Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum.
Generation and analysis of the expressed sequence tags from the mycelium of Ganoderma lucidum.
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DOI：
10.1371/journal.pone.0061127
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发表时间：
2013
期刊：
影响因子：
3.7
通讯作者：
Yang UC
中科院分区：
文献类型：
--
作者：
Huang YH;Wu HY;Wu KM;Liu TT;Liou RF;Tsai SF;Shiao MS;Ho LT;Tzean SS;Yang UC
灵芝（G. lucidum）是一种药用蘑菇，因其潜在的生物效应而在东亚享有盛誉。为了系统地探索与真菌各种表型相关的基因，灵芝基因组联盟开展了表达序列标签（EST）测序项目。使用基于桑格测序的方法，从不同持续时间的灵芝菌丝体的体外培养物中获得了 47,285 个 EST。这些 EST 进一步聚类并合并为 7,774 个非冗余表达位点。从过度表达、选择性剪接和天然反义转录本方面探讨了这些表达的重叠群的特征。我们的结果为探索灵芝转录组及其调控提供了宝贵的信息资源。许多在快速生长的双核菌丝体中过量表达的基因与生长密切相关，例如细胞壁和生物活性化合物的合成。此外，包含推定盒式外显子和保留内含子的 EST 基因组比对是手动策划的，然后用于推断灵芝的主要剪接位点识别机制。此外，我们还查明了许多假定的反义转录本，从中我们注意到两个案例可能揭示了迄今为止尚未发现的生物学途径。为了让用户能够访问该项目的数据和结果的初步分析，我们创建了一个专门的网站：http://csb2.ym.edu.tw/est/。
Ganoderma lucidum (G. lucidum) is a medicinal mushroom renowned in East Asia for its potential biological effects. To enable a systematic exploration of the genes associated with the various phenotypes of the fungus, the genome consortium of G. lucidum has carried out an expressed sequence tag (EST) sequencing project. Using a Sanger sequencing based approach, 47,285 ESTs were obtained from in vitro cultures of G. lucidum mycelium of various durations. These ESTs were further clustered and merged into 7,774 non-redundant expressed loci. The features of these expressed contigs were explored in terms of over-representation, alternative splicing, and natural antisense transcripts. Our results provide an invaluable information resource for exploring the G. lucidum transcriptome and its regulation. Many cases of the genes over-represented in fast-growing dikaryotic mycelium are closely related to growth, such as cell wall and bioactive compound synthesis. In addition, the EST-genome alignments containing putative cassette exons and retained introns were manually curated and then used to make inferences about the predominating splice-site recognition mechanism of G. lucidum. Moreover, a number of putative antisense transcripts have been pinpointed, from which we noticed that two cases are likely to reveal hitherto undiscovered biological pathways. To allow users to access the data and the initial analysis of the results of this project, a dedicated web site has been created at http://csb2.ym.edu.tw/est/.
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影响因子：
30.8
作者：
GISH, W;STATES, DJ
通讯作者：
STATES, DJ
影响因子：
7
作者：
Kan, ZY;Rouchka, EC;States, DJ
通讯作者：
States, DJ
影响因子：
4.4
作者：
Hajjaj, H;Macé, C;Fay, LB
通讯作者：
Fay, LB
DOI：
10.1111/j.1443-9573.2006.00254.x
发表时间：
2006-01-01
期刊：
Chinese journal of digestive diseases
影响因子：
--
作者：
Huang, Zhi Gang;Ran, Zhi Hua;Xiao, Shu Dong
通讯作者：
Xiao, Shu Dong
影响因子：
7
作者：
Liang, Chengzhi;Mao, Long;Stein, Lincoln
通讯作者：
Stein, Lincoln