Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping.
Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping.
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DOI：
10.1016/j.molbiopara.2015.09.002
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发表时间：
2015-08
影响因子：
1.5
通讯作者：
Myler PJ
中科院分区：
文献类型：
--
作者：
Parsons M;Ramasamy G;Vasconcelos EJ;Jensen BC;Myler PJ
自锥虫基因组首次发表以来，管理工作一直在进行中。在这里，我们利用现有的布氏锥虫核糖体分析数据提供证据的核糖体占用（和可能的翻译）的mRNA从225个目前未注释的编码序列（CDS）。这些推定的基因中有一小部分对应于先前注释的基因的额外拷贝，但85%是新的。这些小说CDS的中值大小很小（81 aa），表明过去的注释工作在检测大型CDS方面表现出色。在这里确认的独特CDS中，超过一半在其他锥虫基因组中具有候选直系同源物，其中大多数尚未被注释为蛋白质编码基因。尽管如此，大约三分之一的新CDS仅在T。布氏亚种使用核糖体足迹，RNA-Seq和剪接前导序列作图数据，我们更新了以前的工作，以确定性地修改414个CDS的起始位点，与当前的基因模型相比。这些数据指出了基因组中有几个区域存在改变编码区边界的序列错误。最后，我们将这些数据与我们以前的工作进行了整合，提出了排除683个假定的蛋白质编码基因，并得出了T.布鲁塞。通过核糖体分析和剪接前导序列定位推进布氏锥虫基因组注释。Gowthaman Ramasamy、Elton Vasconcelos、Bryan C.詹森和彼得·J·迈勒核糖体分析和剪接前导序列定位允许识别新的CDS（如图所示），重新定义CDS边界，并排除了许多推定的CDS。
Since the initial publication of the trypanosomatid genomes, curation has been ongoing. Here we make use of existing Trypanosoma brucei ribosome profiling data to provide evidence of ribosome occupancy (and likely translation) of mRNAs from 225 currently unannotated coding sequences (CDSs). A small number of these putative genes correspond to extra copies of previously annotated genes, but 85% are novel. The median size of these novels CDSs is small (81 aa), indicating that past annotation work has excelled at detecting large CDSs. Of the unique CDSs confirmed here, over half have candidate orthologues in other trypanosomatid genomes, most of which were not yet annotated as protein-coding genes. Nonetheless, approximately one-third of the new CDSs were found only in T. brucei subspecies. Using ribosome footprints, RNA-Seq and spliced leader mapping data, we updated previous work to definitively revise the start sites for 414 CDSs as compared to the current gene models. The data pointed to several regions of the genome that had sequence errors that altered coding region boundaries. Finally, we consolidated this data with our previous work to propose elimination of 683 putative genes as protein-coding and arrive at a view of the translatome of slender bloodstream and procyclic culture form T. brucei. Advancing Trypanosoma brucei genome annotation through ribosome profiling and spliced leader mapping Marilyn Parsons. Gowthaman Ramasamy, Elton Vasconcelos, Bryan C. Jensen, and Peter J. Myler Ribosome profiling and spliced leader mapping allowed the identification of novel CDSs (as in the image), redefined CDS boundaries, and ruled out numerous putative CDSs.