Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing

Abstract

Aspergillus oryzae, an important filamentous fungus used in food fermentation and the enzyme industry, has been shown through genome sequencing and various other tools to have prominent features in its genomic composition. However, the functional complexity of the A. oryzae transcriptome has not yet been fully elucidated. Here, we applied direct high-throughput paired-end RNA-sequencing (RNA-Seq) to the transcriptome of A. oryzae under four different culture conditions. With the high resolution and sensitivity afforded by RNA-Seq, we were able to identify a substantial number of novel transcripts, new exons, untranslated regions, alternative upstream initiation codons and upstream open reading frames, which provide remarkable insight into the A. oryzae transcriptome. We were also able to assess the alternative mRNA isoforms in A. oryzae and found a large number of genes undergoing alternative splicing. Many genes and pathways that might be involved in higher levels of protein production in solid-state culture than in liquid culture were identified by comparing gene expression levels between different cultures. Our analysis indicated that the transcriptome of A. oryzae is much more complex than previously anticipated, and these results may provide a blueprint for further study of the A. oryzae transcriptome.

Transcriptional Changes in the Transition from Vegetative Cells to Asexual Development in the Model Fungus Aspergillus nidulans

“…It has been successfully used to elucidate transcriptomes of microbes and higher eukaryotes (see references within reference 11). Thus, this powerful technique arises as an efficient tool for transcriptomic analyses in the genus Aspergillus, as shown in 2010 by Wang and coworkers (11), who published the first RNA-seq-based transcriptomic study of this genus. In these last 2 years, the RNA-seq-based studies involving Aspergillus species analyzed the temperature effect on secondary metabolite synthesis, biofilm formation, the response to lignocellulose, or domestication in A. fumigatus, A. flavus, A. niger, or A. oryzae, respectively (11)(12)(13)(14)(15).…”

Profiling of the transcriptome of Porphyra yezoensis with Solexa sequencing technology

“…The sequencing platforms, such as the Illumina/Solexa Genome Analyzer, GS FLX Titanium System and ABI/SOLiD Gene Sequencer, can sequence in parallel massive amounts of cDNAs [10]. They have been successfully used to investigate the transcriptomes of a wide range of organisms including Pseudosciaena crocea, zebrafish, Aspergillus oryzae, rice, mouse and human [11][12][13][14][15][16]. The next-generation sequencing technologies have also been used in other functional genomics researches including genome annotation, small ncRNA profiling and aberrant transcript detection, which are areas previously covered by microarrays [17].…”

Next-Generation Sequencing Techniques for Eukaryotic Microorganisms: Sequencing-Based Solutions to Biological Problems

“…The inclusion of RNA-seq data in a genome sequencing project allows much better, evidence-based gene predictions during automated annotation without greatly increasing costs. This was the case even for the well-annotated genomes of S. cerevisiae and Schizosaccharomyces pombe (81,115), and RNA-seq data were also used to improve genome annotation of the filamentous fungus Aspergillus oryzae (110).…”

“…This is important when RNA-seq data are to be used for the genomewide quantitative analysis of gene expression, similar to microarray hybridization data. Among eukaryotic microorganisms, RNA-seq has already been used to quantify gene expression for, e.g., yeasts (81,115), A. oryzae (110), and the truffle Tuber melanosporum (69). Compared to microarrays, RNA-seq is still more expensive when large numbers of samples need to be analyzed to compare gene expression under multiple different conditions.…”

“…The yeasts S. cerevisiae and Schizosaccharomyces pombe were among the first species for which RNA-seq studies were performed (81,115); similar studies of filamentous fungi were not long to follow (69,110). In the oomycete Pythium ultimum as well as in the charophyte algae Coleochaete orbicularis and Spirogyra pratensis, NGS was used in combination with Sanger sequencing to establish EST databases (16,106).…”