Sibthorp Christopher, Wu Huihai, Cowley Gwendolyn, Wong Prudence W H, Palaima Paulius, Morozov Igor Y, Weedall Gareth D, Caddick Mark X
Institute of Integrative Biology, University of Liverpool, Biosciences Building, Crown Street, Liverpool L69 7ZB, UK.
BMC Genomics. 2013 Dec 3;14(1):847. doi: 10.1186/1471-2164-14-847.
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.
在超过60年的时间里，丝状真菌构巢曲霉一直是细胞生物学和遗传学中易于处理的模式生物。自2005年以来，它是众多已进行基因组测序的曲霉之一，包括具有医学和工业重要性的物种。为了增进我们对其生物学的了解，并通过改进基因注释提高其作为遗传模型的实用性，我们对构巢曲霉的转录组进行了测序，重点是5'端分析。
链特异性全转录组测序表明，在测试的条件下，80 - 95%的注释基因似乎都有表达。我们估计基因总数应增加约1000个，达到11,800个。关于剪接，8.3%的基因有多个可变转录本，但外显子跳跃的可变剪接非常罕见。对转录本5'端的特异性测序用于全基因组转录起始位点的定位，使我们能够研究7000多个启动子和5'非翻译区。
我们的数据揭示了构巢曲霉转录组的复杂性，并有助于改进基因组注释。这些数据可在AspGD基因组浏览器上查看。
