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Profiling Transposable Elements and Their Epigenetic Effects in Non-model Species

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Plant Epigenetics

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1456))

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Abstract

Taking transposable elements into consideration in surveys of genetic and epigenetic variation remains challenging in species lacking a high-quality reference genome. Here, molecular techniques reducing genome complexity and specifically targeting restructuring and methylation changes in TE genome fractions are described. In particular, methyl-sensitive transposon display (MSTD) uses isoschizomers and PCR amplifications to assess the methylation environment of TE insertions. MSTD offers reliable insights into genome-wide epigenetic changes associated with TEs, especially when used together with similar techniques tracking random sequences.

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References

  1. Hua-Van A, Le Rouzic A, Boutin TS, Filee J, Capy P (2011) The struggle for life of the genome’s selfish architects. Biol Direct 6:19

    Article  PubMed  PubMed Central  Google Scholar 

  2. Hollister JD, Smith LM, Guo YL, Ott F, Weigel D, Gaut BS (2011) Transposable elements and small RNAs contribute to gene expression divergence between Arabidopsis thaliana and Arabidopsis lyrata. Proc Natl Acad Sci U S A 108:2322–2327

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  3. Bonchev G, Parisod C (2013) Transposable elements and microevolutionary changes in natural populations. Mol Ecol Resour 13:765–775

    Article  CAS  PubMed  Google Scholar 

  4. Treangen TJ, Salzberg SL (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat Rev Genet 13:36–46

    CAS  Google Scholar 

  5. Jiang C, Chen C, Huang Z, Liu R, Verdier J (2015) ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data. BMC Bioinformatics 16:72

    Article  PubMed  PubMed Central  Google Scholar 

  6. Kalendar R, Flavell AJ, Ellis THN, Sjakste T, Moisy C, Schulman AH (2011) Analysis of plant diversity with retrotransposon-based molecular markers. Heredity 106:520–530

    Article  CAS  PubMed  Google Scholar 

  7. Syed NH, Flavell AJ (2006) Sequence-specific amplification polymorphisms (SSAPs): a multi-locus approach for analyzing transposon insertions. Nat Protoc 1:2746–2752

    Article  CAS  PubMed  Google Scholar 

  8. Melayah D et al (2004) Distribution of the Tnt1 retrotransposon family in the amphidiploid tobacco (Nicotiana tabacum) and its wild Nicotiana relatives. Biol J Linn Soc Lond 82:639–649

    Article  Google Scholar 

  9. Petit M et al (2007) Differential impact of retrotransposon populations on the genome of allotetraploid tobacco (Nicotiana tabacum). Mol Genet Genomics 278:1–15

    Article  CAS  PubMed  Google Scholar 

  10. Petit M et al (2010) Mobilization of retrotransposons in synthetic allotetraploid tobacco. New Phytol 186:135–147

    Article  CAS  PubMed  Google Scholar 

  11. Kashkush K, Khasdan V (2007) Large-scale survey of cytosine methylation of retrotransposons and the impact of readout transcription from long terminal repeats on expression of adjacent rice genes. Genetics 177:1975–1985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Parisod C, Salmon A, Zerjal T, Tenaillon M, Grandbastien MA, Ainouche M (2009) Rapid structural and epigenetic reorganization near transposable elements in hybrid and allopolyploid genomes in Spartina. New Phytol 184:1003–1015

    Article  CAS  PubMed  Google Scholar 

  13. Cervera MT, Ruiz-Garcia L, Martinez-Zapater JM (2002) Analysis of DNA methylation in Arabidopsis thaliana based on methylation-sensitive AFLP markers. Mol Genet Genomics 268:543–552

    Article  CAS  PubMed  Google Scholar 

  14. Roberts RJ, Vincze T, Posfai J, Macelis D (2010) REBASE - a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38:D234–D236

    Article  CAS  PubMed  Google Scholar 

  15. Senerchia N, Felber F, Parisod C (2015) Genome reorganization in F1 hybrids uncovers the role of retrotransposons in reproductive isolation. Proc R Soc Lond B Biol Sci 282

    Google Scholar 

  16. Gustafsson ALS et al (2014) Genetics of cryptic speciation within an arctic mustard, Draba nivalis. PLoS One 9:e93834

    Article  PubMed  PubMed Central  Google Scholar 

  17. Senerchia N, Wicker T, Felber F, Parisod C (2013) Evolutionary dynamics of LTR retrotransposons in wild wheats assessed with high throughput sequencing. Genome Biol Evol 5:1010–1020

    Article  PubMed  PubMed Central  Google Scholar 

  18. Senerchia N, Felber F, Parisod C (2014) Contrasting evolutionary trajectories of multiple retrotransposons following independent allopolyploidy in wild wheats. New Phytol 202:975–985

    Article  CAS  PubMed  Google Scholar 

  19. Bonin A, Bellemain E, Bronken Edeisen P, Pompanon F, Brochmann C, Taberlet P (2004) How to track and assess genotyping errors in population genetics studies. Mol Ecol 13:3261–3273

    Article  CAS  PubMed  Google Scholar 

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Authors and Affiliations

  1. Laboratory of Evolutionary Botany, Biology Institute, University of Neuchâtel, Rue Emile-Argand 11, 2009, Neuchâtel, Switzerland

    Christian Parisod

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  1. Christian Parisod
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Correspondence to Christian Parisod .

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Editors and Affiliations

  1. Department of Biological Sciences, University of Lethbridge, Lethbridge, Alberta, Canada

    Igor Kovalchuk

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Parisod, C. (2017). Profiling Transposable Elements and Their Epigenetic Effects in Non-model Species. In: Kovalchuk, I. (eds) Plant Epigenetics. Methods in Molecular Biology, vol 1456. Humana Press, Boston, MA. https://doi.org/10.1007/978-1-4899-7708-3_19

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  • DOI: https://doi.org/10.1007/978-1-4899-7708-3_19

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  • Publisher Name: Humana Press, Boston, MA

  • Print ISBN: 978-1-4899-7706-9

  • Online ISBN: 978-1-4899-7708-3

  • eBook Packages: Springer Protocols

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