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

Christopher Sibthorp1, Huihai Wu2, Gwendolyn Cowley1, Prudence W H Wong2, Paulius Palaima1, Igor Y Morozov13, Gareth D Weedall1* and Mark X Caddick1*

Author Affiliations

1 Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK

2 Department of Computer Science, University of Liverpool, Ashton Building, Ashton Street, Liverpool L69 3BX, UK

3 Department of Biomolecular and Sports Sciences, Faculty of Health and Life Sciences, Coventry University, James Starley Building, Coventry CV1 5FB, UK

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BMC Genomics 2013, 14:847  doi:10.1186/1471-2164-14-847

Published: 3 December 2013



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.


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.


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.

Aspergillus nidulans; Transcriptome; RNA-seq; Gene annotation; Alternative splicing; Natural antisense transcripts; Transcription start sites; Transcription factor binding sites