Genome-Wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing

Yanyan Tang; Fengxia Liu; Lubin Tan

doi:10.1007/978-1-0716-1134-0_6

Genome-Wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing

Methods Mol Biol. 2021:2250:75-85. doi: 10.1007/978-1-0716-1134-0_6.

Authors

Yanyan Tang¹, Fengxia Liu², Lubin Tan³

Affiliations

¹ College of Agronomy, Qingdao Agricultural University, Qingdao, China.
² Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China.
³ Department of Plant Genetics and Breeding, China Agricultural University, Beijing, China. tlb9@cau.edu.cn.

PMID: 33900593
DOI: 10.1007/978-1-0716-1134-0_6

Abstract

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.

Keywords: Genotyping; MITE; PTEMD; Targeted high-throughput sequencing.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

DNA Copy Number Variations
DNA Transposable Elements*
Genotyping Techniques
High-Throughput Nucleotide Sequencing
Inverted Repeat Sequences*
Oryza / genetics*
Whole Genome Sequencing

Substances

DNA Transposable Elements