T-lex2: Genotyping, frequency estimation and re-annotation of transposable elements using single or pooled next-generation sequencing data

Nucleic Acids Research

Volumn 43, Issue 4, 2015, Pages

  Fiston Lavier, Anna Sophie ^a,b   Barrón, Maite G ^c,d   Petrov, Dmitri A ^a   González, Josefa ^d  

^a STANFORD UNIVERSITY   (United States)

^b INSTITUT DES SCIENCES DE L EVOLUTION   (France)

^c UNIVERSITAT AUTÒNOMA DE BARCELONA   (Spain)

^d UNIVERSITAT POMPEU FABRA   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL; COMPUTER PROGRAM; DNA SEQUENCE; DROSOPHILA MELANOGASTER; GENETICS; GENOTYPING TECHNIQUE; HIGH THROUGHPUT SEQUENCING; HUMAN; HUMAN GENOME; INSECT GENOME; INTERSPERSED REPEAT; MOLECULAR GENETICS; PROCEDURES; VALIDATION STUDY;

ANIMALS; DROSOPHILA MELANOGASTER; GENOME, HUMAN; GENOME, INSECT; GENOTYPING TECHNIQUES; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; HUMANS; INTERSPERSED REPETITIVE SEQUENCES; MOLECULAR SEQUENCE ANNOTATION; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84941057227     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gku1250     Document Type: Article

References (49)

