Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing
Strategies for identification of mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana by whole genome re-sequencing
复制标题
全基因组重测序鉴定拟南芥碳离子束辐照诱导突变的策略
DOI：
10.1016/j.mrfmmm.2017.12.001
复制
发表时间：
2018-01-01
影响因子：
2.3
通讯作者：
Zhou, Libin
中科院分区：
文献类型：
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作者：
Du, Yan;Luo, Shanwei;Zhou, Libin
重离子束辐照是一种强有力的物理诱变剂，已被用于在植物中产生许多突变材料。这些材料是后基因组时代功能基因组学研究的重要资源。新一代测序技术的出现促进了功能基因组学和分子育种的研究。从全基因组重测序中可以收集到丰富的信息;然而，了解全基因组范围内的分子突变谱，以及识别给定表型的致病基因对研究人员来说是一个具有挑战性的问题。NGS产生的巨大输出使得捕获关键信息变得困难。因此，探索一种有效的全基因组突变扫描数据筛选策略具有重要意义。本研究使用了来自一个实验室野生型（哥伦比亚）和11个来自碳离子束辐照的M-3拟南芥品系的重测序数据。用于分析的样品数量和不同组合都会影响筛分结果。结果表明，使用6个样本足以过滤掉共享突变（背景干扰）位点，并确定整个基因组中的真正突变位点。通过结合传统的粗图克隆，可以进一步缩小候选突变位点的最终数量。我们的研究结果证明了平行测序分析作为鉴定碳离子束照射诱导的突变的有效工具的可行性。我们首次提出了不同的分析策略来处理大量的并行测序数据集，以低假阳性率检测拟南芥中碳离子束辐照诱导的突变，以及识别导致突变表型的核苷酸变化。
Heavy-ion beam irradiation is a powerful physical mutagen that has been used to create numerous mutant materials in plants. These materials are an essential resource for functional genomics research in the post-genome era. The advent of Next-Generation Sequencing (NGS) technology has promoted the study of functional genomics and molecular breeding. A wealth of information can be gathered from whole genome re-sequencing; however, understanding the molecular mutation profile at genome wide, as well as identifying causal genes for a given phenotype are big challenging issues for researchers. The huge outputs created by NGS make it difficult to capture key information. It is worthy to explore an effective and efficient data-sieving strategy for mutation scanning at whole genome scale. Re-sequencing data from one laboratory wild type (Columbia) and eleven M-3 Arabidopsis thaliana lines derived from carbon-ion beam irradiation were used in present study. Both the number and different combinations of samples used for analysis affected the sieving results. The result indicated that using six samples was sufficient to filter out the shared mutation (background interference) sites as well as to identify the true mutation sites in the whole genome. The final number of candidate mutation sites could be further narrowed down by combining traditional rough map-based cloning. Our results demonstrated the feasibility of a parallel sequencing analysis as an efficient tool for the identification of mutations induced by carbon-ion beam irradiation. For the first time, we presented different analysis strategies for handling massive parallel sequencing data sets to detect the mutations induced by carbon-ion beam irradiation in Arabidopsis thaliana with low false-positive rate, as well as to identify the causative nucleotide changes responsible for a mutant phenotype.