School of Bioscience and Bioengineering, South China University of Technology, Guangzhou, Guangdong, China.
Nucleic Acids Res. 2010 Aug;38(15):5075-87. doi: 10.1093/nar/gkq256. Epub 2010 Apr 14.
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.
米曲霉，一种在食品发酵和酶工业中重要的丝状真菌，通过基因组测序和各种其他工具表明，其基因组组成具有显著特征。然而，米曲霉转录组的功能复杂性尚未被完全阐明。在这里，我们应用直接高通量配对末端 RNA-seq（RNA-Seq）技术对四种不同培养条件下的米曲霉转录组进行了研究。通过 RNA-Seq 提供的高分辨率和灵敏度，我们能够鉴定出大量新的转录本、新外显子、非翻译区、上游起始密码子和上游开放阅读框，这为米曲霉转录组提供了重要的见解。我们还能够评估米曲霉中 mRNA 异构体的情况，发现了大量发生可变剪接的基因。通过比较不同培养条件下的基因表达水平，我们鉴定出了许多可能与固体培养中比液体培养中更高水平的蛋白质生产有关的基因和途径。我们的分析表明，米曲霉的转录组比以前预期的要复杂得多，这些结果可能为进一步研究米曲霉转录组提供蓝图。
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