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

Abstract

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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-14-847) contains supplementary material, which is available to authorized users.

Characterization of Natural Antisense Transcript, Sclerotia Development and Secondary Metabolism by Strand-Specific RNA Sequencing of Aspergillus flavus

“…This means NATs in A. flavus might regulate gene expression mainly at the post-transcriptional level, which is consistent with the conclusion reported by Donaldson et al [28]. The inside-biased NAT distribution in A. flavus , however, was different from the 3′-biased antisense transcription in A. nidulans [72] and the mammalian NAT distribution, where NATs are usually enriched in the region of the 250 bp upstream sequence and the 1.5 kb downstream sequence [26]. The transcriptional level of A. flavus genes with NATs (average RPKM 253.59) was much higher compared to genes without NATs (average RPKM 54.50; Fig.…”

Beyond Asexual Development: Modifications in the Gene Expression Profile Caused by the Absence of the Aspergillus nidulans Transcription Factor FlbB

“…In contrast to our RNA-seq results, the An4394 transcript was not detected in the VG (0 hr) in these experiments. This observation is in agreement with results described by Sibthorp et al (2013) that reported low reads per kilobase per million mapped reads (RPKM) levels for An4394 in either minimal or complete Aspergillus culture medium. Furthermore, we were unable to detect the An4394::GFP chimera in vegetative hyphae either by fluorescence microscopy or by Western blot.…”

Transcriptome analysis of smut fungi reveals widespread intergenic transcription and conserved antisense transcript expression

“…The larger increase for U. maydis was likely due to sequencing RNA from haploids, dikaryons, and teliospores (dormant and germinating) while only RNA from haploids was sequenced for U. hordei and only RNA from haploids and dikaryons for S. reilianum . Increased numbers of detected transcripts were also observed by analyses of deep RNA-seq data of F. graminearum yielding a 1.2-fold increase and that of Aspergillus nidulans yielding a 4.2-fold increase [38, 40]. Among the novel transcripts detected in our study, a small number have putative ORFs.…”