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

Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L - Nucleic Acids Res. (2010)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China.

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.

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AS events in the A. oryzae transcriptome. (A) The schematic depicts the six primary types of AS events in the A. oryzae transcriptome. The red curve indicates the expression levels (log2 of reads count). The orange bar denotes the exons and the red knuckle line highlights the linkage between two exons that were supported by at least two distinct junction reads. The vertical line shows the transcript start or end sites. MXE were not detected in our data. (B) A length comparison between RIs and CEs. Vertical coordinates represents the cumulative percentage of RIs or CEs of different lengths. (C) The numbers of each type of AS event in A. oryzae detected by RNA-Seq.
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Figure 5: AS events in the A. oryzae transcriptome. (A) The schematic depicts the six primary types of AS events in the A. oryzae transcriptome. The red curve indicates the expression levels (log2 of reads count). The orange bar denotes the exons and the red knuckle line highlights the linkage between two exons that were supported by at least two distinct junction reads. The vertical line shows the transcript start or end sites. MXE were not detected in our data. (B) A length comparison between RIs and CEs. Vertical coordinates represents the cumulative percentage of RIs or CEs of different lengths. (C) The numbers of each type of AS event in A. oryzae detected by RNA-Seq.

Mentions: AS is crucial for proteomic diversity and functional complexity in higher organisms (25–28). To assess the genome-wide extent of AS events in A. oryzae, we performed computational analysis to determine the known and putative splicing junctions and then identified sequence reads mapping to these regions using stringent criteria (see ‘Materials and methods’ section). We examined seven common types of AS events, including A5SS, A3SS, SE, RI, MXE, AFE and ALE (14), and found that 1032 A. oryzae genes underwent AS with 1375 AS events (Supplementary Table S9, Figure 5A and C). All types of AS events were detected except MXE. For our data, 76.98% of all A. oryzae genes contained two or more exons, and of these 11.10% produced two or more AS isoforms. Therefore, of the total number of A. oryzae genes, 8.55% were estimated to undergo AS.Figure 5.


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

Wang B, Guo G, Wang C, Lin Y, Wang X, Zhao M, Guo Y, He M, Zhang Y, Pan L - Nucleic Acids Res. (2010)

AS events in the A. oryzae transcriptome. (A) The schematic depicts the six primary types of AS events in the A. oryzae transcriptome. The red curve indicates the expression levels (log2 of reads count). The orange bar denotes the exons and the red knuckle line highlights the linkage between two exons that were supported by at least two distinct junction reads. The vertical line shows the transcript start or end sites. MXE were not detected in our data. (B) A length comparison between RIs and CEs. Vertical coordinates represents the cumulative percentage of RIs or CEs of different lengths. (C) The numbers of each type of AS event in A. oryzae detected by RNA-Seq.
© Copyright Policy - creative-commons
Related In: Results  -  Collection

License
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Figure 5: AS events in the A. oryzae transcriptome. (A) The schematic depicts the six primary types of AS events in the A. oryzae transcriptome. The red curve indicates the expression levels (log2 of reads count). The orange bar denotes the exons and the red knuckle line highlights the linkage between two exons that were supported by at least two distinct junction reads. The vertical line shows the transcript start or end sites. MXE were not detected in our data. (B) A length comparison between RIs and CEs. Vertical coordinates represents the cumulative percentage of RIs or CEs of different lengths. (C) The numbers of each type of AS event in A. oryzae detected by RNA-Seq.
Mentions: AS is crucial for proteomic diversity and functional complexity in higher organisms (25–28). To assess the genome-wide extent of AS events in A. oryzae, we performed computational analysis to determine the known and putative splicing junctions and then identified sequence reads mapping to these regions using stringent criteria (see ‘Materials and methods’ section). We examined seven common types of AS events, including A5SS, A3SS, SE, RI, MXE, AFE and ALE (14), and found that 1032 A. oryzae genes underwent AS with 1375 AS events (Supplementary Table S9, Figure 5A and C). All types of AS events were detected except MXE. For our data, 76.98% of all A. oryzae genes contained two or more exons, and of these 11.10% produced two or more AS isoforms. Therefore, of the total number of A. oryzae genes, 8.55% were estimated to undergo AS.Figure 5.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China.

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.

Show MeSH