 5, 2012

Summary

This summary is machine-generated.

This study develops genomic resources for Enchytraeus albidus, a key species in ecotoxicology. New Expressed Sequence Tags and a database (EnchyBASE) aid understanding of toxicity mechanisms through transcriptomic analysis.

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Area of Science:

Environmental Toxicology
Molecular Biology
Bioinformatics

Background:

Enchytraeus albidus is crucial for ecological risk assessment, with population-level endpoints like reproduction and survival commonly used.
Transcriptomic analysis offers insights into the molecular mechanisms underlying toxicity responses in this species.

Purpose of the Study:

To create suppressive subtractive hybridization (SSH) libraries for identifying differentially expressed genes in E. albidus after exposure to metals and pesticides.
To sequence and characterize these Expressed Sequence Tags (ESTs).
To develop a publicly accessible genomic database for E. albidus.

Main Methods:

Development of SSH libraries.
Sequencing and characterization of approximately 2100 ESTs.
Assembly of ESTs into clusters and assignment of protein homology and Gene Ontology (GO) terms.
Creation of the EnchyBASE database.

Main Results:

41% of ESTs matched known proteins, and 37% were assigned Gene Ontology terms.
5.5% of sequences were mapped to metabolic pathways using KEGG.
A custom oligonucleotide microarray was designed based on the new sequencing data.
The EnchyBASE database was launched, containing ESTs from E. albidus.

Conclusions:

The generated genomic data and EnchyBASE database provide valuable resources for functional genomics and transcriptomic studies in E. albidus.
These resources will enhance the understanding of toxicity mechanisms and support ecological risk assessment.
Future extensions of EnchyBASE aim to include other enchytraeid species.