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

  • Sardu, Alessandro Department of Biology, Division of Biochemistry, University of Fribourg, Switzerland
  • Treu, Laura Department of Environmental Engineering, Technical University of Denmark, Lyngby, Denmark
  • Campanaro, Stefano Department of Biology, University of Padova, Italy
    01.12.2014
Published in:
  • BMC Genomics. - 2014, vol. 15, no. 1, p. 1045
Saccharomyces cerevisiae
Saccharomyces sensu stricto
Transcriptome assembly software
Transcriptome variability
UTR
Non coding RNA
Cell wall
Reproductive process in single celled organism
English 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.
Faculty
Faculté des sciences et de médecine
Department
Département de Biologie
Language
  • English
Classification
Biological sciences
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https://folia.unifr.ch/unifr/documents/304076
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