title: 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.
authors.affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China.
authors.forename: Bin
authors.initials: B
authors.lastname: Wang
authors.forename: Guangwu
authors.initials: G
authors.lastname: Guo
authors.forename: Chao
authors.initials: C
authors.lastname: Wang
authors.forename: Ying
authors.initials: Y
authors.lastname: Lin
authors.forename: Xiaoning
authors.initials: X
authors.lastname: Wang
authors.forename: Mouming
authors.initials: M
authors.lastname: Zhao
authors.forename: Yong
authors.initials: Y
authors.lastname: Guo
authors.forename: Minghui
authors.initials: M
authors.lastname: He
authors.forename: Yong
authors.initials: Y
authors.lastname: Zhang
authors.forename: Li
authors.initials: L
authors.lastname: Pan
mesh_terms: 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
chemical_list: D012333:RNA, Messenger; D020506:Untranslated Regions
references.citation: Genome Biol. 2008;9(3):R50
references.pmid: 18321378
references.citation: Biosci Biotechnol Biochem. 2008 Nov;72(11):2998-3001
references.pmid: 18997417
references.citation: Mol Plant Microbe Interact. 2004 Dec;17(12):1337-47
references.pmid: 15597739
references.citation: Appl Microbiol Biotechnol. 2001 Oct;57(1-2):131-7
references.pmid: 11693910
references.citation: Nature. 2008 Jun 26;453(7199):1239-43
references.pmid: 18488015
references.citation: Nat Methods. 2008 Jul;5(7):621-8
references.pmid: 18516045
references.citation: J Biol Chem. 1995 Feb 10;270(6):2411-4
references.pmid: 7852296
references.citation: J Biol Chem. 2003 Nov 7;278(45):45011-20
references.pmid: 12941955
references.citation: Appl Environ Microbiol. 2006 May;72(5):3448-57
references.pmid: 16672490
references.citation: Nat Genet. 2008 Dec;40(12):1413-5
references.pmid: 18978789
references.citation: Bioinformatics. 2009 Apr 15;25(8):1091-3
references.pmid: 19237447
references.citation: Nature. 2005 Dec 22;438(7071):1157-61
references.pmid: 16372010
references.citation: Science. 2008 Aug 15;321(5891):956-60
references.pmid: 18599741
references.citation: J Biosci Bioeng. 2000;90(1):118-20
references.pmid: 16232829
references.citation: Bioinformatics. 2008 Mar 1;24(5):637-44
references.pmid: 18218656
references.citation: Annu Rev Microbiol. 2005;59:407-50
references.pmid: 16153175
references.citation: BMC Genomics. 2008 May 23;9:245
references.pmid: 18500999
references.citation: Proc Natl Acad Sci U S A. 2008 Mar 18;105(11):4387-92
references.pmid: 18332432
references.citation: Nature. 2008 Nov 27;456(7221):470-6
references.pmid: 18978772
references.citation: Science. 2005 Feb 25;307(5713):1321-4
references.pmid: 15653466
references.citation: DNA Res. 2007 Apr;14(2):47-57
references.pmid: 17540709
references.citation: Nature. 2009 Mar 5;458(7234):97-101
references.pmid: 19136943
references.citation: Trends Biotechnol. 2005 Sep;23(9):468-74
references.pmid: 15967521
references.citation: Nat Rev Genet. 2004 Oct;5(10):773-82
references.pmid: 15510168
references.citation: Nat Methods. 2008 Jul;5(7):613-9
references.pmid: 18516046
references.citation: Cell. 2001 Dec 28;107(7):827-30
references.pmid: 11779459
references.citation: Mol Microbiol. 2004 Sep;53(6):1731-42
references.pmid: 15341651
references.citation: Bioinformatics. 2008 Mar 1;24(5):713-4
references.pmid: 18227114
references.citation: Science. 2008 Jun 6;320(5881):1344-9
references.pmid: 18451266
references.citation: Cell. 2000 Jun 23;101(7):741-51
references.pmid: 10892745
references.citation: Nat Genet. 2002 Jan;30(1):13-9
references.pmid: 11753382
references.citation: Bioinformatics. 2005 Sep 15;21(18):3674-6
references.pmid: 16081474
references.citation: Genome Res. 2009 Apr;19(4):657-66
references.pmid: 19181841
references.citation: Mol Microbiol. 2003 Aug;49(4):859-67
references.pmid: 12890013
references.citation: Bioinformatics. 2010 Jan 1;26(1):136-8
references.pmid: 19855105
references.citation: J Biosci Bioeng. 1999;88(5):472-8
references.pmid: 16232647
references.citation: PLoS Biol. 2004 Aug;2(8):E246
references.pmid: 15314660
references.citation: Gene. 1998 Jan 30;207(2):127-34
references.pmid: 9511753
references.citation: BMC Genomics. 2007 Sep 24;8:334
references.pmid: 17892571
references.citation: Appl Environ Microbiol. 2005 May;71(5):2737-47
references.pmid: 15870366
references.citation: Fungal Genet Biol. 2008 Feb;45(2):139-51
references.pmid: 17967552
references.citation: PLoS Biol. 2004 Aug;2(8):E235
references.pmid: 15314654
references.citation: Mol Cell Biol. 2000 Nov;20(21):7955-70
references.pmid: 11027266
references.citation: BMC Genomics. 2006 Feb 22;7:32
references.pmid: 16504068
references.citation: Appl Microbiol Biotechnol. 2004 Jul;65(1):74-83
references.pmid: 15221230
references.citation: Curr Genet. 2002 Jul;41(4):275-81
references.pmid: 12172969