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

BMC Genomics

Research Article

Prudence W H Wong¹  Huihai Wu¹  Christopher Sibthorp²  Gwendolyn Cowley²  Gareth D Weedall²  Paulius Palaima²  Mark X Caddick²  Igor Y Morozov³ 

[1] Department of Computer Science, University of Liverpool, Ashton Building, Ashton Street, L69 3BX, Liverpool, UK;Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, Liverpool, UK;Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, L69 7ZB, Liverpool, UK;Department of Biomolecular and Sports Sciences, Faculty of Health and Life Sciences, Coventry University, James Starley Building, CV1 5FB, Coventry, UK;

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

DOI  :  10.1186/1471-2164-14-847

 received in 2013-08-15, accepted in 2013-11-15,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundThe 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.ResultsStrand-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.ConclusionsOur 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.

【 授权许可】

Unknown   
© Sibthorp et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.