Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions.
BACKGROUND: 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...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3978026?pdf=render |
| _version_ | 1818440794870120448 |
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| author | Xu-Ping Shentu Wei-Ping Liu Xiao-Huan Zhan Yi-Peng Xu Jian-Feng Xu Xiao-Ping Yu Chuan-Xi Zhang |
| author_facet | Xu-Ping Shentu Wei-Ping Liu Xiao-Huan Zhan Yi-Peng Xu Jian-Feng Xu Xiao-Ping Yu Chuan-Xi Zhang |
| author_sort | Xu-Ping Shentu |
| collection | DOAJ |
| description | BACKGROUND: 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. RESULTS: 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. CONCLUSION: 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. |
| first_indexed | 2024-12-14T18:18:01Z |
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| id | doaj.art-ef64d8e17c4c42d9866dca78bf52620b |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T18:18:01Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-ef64d8e17c4c42d9866dca78bf52620b2022-12-21T22:52:09ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0194e9420310.1371/journal.pone.0094203Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions.Xu-Ping ShentuWei-Ping LiuXiao-Huan ZhanYi-Peng XuJian-Feng XuXiao-Ping YuChuan-Xi ZhangBACKGROUND: 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. RESULTS: 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. CONCLUSION: 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.http://europepmc.org/articles/PMC3978026?pdf=render |
| spellingShingle | Xu-Ping Shentu Wei-Ping Liu Xiao-Huan Zhan Yi-Peng Xu Jian-Feng Xu Xiao-Ping Yu Chuan-Xi Zhang Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. PLoS ONE |
| title | Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. |
| title_full | Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. |
| title_fullStr | Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. |
| title_full_unstemmed | Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. |
| title_short | Transcriptome sequencing and gene expression analysis of Trichoderma brevicompactum under different culture conditions. |
| title_sort | transcriptome sequencing and gene expression analysis of trichoderma brevicompactum under different culture conditions |
| url | http://europepmc.org/articles/PMC3978026?pdf=render |
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