1. Gilad, Y., Pritchard, J. K. And Thornton, K. (2009) Characterizing natural variation using next-generation sequencing technologies. Trends Genet., 25, 463-471.
2. Koboldt, D. C., Steinberg, K. M., Larson, D. E., Wilson, R. K. And Mardis, E. R. (2013) The next-generation sequencing revolution and its impact on genomics. Cell, 155, 27-38.
3. Shapiro, E., Biezuner, T. And Linnarsson, S. (2013) Single-cell sequencing-based technologies will revolutionize whole-organism science. Nat. Rev. Genet., 14, 618-630.
4. Treangen, T. J. And Salzberg, S. L. (2012) Repetitive DNA and next-generation sequencing: computational challenges and solutions. Nat. Rev. Genet., 13, 36-46.
5. Wicker, T., Sabot, F., Hua-Van, A., Bennetzen, J. L., Capy, P., Chalhoub, B., Flavell, A., Leroy, P., Morgante, M., Panaud, O. et al. (2007) A unified classification system for eukaryotic transposable elements. Nat. Rev. Genet., 8, 973-982.
6. Kapitonov, V. V. And Jurka, J. (2008) A universal classification of eukaryotic transposable elements implemented in Repbase. Nat. Rev. Genet., 9, 411-412; author reply 414.
7. Biemont, C. (2010) A brief history of the status of transposable elements: from junk DNA to major players in evolution. Genetics, 186, 1085-1093.
8. de Koning, A. P., Gu, W., Castoe, T. A., Batzer, M. A. And Pollock, D. D. (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet., 7, e1002384.
9. Devos, K. M., Beales, J., Ogihara, Y. And Doust, A. N. (2005) Comparative sequence analysis of the phytochrome C gene and its upstream region in allohexaploid wheat reveals new data on the evolution of its three constituent genomeS. Plant Mol. Biol., 58, 625-641.
10. Ewing, A. D. And Kazazian, H. H. Jr. (2011) Whole-genome resequencing allows detection of many rare LINE-1 insertion alleles in humans. Genome Res., 21, 985-990.
11. Iskow, R. C., McCabe, M. T., Mills, R. E., Torene, S., Pittard, W. S., Neuwald, A. F., Van Meir, E. G., Vertino, P. M. And Devine, S. E. (2010) Natural mutagenesis of human genomes by endogenous retrotransposons. Cell, 141, 1253-1261.
12. Cowley, M. And Oakey, R. J. (2013) Transposable elements re-wire and fine-tune the transcriptome. PLoS Genet., 9, e1003234.
13. Casacuberta, E. And Gonzalez, J. (2013) The impact of transposable elements in environmental adaptation. Mol. Ecol., 22, 1503-1517.
14. Magwire, M. M., Bayer, F., Webster, C. L., Cao, C. And Jiggins, F. M. (2011) Successive increases in the resistance of Drosophila to viral infection through a transposon insertion followed by a Duplication. PLoS Genet., 7, e1002337.
15. Guio, L., Barron, M. G. And Gonzalez, J. (2014) The transposable element Bari-Jheh mediates oxidative stress response in Drosophila. Mol. Ecol., 23, 2020-2030.
16. Mateo, L., Ullastres, A. And Gonzalez, J. (2014) A transposable element insertion confers xenobiotic resistance in Drosophila. PLoS Genet., 10, e1004560.
17. Akagi, K., Li, J. And Symer, D. E. (2013) How do mammalian transposons induce genetic variation? A conceptual framework: The age, structure, allele frequency, and genome context of transposable elements may define their wide-ranging biological impacts. Bioessays, 35, 397-407.
18. Chenais, B., Caruso, A., Hiard, S. And Casse, N. (2012) The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments. Gene, 509, 7-15.
19. Hua-Van, A., Le Rouzic, A., Boutin, T. S., Filee, J. And Capy, P. (2011) The struggle for life of the genome's selfish architects. Biol. Direct., 6 19.
20. Makalowski, W., Pande, A., Gotea, V. And Makalowska, I. (2012) Transposable elements and their identification. Methods Mol. Biol., 855, 337-359.
21. Linheiro, R. S. And Bergman, C. M. (2012) Whole genome resequencing reveals natural target site preferences of transposable elements in Drosophila melanogaster. PloS ONE, 7, e30008.
22. Hormozdiari, F., Hajirasouliha, I., Dao, P., Hach, F., Yorukoglu, D., Alkan, C., Eichler, E. E. And Sahinalp, S. C. (2010) Next-generation VariationHunter: combinatorial algorithms for transposon insertion discovery. Bioinformatics, 26, i350-i357.
23. Keane, T. M., Wong, K. And Adams, D. J. (2013) RetroSeq: Transposable element discovery from next-generation sequencing data. Bioinformatics, 29, 389-390.
24. Lee, E., Iskow, R., Yang, L., Gokcumen, O., Haseley, P., Luquette, L. J. 3rd, Lohr, J. G., Harris, C. C., Ding, L., Wilson, R. K. et al. (2012) Landscape of somatic retrotransposition in human cancers. Science, 337, 967-971.
