Survey of the transcriptome of Aspergillus oryzae via massively parallel mRNA sequencing.
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.
Wang
Bin
B
School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China.
Guo
Guangwu
G
Wang
Chao
C
Lin
Ying
Y
Wang
Xiaoning
X
Zhao
Mouming
M
Guo
Yong
Y
He
Minghui
M
Zhang
Yong
Y
Pan
Li
L
D017398:Alternative Splicing; D001236:Aspergillus oryzae / Q000235:genetics* / Q000378:metabolism; D020869:Gene Expression Profiling; D015966:Gene Expression Regulation, Fungal; D016681:Genome, Fungal; D012333:RNA, Messenger / Q000737:chemistry / Q000378:metabolism; D017423:Sequence Analysis, RNA; D014158:Transcription, Genetic; D020506:Untranslated Regions
D012333:RNA, Messenger; D020506:Untranslated Regions
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