Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly
Alessandro Sardu, Laura Treu, Stefano Campanaro1
1Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy. stefano.campanaro@unipd.it.
BMC Genomics
|December 3, 2014
Summary
A new software, ORA (Overlapped Reads Assembler), enables reliable transcriptome structure analysis in lower eukaryotes. This tool identified variable untranslated regions (UTRs) in yeast strains and potential regulatory roles for non-coding RNAs.
Area of Science:
- Genomics
- Molecular Biology
- Bioinformatics
Background:
- RNA sequencing (RNA-seq) is crucial for gene expression analysis and transcriptome reconstruction.
- Limited software exists for transcriptome structure analysis in lower eukaryotes, hindering comparative studies.
- This gap restricts understanding of inter-species and inter-strain transcriptional differences.
Purpose of the Study:
- To develop novel software for analyzing transcriptome structure in organisms with few introns.
- To enable reliable determination of untranslated regions (UTRs) and polycistronic transcripts.
- To facilitate comparative transcriptome analysis across different yeast species and strains.
Main Methods:
- Development of the Overlapped Reads Assembler (ORA) software.
- Analysis of the transcriptional landscape of six Saccharomyces cerevisiae strains during fermentation.
- Comparative transcriptome analysis across Saccharomyces genus species.
Main Results:
- ORA provides simple and reliable transcriptome structure analysis, including UTR size and position.
- Comparative analysis of S. cerevisiae strains revealed differences in transcript UTRs.
- Conservation of non-coding RNAs within the Saccharomyces genus was examined, suggesting potential functions.
Conclusions:
- ORA demonstrates high reliability compared to existing software and previous studies.
- The software detected variable UTRs among S. cerevisiae strains.
- A regulatory role is proposed for conserved non-coding RNAs in Saccharomyces, particularly those antisense to meiosis and cell wall biosynthesis genes.
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