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Background  The filamentous fungus  Aspergillus nidulans  has been a tractable model organism for cell biology and genetics for over 60 years. It is among a large number of Aspergilli whose genomes have been sequenced since 2005, including medically and industrially important species. In order to advance our knowledge of its biology and increase its utility as a genetic model by improving gene annotation we sequenced the transcriptome of  A. nidulans  with a focus on 5′ end analysis.    Results  Strand-specific whole transcriptome sequencing showed that 80-95% of annotated genes appear to be expressed across the conditions tested. We estimate that the total gene number should be increased by approximately 1000, to 11,800. With respect to splicing 8.3% of genes had multiple alternative transcripts, but alternative splicing by exon-skipping was very rare. 75% of annotated genes showed some level of antisense transcription and for one gene,  meaB , we demonstrated the antisense transcript has a regulatory role. Specific sequencing of the 5’ ends of transcripts was used for genome wide mapping of transcription start sites, allowing us to interrogate over 7000 promoters and 5′ untranslated regions.    Conclusions  Our data has revealed the complexity of the  A. nidulans  transcriptome and contributed to improved genome annotation. The data can be viewed on the AspGD genome browser.    Electronic supplementary material  The online version of this article (doi:10.1186/1471-2164-14-847) contains supplementary material, which is available to authorized users.

Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters