Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software

BMC Genomics

Stefano Campanaro³  Laura Treu²  Alessandro Sardu¹ 

[1]Department of Biology, Division of Biochemistry, University of Fribourg, CH-1700 Fribourg, Switzerland

[2]Department of Environmental Engineering, Technical University of Denmark, DK-2800 Kgs. Lyngby, Denmark

[3]Department of Biology, University of Padova, Via Ugo Bassi 58/b, 35131 Padova, Italy

关键词: Reproductive process in single-celled organism;    Cell wall;    Non-coding RNA;    UTR;    Transcriptome variability;    Transcriptome assembly software;    Saccharomyces sensu-stricto;    Saccharomyces cerevisiae;   

Others  :  1090225
DOI  :  10.1186/1471-2164-15-1045

 received in 2014-09-18, accepted in 2014-11-20,  发布年份 2014

【 摘 要 】

Background

RNA-seq studies have an important role for both large-scale analysis of gene expression and for transcriptome reconstruction. However, the lack of software specifically developed for the analysis of the transcriptome structure in lower eukaryotes, has so far limited the comparative studies among different species and strains.

Results

In order to fill this gap, an innovative software called ORA (Overlapped Reads Assembler) was developed. This software allows a simple and reliable analysis of the transcriptome structure in organisms with a low number of introns. It can also determine the size and the position of the untranslated regions (UTR) and of polycistronic transcripts. As a case study, we analyzed the transcriptional landscape of six S. cerevisiae strains in two different key steps of the fermentation process. This comparative analysis revealed differences in the UTR regions of transcripts. By extending the transcriptome analysis to yeast species belonging to the Saccharomyces genus, it was possible to examine the conservation level of unknown non-coding RNAs and their putative functional role.

Conclusions

By comparing the results obtained using ORA with previous studies and with the transcriptome structure determined with other software, it was proven that ORA has a remarkable reliability. The results obtained from the training set made it possible to detect the presence of transcripts with variable UTRs between S. cerevisiae strains. Finally, we propose a regulatory role for some non-coding transcripts conserved within the Saccharomyces genus and localized in the antisense strand to genes involved in meiosis and cell wall biosynthesis.

【 授权许可】

   
2014 Sardu et al.; licensee BioMed Central Ltd.

【 图 表 】

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