Abstract
The recent development of next-generation sequencing (NGS) technologies allowed various authors to imagine, test, and validate new approaches for TE analysis, in their nature, type, activity, or quantity. In this chapter, we describe briefly the technologies used, then the various approaches and methods used already, and finally some potential new methods. In contrast to the more molecular chapters of the book, the approaches described here are purely bioinformatics, and have a set of NGS data as a starting point. Moreover, as these analyses are quite recent in the field, most of them were only performed once, and we cannot be sure that they could be reused in other species or context than the original one. However, there are a lot of interesting approaches and results that NGS can provide in the TE field.
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Abbreviations
- BAC:
-
Bacterial artificial chromosome
- LTR:
-
Long terminal repeat
- NGS:
-
Next-generation sequencing
- siRNA:
-
Small interfering RNA
- SNP:
-
Single-nucleotide polymorphism
- TE:
-
Transposable element
- VS:
-
Structural variant
References
Wicker T, et al. (2008) Low-pass shotgun sequencing of the barley genome facilitates rapid identification of genes, conserved non-coding sequences and novel repeats. BMC Genomics 9:518
Kurtz S, et al. (2008) A new method to compute K-mer frequencies and its application to annotate large repetitive plant genomes. BMC Genomics 9:517
Marçais G, Kingsford C (2011) A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770
Gnerre S, et al. (2011) High-quality draft assemblies of mammalian genomes from massively parallel sequence data. Proc Natl Acad Sci USA 108:1513–1518
Argout X, et al. (2010) The genome of Theobroma cacao. Nat Genet 43:101–108
Marioni JC, et al. (2008) RNA-seq: An assessment of technical reproducibility and comparison with gene expression arrays. Genome Res 18:1509–1517
Blumenstiel JP (2011) Evolutionary dynamics of transposable elements in a small RNA world. Trends in Genetics 27:23–31
Sabot F, et al. (2011) Transpositional landscape of rice genome revealed by Paired-End Mapping of high-throughput resequencing data. Plant J doi: 10.1111/j.1365-313X.2011.04492.x. [Epub ahead of print]
Mirouze M, et al. (2009) Selective epigenetic control of retrotransposition in Arabidopsis. Nature 461:427–430
Fiston-Lavier A, et al. (2010) T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res 39:e36
Li H, Durbin R (2009) Fast and accurate short read alignment with Burrows–Wheeler transform. Bioinformatics 25:1754–1760
Langmead B, et al. (2009) Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10:R25
Li H, Ruan J, Durbin R (2008) Mapping short DNA sequencing reads and calling variants using mapping quality scores. Genome Res 18:1851–1858
Li R, et al. (2009) SOAP2: an improved ultrafast tool for short read alignment. Bioinformatics 25:1966–1967
Slater G, Birney E (2005) Automated generation of heuristics for biological sequence comparison. BMC Bioinformatics 6:31
Trapnell C, et al. (2010) Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotech 28:511–515
Trapnell C, Pachter L, Salzberg SL (2009) TopHat: discovering splice junctions with RNA-Seq. Bioinformatics 25:1105–1111
Frith MC, Wan R, Horton P (2010) Incorporating sequence quality data into alignment improves DNA read mapping. Nucl. Acids Res 38:e100
Zerbino, D.R., Birney, E., 2008. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Research 18, 821–829
Simpson JT, et al. (2009) ABySS: A parallel assembler for short read sequence data. Genome Res 19:1117–1123
Robertson G, et al. (2010) De novo assembly and analysis of RNA-seq data. Nat Meth 7:909–912
DeBarry J, Liu R, Bennetzen J (2008) Discovery and assembly of repeat family pseudomolecules from sparse genomic sequence data using the Assisted Automated Assembler of Repeat Families (AAARF) algorithm. BMC Bioinformatics 9:235
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Chaparro, C., Sabot, F. (2012). Methods and Software in NGS for TE Analysis. In: Bigot, Y. (eds) Mobile Genetic Elements. Methods in Molecular Biology, vol 859. Humana Press. https://doi.org/10.1007/978-1-61779-603-6_6
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DOI: https://doi.org/10.1007/978-1-61779-603-6_6
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