25. Robb, S. M., Lu, L., Valencia, E., Burnette, J. M. 3rd, Okumoto, Y., Wessler, S. R. And Stajich, J. E. (2013) The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. G3, 3, 949-957.
26. Kofler, R., Betancourt, A. J. And Schlotterer, C. (2012) Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet., 8, e1002487.
27. Wu, J., Lee, W. P., Ward, A., Walker, J. A., Konkel, M. K., Batzer, M. A. And Marth, G. T. (2014) Tangram: A comprehensive toolbox for mobile element insertion detection. BMC Genom., 15, 795.
28. Zhuang, J., Wang, J., Theurkauf, W. And Weng, Z. (2014) TEMP: A computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res., 42, 6826-6838.
29. J. M., Cridland. And Thornton, K. R. (2010) Validation of rearrangement break points identified by paired-end sequencing in natural populations of Drosophila melanogaster. Genome biol. evol., 2, 83-101.
30. Platzer, A., Nizhynska, V. And Long, Q. (2012) TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data. Biology, 1, 395-410.
31. Fiston-Lavier, A. S., Carrigan, M., Petrov, D. A. And Gonzalez, J. (2011) T-lex: A program for fast and accurate assessment of transposable element presence using next-generation sequencing data. Nucleic Acids Res., 39, e36.
32. Lerat, E. (2010) Identifying repeats and transposable elements in sequenced genomes: how to find your way through the dense forest of programs. Heredity (Edinb), 104, 520-533.
33. Kent, W. J. (2002) BLAT-the BLAST-like alignment tool. Genome Res., 12, 656-664.
34. David, M., Dzamba, M., Lister, D., Ilie, L. And Brudno, M. (2011) SHRiMP2: sensitive yet practical SHort Read Mapping. Bioinformatics, 27, 1011-1012.
35. Rumble, S. M., Lacroute, P., Dalca, A. V., Fiume, M., Sidow, A. And Brudno, M. (2009) SHRiMP: Accurate mapping of short color-space readS. PLoS Comput. Biol., 5, e1000386.
36. Mackay, T. F., Richards, S., Stone, E. A., Barbadilla, A., Ayroles, J. F., Zhu, D., Casillas, S., Han, Y., Magwire, M. M., Cridland, J. M. et al. (2012) The Drosophila melanogaster Genetic Reference Panel. Nature, 482, 173-178.
37. Petrov, D. A., Fiston-Lavier, A. S., Lipatov, M., Lenkov, K. And Gonzalez, J. (2011) Population genomics of transposable elements in Drosophila melanogaster. Mol. Biol. Evol., 28, 1633-1644.
38. Gonzalez, J., Lenkov, K., Lipatov, M., Macpherson, J. M. And Petrov, D. A. (2008) High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol., 6, e251.
39. Zhu, Y., Bergland, A. O., Gonzalez, J. And Petrov, D. A. (2012) Empirical validation of pooled whole genome population re-sequencing in Drosophila melanogaster. PloS ONE, 7, e41901.
40. Stewart, C., Kural, D., Stromberg, M. P., Walker, J. A., Konkel, M. K., Stutz, A. M., Urban, A. E., Grubert, F., Lam, H. Y., Lee, W. P. et al. (2011) A comprehensive map of mobile element insertion polymorphisms in humanS. PLoS Genet., 7, e1002236.
41. Gonzalez, J., Karasov, T. L., Messer, P. W. And Petrov, D. A. (2010) Genome-wide patterns of adaptation to temperate environments associated with transposable elements in Drosophila. PLoS Genet., 6, e1000905.
42. Ellinghaus, D., Kurtz, S. And Willhoeft, U. (2008) LTRharvest, an efficient and flexible software for de novo detection of LTR retrotransposons. BMC Bioinformat., 9, 18.
43. Szak, S. T., Pickeral, O. K., Makalowski, W., Boguski, M. S., Landsman, D. And Boeke, J. D. (2002) Molecular archeology of L1 insertions in the human genome. Genome Biol., 3, research0052.
44. Rawal, K. And Ramaswamy, R. (2011) Genome-wide analysis of mobile genetic element insertion sites. Nucleic Acids Res., 39, 6864-6878.
45. Kapitonov, V. V. And Jurka, J. (2003) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc. Natl. Acad. Sci. U.S.A., 100, 6569-6574.
46. Berezikov, E., Bucheton, A. And Busseau, I. (2000) A search for reverse transcriptase-coding sequences reveals new non-LTR retrotransposons in the genome of Drosophila melanogaster. Genome Biol., 1, RESEARCH0012.
47. Dunsmuir, P., Brorein, W. J. Jr, Simon, M. A. And Rubin, G. M. (1980) Insertion of the Drosophila transposable element copia generates a 5 base pair duplication. Cell, 21, 575-579.
48. Rubin, G. M., Brorein, W. J. Jr, Dunsmuir, P., Flavell, A. J., Levis, R., Strobel, E., Toole, J. J. And Young, E. (1981) Copia-like transposable elements in the Drosophila genome. Cold Spring Harb. Symp. Quant. Biol., 45, 619-628.
49. Chaparro, C. And Sabot, F. (2012) Methods and software in NGS for TE analysis. Methods Mol. Biol., 859, 105-114.