College of Agronomy, Qingdao Agricultural University, Qingdao, China.
Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
Methods Mol Biol. 2021;2250:75-85. doi: 10.1007/978-1-0716-1134-0_6.
Miniature inverted-repeat transposable elements (MITEs) are a subset of short, non-autonomous class II transposable elements and also a major source of eukaryotic genomic variation. Therefore, genome-wide identification of MITE insertions can help to shed light on their copy number variation and genome insertion features. Here, we present a protocol for targeted MITE identification and genotyping by high-throughput sequencing. By introducing genome-wide detection of the rice mJing MITE as an example, we describe DNA extraction, DNA fragmentation, targeted DNA fragment enrichment, library construction for high-throughput sequencing, and sequence analysis.
微型反向重复转座元件 (MITEs) 是短的非自主类 II 转座元件的一个子集，也是真核生物基因组变异的主要来源。因此，全基因组鉴定 MITE 插入有助于揭示它们的拷贝数变异和基因组插入特征。在这里，我们提出了一种通过高通量测序进行靶向 MITE 鉴定和基因分型的方案。通过引入水稻 mJing MITE 的全基因组检测作为示例，我们描述了 DNA 提取、DNA 片段化、靶向 DNA 片段富集、高通量测序文库构建和序列分析。
