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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.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-15-1045) contains supplementary material, which is available to authorized users.

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