Shentu Xu-Ping, Liu Wei-Ping, Zhan Xiao-Huan, Xu Yi-Peng, Xu Jian-Feng, Yu Xiao-Ping, Zhang Chuan-Xi
Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China; Institute of Insect Science, Zhejiang University, Hangzhou, China.
Zhejiang Provincial Key Laboratory of Biometrology and Inspection & Quarantine, College of Life Sciences, China Jiliang University, Hangzhou, China.
PLoS One. 2014 Apr 7;9(4):e94203. doi: 10.1371/journal.pone.0094203. eCollection 2014.
Trichoderma brevicompactum is the Trichoderma species producing simple trichothecenes-trichodermin, a potential antifungal antibiotic and a protein synthesis inhibitor. However, the biosynthetic pathway of trichodermin in Trichoderma is not completely clarified. Therefore, transcriptome and gene expression profiling data for this species are needed as an important resource to better understand the mechanism of the trichodermin biosynthesis and provide a blueprint for further study of T. brevicompactum.
In this study, de novo assembly of the T. brevicompactum transcriptome using the short-read sequencing technology (Illumina) was performed. In addition, two digital gene expression (DGE) libraries of T. brevicompactum under the trichodermin-producing and trichodermin-nonproducing culture conditions, respectively, were constructed to identify the differences in gene expression. A total of 23,351 unique transcripts with a mean length of 856 bp were obtained by a new Trinity de novo assembler. The variations of the gene expression under different culture conditions were also identified. The expression profiling data revealed that 3,282 unique transcripts had a significantly differential expression under the trichodermin-producing condition, as compared to the trichodermin-nonproducing condition. This study provides a large amount of transcript sequence data that will contribute to the study of the trichodermin biosynthesis in T. brevicompactum. Furthermore, quantitative real-time PCR (qRT-PCR) was found to be useful to confirm the differential expression of the unique transcripts.
Our study provides considerable gene expression information of T. brevicompactum at the transcriptional level,which will help accelerate the research on the trichodermin biosynthesis. Additionally, we have demonstrated the feasibility of using the Illumina sequencing based DGE system for gene expression profiling, and have shed new light on functional studies of the genes involved in T. brevicompactum biosynthesis.
短小木霉是一种能产生简单单端孢霉烯族毒素——木霉菌素的木霉属物种，木霉菌素是一种潜在的抗真菌抗生素和蛋白质合成抑制剂。然而，木霉属中木霉菌素的生物合成途径尚未完全阐明。因此，需要该物种的转录组和基因表达谱数据作为重要资源，以更好地理解木霉菌素生物合成的机制，并为进一步研究短小木霉提供蓝图。
在本研究中，利用短读长测序技术（Illumina）对短小木霉转录组进行了从头组装。此外，分别构建了短小木霉在产木霉菌素和不产木霉菌素培养条件下的两个数字基因表达（DGE）文库，以鉴定基因表达的差异。通过一种新的Trinity从头组装器获得了总共23351个独特转录本，平均长度为856 bp。还鉴定了不同培养条件下基因表达的变化。表达谱数据显示，与不产木霉菌素的条件相比，在产木霉菌素的条件下有3282个独特转录本具有显著差异表达。本研究提供了大量转录序列数据，将有助于研究短小木霉中木霉菌素的生物合成。此外，发现定量实时PCR（qRT-PCR）可用于确认独特转录本的差异表达。
我们的研究在转录水平上提供了大量短小木霉的基因表达信息，这将有助于加速对木霉菌素生物合成的研究。此外，我们证明了使用基于Illumina测序的DGE系统进行基因表达谱分析的可行性，并为参与短小木霉生物合成的基因的功能研究提供了新的线索。
