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Updated: May 30, 2026
09:12
Comparative RNA Structure Analysis of Nascent and Mature Transcripts in Saccharomyces cerevisiae
Published on: February 27, 2026
Identification and annotation of noncoding RNAs in Saccharomycotina
José Almeida Cruz1, Eric Westhof
1Architecture et Réactivité de l'ARN, Institut de Biologie Moléculaire et Cellulaire du CNRS, Université de Strasbourg, 15 rue René-Descartes, 67084 Strasbourg cedex, France. J.Cruz@ibmc.u-strasbg.fr
Comptes Rendus Biologies
|August 9, 2011
Summary
We developed two automatic pipelines for non-coding RNA (ncRNA) gene annotation in genomes. These pipelines successfully identified 693 ncRNA genes across 10 Saccharomycotina genomes, highlighting their utility in large-scale projects.
Area of Science:
- Genomics
- Bioinformatics
- Molecular Biology
Background:
- Non-coding RNAs (ncRNAs) play crucial roles in biological processes, necessitating their accurate annotation in genome sequencing.
- Identifying ncRNAs requires specialized bioinformatics tools distinct from those used for protein-coding genes.
Purpose of the Study:
- To develop and evaluate automated pipelines for comprehensive ncRNA gene discovery in eukaryotic genomes.
- To assess the efficiency of these pipelines in identifying known and novel ncRNAs within the Saccharomycotina subphylum.
Main Methods:
- Assembly of two distinct automated annotation pipelines integrating existing bioinformatics tools.
- Application of homology-based and de novo search strategies for ncRNA identification.
- Systematic analysis of 10 Saccharomycotina genomes using the developed pipelines.
Main Results:
- Successful annotation of 693 ncRNA genes across the 10 Saccharomycotina genomes analyzed.
- Achieved 81% of expected ncRNA gene annotation based on Saccharomyces cerevisiae as a reference.
- Discovery of several novel ncRNAs previously uncharacterized in the Saccharomycotina clade.
Conclusions:
- Automated ncRNA search pipelines are feasible and effective for large-scale genome annotation projects.
- These pipelines enhance the discovery of both known and novel ncRNAs, contributing to a deeper understanding of genomic function.
- The developed approach is valuable for multi-genome sequencing initiatives requiring efficient ncRNA identification.
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