Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology.
Detection of active transposable elements in Arabidopsis thaliana using Oxford Nanopore Sequencing technology.
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DOI：
10.1186/s12864-017-3753-z
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发表时间：
2017-07-17
期刊：
影响因子：
4.4
通讯作者：
Panaud O
中科院分区：
文献类型：
--
作者：
Debladis E;Llauro C;Carpentier MC;Mirouze M;Panaud O
转座元件（TE）有助于大多数真核生物基因组的结构和功能动力学。由于它们倾向于密集地填充植物和动物基因组，转座对基因组多样性的影响的精确估计已被认为是当今基因组学的主要挑战之一。新一代测序（NGS）技术的发展为转座元件相关结构变异体（TEASV）的高通量检测提供了新的方法，为群体基因组学研究开辟了新的前景。然而，这些依赖于产生短读段（高达350个核苷酸）的Illumina平台。序列读段大小的这种限制可能导致高错误发现率（FDR），因此限制了TEASV的检测能力，特别是在大的复杂基因组的情况下。最新的测序技术，如Oxford Nanopore Technologies（ONT），可以产生长至100个碱基的读数，因此代表了植物和动物中TEASV检测的有前途的工具。我们提出了一个试点实验的结果TEASV检测模式植物拟南芥使用ONT测序，并表明它可以有效地用于检测TE运动。我们使用具有R7化学的MinIon装置产生了约0.8X的met 1衍生的表观遗传重组近交系（epiRIL）的基因组覆盖率。我们能够检测到LTR-逆转录转座子Evadé（EVD）的9个新拷贝。我们还证明了DNA转座子CACTA，CAC 1的活性。即使在低序列覆盖率（0.8X）下，ONT测序也允许我们可靠地检测拟南芥基因组中的几个TE插入。长读段长度允许由TE活性引起的结构变异的精确且明确的映射。这表明TEASV检测的读段长度和基因组覆盖率之间的权衡可能有利于前者。如果该技术在降低错误率和操作成本方面进一步改进，它可以有效地用于种群水平的多样性研究。本文的在线版本（doi：10.1186/s12864-017-3753-z）包含补充材料，可供授权用户使用。
Transposables elements (TEs) contribute to both structural and functional dynamics of most eukaryotic genomes. Because of their propensity to densely populate plant and animal genomes, the precise estimation of the impact of transposition on genomic diversity has been considered as one of the main challenges of today’s genomics. The recent development of NGS (next generation sequencing) technologies has open new perspectives in population genomics by providing new methods for high throughput detection of Transposable Elements-associated Structural Variants (TEASV). However, these have relied on Illumina platform that generates short reads (up to 350 nucleotides). This limitation in size of sequence reads can cause high false discovery rate (FDR) and therefore limit the power of detection of TEASVs, especially in the case of large, complex genomes. The newest sequencing technologies, such as Oxford Nanopore Technologies (ONT) can generate kilobases-long reads thus representing a promising tool for TEASV detection in plant and animals. We present the results of a pilot experiment for TEASV detection on the model plant species Arabidopsis thaliana using ONT sequencing and show that it can be used efficiently to detect TE movements. We generated a ~0.8X genome coverage of a met1-derived epigenetic recombinant inbred line (epiRIL) using a MinIon device with R7 chemistry. We were able to detect nine new copies of the LTR-retrotransposon Evadé (EVD). We also evidenced the activity of the DNA transposon CACTA, CAC1. Even at a low sequence coverage (0.8X), ONT sequencing allowed us to reliably detect several TE insertions in Arabidopsis thaliana genome. The long read length allowed a precise and un-ambiguous mapping of the structural variations caused by the activity of TEs. This suggests that the trade-off between read length and genome coverage for TEASV detection may be in favor of the former. Should the technology be further improved both in terms of lower error rate and operation costs, it could be efficiently used in diversity studies at population level. The online version of this article (doi:10.1186/s12864-017-3753-z) contains supplementary material, which is available to authorized users.
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