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Genetic Mapping of Thermotolerance Differences Between Species of Saccharomyces Yeast via Genome-Wide Reciprocal Hemizygosity Analysis

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Genome-wide annotation of transcript boundaries using bacterial Rend-seq datasets.

Andreas C Lawaetz¹, Lauren A Cowley^1,2, Emma L Denham¹

¹Life Sciences Department, University of Bath, Claverton Down, Bath, BA2 7AY, UK.

Microbial Genomics

|April 26, 2024

Summary

This study introduces pyRAP, a new software tool that precisely maps RNA transcripts in bacterial genomes. pyRAP improves genome annotations by identifying novel transcripts and non-coding RNAs, enhancing RNA-seq data analysis.

Keywords:

Bacillus subtilis Escherichia coli Rend-seq Staphylococcus aureus pyRAP sRNA

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A Fast and Reliable Pipeline for Bacterial Transcriptome Analysis Case study: Serine-dependent Gene Regulation in Streptococcus pneumoniae

Published on: April 25, 2015

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Accurate genome annotation is crucial for RNA-seq analysis and understanding gene regulation.
Existing genome annotations often lack detailed information on untranslated regions (UTRs) and non-coding RNAs.
Current methods struggle to integrate diverse RNA-seq data, leading to misrepresentation of transcript elements.

Purpose of the Study:

To develop a computational tool for precise genome-wide transcript boundary resolution.
To improve the accuracy of annotation for untranslated regions and non-coding RNAs.
To facilitate the analysis of diverse RNA-seq datasets, including Rend-seq.

Main Methods:

Development of pyRAP (python Rend-seq Annotation Pipeline), a software package for analyzing Rend-seq data.
Application of pyRAP to identify transcript boundaries at single-nucleotide resolution.
Generation of updated annotation files for key bacterial species.

Main Results:

pyRAP successfully identified novel transcripts, transcript isoforms, and RNase-dependent small RNA (sRNA) processing events.
In *Bacillus subtilis*, 63 novel transcripts and thousands of UTRs and non-coding RNAs were annotated.
In *Escherichia coli* and *Staphylococcus aureus*, pyRAP identified numerous novel transcripts and annotated extensive UTR and non-coding RNA elements.
Updated annotation files for *B. subtilis*, *E. coli*, and *S. aureus* were generated.

Conclusions:

pyRAP accurately resolves transcript boundaries, overcoming limitations in current genome annotations.
The pipeline enhances the discovery of novel transcripts and non-coding RNAs in bacterial genomes.
Updated annotation files produced by pyRAP will benefit microbial genomics research.