Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum.
Deep RNA sequencing reveals a high frequency of alternative splicing events in the fungus Trichoderma longibrachiatum.
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深度 RNA 测序揭示了真菌长支木霉 (Trichoderma longibrachiatum) 中存在高频率的选择性剪接事件
DOI：
10.1186/s12864-015-1251-8
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发表时间：
2015-02-06
期刊：
影响因子：
4.4
通讯作者：
Song XY
中科院分区：
文献类型：
--
作者：
Xie BB;Li D;Shi WL;Qin QL;Wang XW;Rong JC;Sun CY;Huang F;Zhang XY;Dong XW;Chen XL;Zhou BC;Zhang YZ;Song XY
背景：选择性剪接对高等生物蛋白质组多样性和功能复杂性至关重要。然而，在真菌中的选择性剪接景观仍然是难以捉摸的。结果：丝状真菌长枝木霉的转录组的深度测序使用Illumina Solexa技术。共发现14305个剪接点。选择性剪接事件的分析显示，所有选择性剪接事件的数量（10034），内含子保留，（IR，9369），5'端可变剪接位点（A5SS，167）和可变3'剪接位点（A3SS，302）分别比使用Illumina Solexa技术在真菌Aspergillus spermatitis中观察到的那些高7.3、7.4、5.1和5.9倍。这种出乎意料的高比例的选择性剪接表明，选择性剪接是重要的转录组的多样性T。长臂肌选择性剪接的内含子比组成型内含子具有更长的长度、更高的GC含量和更低的剪接位点得分。进一步的分析表明，异构体的相对频率与剪接位点得分的异构体。此外，比较转录组学确定，大多数酶相关的糖酵解和柠檬酸循环和乙醛酸循环，以及一些碳水化合物活性酶的转录regulated.Conclusions：这项研究，包括一个全面的分析的选择性剪接景观在丝状真菌T。longibrachiatum，揭示了一个意想不到的高比率的选择性剪接事件，并提供了新的见解转录组多样性的真菌。
Background:Alternative splicing is crucial for proteome diversity and functional complexity in higher organisms. However, the alternative splicing landscape in fungi is still elusive.Results:The transcriptome of the filamentous fungus Trichoderma longibrachiatum was deep sequenced using Illumina Solexa technology. A total of 14305 splice junctions were discovered. Analyses of alternative splicing events revealed that the number of all alternative splicing events (10034), intron retentions (IR, 9369), alternative 5' splice sites (A5SS, 167), and alternative 3' splice sites (A3SS, 302) is 7.3, 7.4, 5.1, and 5.9-fold higher, respectively, than those observed in the fungus Aspergillus oryzae using Illumina Solexa technology. This unexpectedly high ratio of alternative splicing suggests that alternative splicing is important to the transcriptome diversity of T. longibrachiatum. Alternatively spliced introns had longer lengths, higher GC contents, and lower splice site scores than constitutive introns. Further analysis demonstrated that the isoform relative frequencies were correlated with the splice site scores of the isoforms. Moreover, comparative transcriptomics determined that most enzymes related to glycolysis and the citrate cycle and glyoxylate cycle as well as a few carbohydrate-active enzymes are transcriptionally regulated.Conclusions:This study, consisting of a comprehensive analysis of the alternative splicing landscape in the filamentous fungus T. longibrachiatum, revealed an unexpectedly high ratio of alternative splicing events and provided new insights into transcriptome diversity in fungi.
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影响因子：
46.9
作者：
Trapnell C;Williams BA;Pertea G;Mortazavi A;Kwan G;van Baren MJ;Salzberg SL;Wold BJ;Pachter L
通讯作者：
Pachter L
影响因子：
14.9
作者：
Drabenstot, SD;Kupfer, DM;Murphy, JW
通讯作者：
Murphy, JW
影响因子：
56.9
作者：
Loftus, BJ;Fung, E;Hyman, RW
通讯作者：
Hyman, RW
影响因子：
--
作者：
Kupfer, DM;Drabenstot, SD;Murphy, JW
通讯作者：
Murphy, JW
影响因子：
12.3
作者：
Langmead B;Trapnell C;Pop M;Salzberg SL
通讯作者：
Salzberg SL