Article thumbnail

T-lex: a program for fast and accurate assessment of transposable element presence using next-generation sequencing data

By Anna-Sophie Fiston-Lavier, Matthew Carrigan, Dmitri A. Petrov and Josefa González


Transposable elements (TEs) are repetitive DNA sequences that are ubiquitous, extremely abundant and dynamic components of practically all genomes. Much effort has gone into annotation of TE copies in reference genomes. The sequencing cost reduction and the newly available next-generation sequencing (NGS) data from multiple strains within a species offer an unprecedented opportunity to study population genomics of TEs in a range of organisms. Here, we present a computational pipeline (T-lex) that uses NGS data to detect the presence/absence of annotated TE copies. T-lex can use data from a large number of strains and returns estimates of population frequencies of individual TE insertions in a reasonable time. We experimentally validated the accuracy of T-lex detecting presence or absence of 768 previously identified TE copies in two resequenced Drosophila melanogaster strains. Approximately 95% of the TE insertions were detected with 100% sensitivity and 97% specificity. We show that even at low levels of coverage T-lex produces accurate results for TE copies that it can identify reliably but that the rate of ‘no data’ calls increases as the coverage falls below 15×. T-lex is a broadly applicable and flexible tool that can be used in any genome provided the availability of the reference genome, individual TE copy annotation and NGS data

Topics: Methods Online
Publisher: Oxford University Press
OAI identifier:
Provided by: PubMed Central

To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.

Suggested articles


  1. (2009). A recent adaptive transposable element insertion near highly conserved developmental loci in Drosophila melanogaster.
  2. (2007). A unified classification system for eukaryotic transposable elements.
  3. (2006). Birth of a chimeric primate gene by capture of the transposase gene from a mobile element.
  4. (2006). Dramatic amplification of a rice transposable element during recent domestication.
  5. (2007). Effect of divergence time and recombination rate on molecular evolution of Drosophila INE-1 transposable elements and other candidates for neutrally evolving sites.
  6. (2002). Evolution of a polymorphic regulatory element in interferon-gamma through transposition and mutation.
  7. (2006). Genetics: junk DNA as an evolutionary force.
  8. Genome 10K Community of Scientists: a proposal to obtain whole-genome sequence for 10,000 vertebrate species.
  9. (2008). Genome sequence of the metazoan plant-parasitic nematode Meloidogyne incognita.
  10. (2010). Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila.
  11. (2008). High rate of recent transposable element-induced adaptation in Drosophila melanogaster.
  12. (2008). Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.
  13. (2001). Initial sequencing and analysis of the human genome.
  14. (2008). Mapping short DNA sequencing reads and calling variants using mapping quality scores.
  15. (2002). Mobile DNA II.
  16. (2001). Perspective: transposable elements, parasitic DNA, and genome evolution.
  17. (2010). Population genomics of transposable elements in Drosophila melanogaster.
  18. (2000). Primer3 on the WWW for general users and for biologist programmers.
  19. (2005). Repbase Update, a database of eukaryotic repetitive elements.
  20. (2009). SHRiMP: accurate mapping of short color-space reads.
  21. (2010). SoyTEdb: a comprehensive database of transposable elements in the soybean genome.
  22. (2009). The 1001 genomes project for Arabidopsis thaliana.
  23. (1994). The distribution of transposable elements within and between chromosomes in a population of Drosophila melanogaster. III. Element abundances in heterochromatin.
  24. (2010). The evolution of transposable elements in natural populations of self-fertilizing Arabidopsis thaliana and its outcrossing relative Arabidopsis lyrata.
  25. (2000). The genome sequence of Drosophila melanogaster.
  26. (2005). The repetitive landscape of the chicken genome.
  27. (2002). The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective.
  28. (2004). Transposable element annotation of the rice genome.
  29. (2007). Transposable elements and the epigenetic regulation of the genome.
  30. (2009). Transposable elements in reptilian and avian (sauropsida) genomes.
  31. (1998). Transposition mediated by RAG1 and RAG2 and its implications for the evolution of the immune system.
  32. (2007). Transposition of the rice miniature inverted repeat transposable element mPing in Arabidopsis thaliana.
  33. (1993). Transposons in place of telomeric repeats at a Drosophila telomere.
  34. (2009). Unexpected consequences of a sudden and massive transposon amplification on rice gene expression.
  35. (2001). Virtual PCR.