Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters.
Transcriptome analysis of the filamentous fungus Aspergillus nidulans directed to the global identification of promoters.
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DOI：
10.1186/1471-2164-14-847
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发表时间：
2013-12-03
期刊：
影响因子：
4.4
通讯作者：
Caddick MX
中科院分区：
文献类型：
--
作者：
Sibthorp C;Wu H;Cowley G;Wong PW;Palaima P;Morozov IY;Weedall GD;Caddick MX
60多年来，丝状真菌细粒曲霉（Aspergillus nidulans）一直是细胞生物学和遗传学研究的一种可处理的模式生物。自2005年以来，包括医学和工业上重要的物种在内的大量曲霉菌基因组已被测序，它是其中之一。为了提高我们对其生物学的认识，并通过改进基因注释来提高其作为遗传模型的实用性，我们对毛竹的转录组进行了测序，重点进行了5 '端分析。链特异性全转录组测序显示，80-95%的注释基因似乎在测试条件下表达。我们估计基因总数应该增加大约1000个，达到11800个。在剪接方面，8.3%的基因有多个备选转录本，但外显子跳变的备选剪接非常罕见。75%的注释基因显示出一定程度的反义转录，对于一个基因meaB，我们证明了反义转录具有调控作用。转录本的5 ‘端特异性测序用于转录起始位点的全基因组定位，使我们能够询问超过7000个启动子和5 ’未翻译区域。我们的数据揭示了A. nidulans转录组的复杂性，并有助于改进基因组注释。这些数据可以在AspGD基因组浏览器上查看。本文的在线版本（doi:10.1186/1471-2164-14-847）包含补充材料，可供授权用户使用。
The filamentous fungus Aspergillus nidulans has been a tractable model organism for cell biology and genetics for over 60 years. It is among a large number of Aspergilli whose genomes have been sequenced since 2005, including medically and industrially important species. In order to advance our knowledge of its biology and increase its utility as a genetic model by improving gene annotation we sequenced the transcriptome of A. nidulans with a focus on 5′ end analysis. Strand-specific whole transcriptome sequencing showed that 80-95% of annotated genes appear to be expressed across the conditions tested. We estimate that the total gene number should be increased by approximately 1000, to 11,800. With respect to splicing 8.3% of genes had multiple alternative transcripts, but alternative splicing by exon-skipping was very rare. 75% of annotated genes showed some level of antisense transcription and for one gene, meaB, we demonstrated the antisense transcript has a regulatory role. Specific sequencing of the 5’ ends of transcripts was used for genome wide mapping of transcription start sites, allowing us to interrogate over 7000 promoters and 5′ untranslated regions. Our data has revealed the complexity of the A. nidulans transcriptome and contributed to improved genome annotation. The data can be viewed on the AspGD genome browser. The online version of this article (doi:10.1186/1471-2164-14-847) contains supplementary material, which is available to authorized users.
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