A new approach for annotation of transposable elements using small RNA mapping.
A new approach for annotation of transposable elements using small RNA mapping.
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DOI：
10.1093/nar/gkv257
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发表时间：
2015-07-27
影响因子：
14.9
通讯作者：
Jackson SA
中科院分区：
文献类型：
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作者：
El Baidouri M;Kim KD;Abernathy B;Arikit S;Maumus F;Panaud O;Meyers BC;Jackson SA
转座因子（te）是在大多数生物体中发现的可移动的基因组DNA序列。它们如此密集地分布在许多真核生物物种的基因组中，以至于它们通常是主要成分。在过去的几十年里，随着许多植物基因组测序项目的快速产生，迫切需要改进TE注释作为全基因组研究的先决条件。与使用RNA-seq进行基因注释类似，我们提出了一种新的TE从头注释方法，该方法使用作为TE沉默途径一部分的24个nt- sirna作为向导。我们将这种名为TASR （for Transposon Annotation using Small RNAs）的新方法用于拟南芥、水稻和大豆的TE从头注释，并证明该策略可以成功应用于植物的TE从头注释。可执行PERL可从http://tasr-pipeline.sourceforge.net/下载
Transposable elements (TEs) are mobile genomic DNA sequences found in most organisms. They so densely populate the genomes of many eukaryotic species that they are often the major constituents. With the rapid generation of many plant genome sequencing projects over the past few decades, there is an urgent need for improved TE annotation as a prerequisite for genome-wide studies. Analogous to the use of RNA-seq for gene annotation, we propose a new method for de novo TE annotation that uses as a guide 24 nt-siRNAs that are a part of TE silencing pathways. We use this new approach, called TASR (for Transposon Annotation using Small RNAs), for de novo annotation of TEs in Arabidopsis, rice and soybean and demonstrate that this strategy can be successfully applied for de novo TE annotation in plants. Executable PERL is available for download from: http://tasr-pipeline.sourceforge.net/