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

Genomics
Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing
Bin Wang1, Guangwu Guo2,3,4, Chao Wang1, Ying Lin1, Xiaoning Wang1, Mouming Zhao5, Yong Guo1, Minghui He1,4, Yong Zhang4,* and Li Pan1,*

1School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong 510006, 2Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100029, 3Graduate University of Chinese Academy Sciences, Beijing 100049, 4Beijing Genomics Institute at Shenzhen, Shenzhen 518000 and 5College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, Guangdong 510641, China

*To whom correspondence should be addressed. Tel: ; Fax: +86 20 39380698; Email: btlipan@scut.edu.cn

Correspondence may also be addressed to Yong Zhang. Tel/Fax: +86 755 25274032; Email: zhangy@genomics.org.cn

Received November 21, 2009. Revised March 16, 2010. Accepted March 26, 2010.

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.