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

Part of the Methods in Molecular Biology book series (MIMB,volume 2250)

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.

Key words

  • MITE
  • Targeted high-throughput sequencing
  • PTEMD
  • Genotyping

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  • DOI: 10.1007/978-1-0716-1134-0_6
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References

  1. Bureau TE, Ronald PC, Wessler SR (1996) A computer-based systematic survey reveals the predominance of small inverted-repeat elements in wild-type rice genes. Proc Natl Acad Sci U S A 93(16):8524–8529

    CAS  CrossRef  Google Scholar 

  2. Jiang N, Bao Z, Zhang X et al (2003) An active DNA transposon family in rice. Nature 421:163–167

    CAS  CrossRef  Google Scholar 

  3. Lu C, Chen J, Zhang Y et al (2012) Miniature inverted-repeat transposable elements (MITEs) have been accumulated through amplification bursts and play important roles in gene expression and species diversity in Oryza sativa. Mol Biol Evol 29:1005–1017

    CAS  CrossRef  Google Scholar 

  4. Hirsch CD, Springer NM (2017) Transposable element influences on gene expression in plants. Biochim Biophys Acta Gene Regul Mech 1860:157–165

    CAS  CrossRef  Google Scholar 

  5. Stapley J, Santure AW, Dennis SR (2015) Transposable elements as agents of rapid adaptation may explain the genetic paradox of invasive species. Mol Ecol 24:2241–2252

    CAS  CrossRef  Google Scholar 

  6. Niu XM, Xu YC, Li ZW et al (2019) Transposable elements drive rapid phenotypic variation in Capsella rubella. Proc Natl Acad Sci U S A 116:6908–6913

    CAS  CrossRef  Google Scholar 

  7. Mills RE, Luttig CT, Larkins CE et al (2006) An initial map of insertion and deletion (INDEL) variation in the human genome. Genome Res 16:1182–1190

    CAS  CrossRef  Google Scholar 

  8. Kang H, Zhu D, Lin R et al (2016) A novel method for identifying polymorphic transposable elements via scanning of high-throughput short reads. DNA Res 23:241–251

    CAS  CrossRef  Google Scholar 

  9. Tu Z (2001) Eight novel families of miniature inverted repeat transposable elements in the African malaria mosquito, Anopheles gambiae. Proc Natl Acad Sci U S A 98:1699–1704

    CAS  CrossRef  Google Scholar 

  10. Santiago N, Herráiz C, Goñi JR et al (2002) Genome-wide analysis of the emigrant family of MITE of Arabidopsis thaliana. Mol Biol Evol 19:2285–2293

    CAS  CrossRef  Google Scholar 

  11. Han Y, Wessler SR (2010) MITE-Hunter: a program for discovering miniature inverted-repeat transposable elements from genomic sequences. Nucleic Acids Res 38:e199

    CrossRef  Google Scholar 

  12. Yang G, Hall TC (2003) MAK, a computational tool kit for automated MITE analysis. Nucleic Acids Res 31:3659–3665

    CAS  CrossRef  Google Scholar 

  13. Yang G (2013) MITE Digger, an efficient and accurate algorithm for genome wide discovery of miniature inverted repeat transposable elements. BMC Bioinformatics 14:186

    CrossRef  Google Scholar 

  14. Chen J, Hu Q, Zhang Y et al (2014) P-MITE: a database for plant minimature inverted-repeat transposable elements. Nucleic Acids Res 42:D1176–D1181

    CAS  CrossRef  Google Scholar 

  15. Zhuang J, Wang J, Theurkauf W et al (2014) TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res 42:6826–6838

    CAS  CrossRef  Google Scholar 

  16. Williams-Carrier R, Stiffler N, Belcher S et al (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J 63:167–177

    CAS  PubMed  Google Scholar 

  17. Tang Y, Ma X, Zhao S et al (2019) Identification of an active miniature inverted-repeat transposable element mJing and its diversification in rice. Plant J 98:639–653

    CAS  CrossRef  Google Scholar 

  18. Bentley DR, Balasubramanian S, Swerdlow HP et al (2008) Accurate whole human genome sequencing using reversible terminator chemistry. Nature 456:53–59

    CAS  CrossRef  Google Scholar 

  19. Murray M, Thompson W (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325

    CAS  CrossRef  Google Scholar 

  20. Ye K, Schulz MH, Long Q et al (2009) Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads. Bioinformatics 25:2865–2871

    CAS  CrossRef  Google Scholar 

  21. Martin M (2011) Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBnet J 17:10–12

    CrossRef  Google Scholar 

  22. Langmead B, Salzberg SL (2012) Fast gapped-read alignment with Bowtie 2. Nat Methods 9:357–359

    CAS  CrossRef  Google Scholar 

  23. Tamura K, Stecher G, Peterson D et al (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729

    CAS  CrossRef  Google Scholar 

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Acknowledgement

This work was supported by Chinese Universities Scientific Fund (Grant No. 2019TC087).

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Correspondence to Lubin Tan .

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Tang, Y., Liu, F., Tan, L. (2021). Genome-Wide Identification of Miniature Inverted-Repeat Transposable Elements by Targeted High-Throughput Sequencing. In: Cho, J. (eds) Plant Transposable Elements. Methods in Molecular Biology, vol 2250. Humana, New York, NY. https://doi.org/10.1007/978-1-0716-1134-0_6

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  • DOI: https://doi.org/10.1007/978-1-0716-1134-0_6

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  • Publisher Name: Humana, New York, NY

  • Print ISBN: 978-1-0716-1133-3

  • Online ISBN: 978-1-0716-1134-0

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