ITIS, a bioinformatics tool for accurate identification of transposon insertion sites using next-generation sequencing data

BMC Bioinformatics

Volumn 16, Issue 1, 2015, Pages

  Jiang, Chuan ^a,b   Chen, Chao ^a,b   Huang, Ziyue ^a   Liu, Renyi ^a   Verdier, Jerome ^a  

^a Shanghai Jiao Tong University Affiliated Sixth People s Hospital   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; CELL CULTURE; CHROMOSOMES; GENETIC ENGINEERING; MUTAGENESIS;

FORWARD GENETICS; INSERTION SITE; ITIS; MEDICAGO TRUNCATULA; TNT1; TRANSPOSABLE ELEMENTS;

GENES;

HEXAPODA; MAMMALIA; MEDICAGO TRUNCATULA;

TRANSPOSON;

ALGORITHM; BARREL MEDIC; BIOLOGY; COMPUTER PROGRAM; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; PROCEDURES; TRANSPOSON; VALIDATION STUDY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DNA TRANSPOSABLE ELEMENTS; HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; MEDICAGO TRUNCATULA; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 84928712512     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/s12859-015-0507-2     Document Type: Article

References (35)

1. Slotkin RK, Martienssen R. Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet. 2007;8(4):272-85.
2. Carlson CM, Dupuy AJ, Fritz S, Roberg-Perez KJ, Fletcher CF, Largaespada DA. Transposon mutagenesis of the mouse germline. Genetics. 2003;165(1):243-56.
3. Ross-Macdonald P, Coelho PS, Roemer T, Agarwal S, Kumar A, Jansen R, et al. Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature. 1999;402(6760):413-8.
4. Bazopoulou D, Tavernarakis N. The NemaGENETAG initiative: large scale transposon insertion gene-tagging in Caenorhabditis elegans. Genetica. 2009;137(1):39-46.
5. Thibault ST, Singer MA, Miyazaki WY, Milash B, Dompe NA, Singh CM, et al. A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat Genet. 2004;36(3):283-7.
6. Rosso MG, Li Y, Strizhov N, Reiss B, Dekker K, Weisshaar B. An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol Biol. 2003;53(1-2):247-59.
7. Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, et al. Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J. 2008;54(2):335-47.
8. Verdier J, Kakar K, Gallardo K, Le Signor C, Aubert G, Schlereth A, et al. Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling. Plant Mol Biol. 2008;67(6):567-80.
9. Verdier J, Lalanne D, Pelletier S, Torres-Jerez I, Righetti K, Bandyopadhyay K, et al. A regulatory network-based approach dissects late maturation processes related to the acquisition of desiccation tolerance and longevity of Medicago truncatula seeds. Plant Physiol. 2013;163(2):757-74.
10. Zhang F, Wang YW, Li GF, Tang YH, Kramer EM, Tadege M. STENOFOLIA Recruits TOPLESS to Repress ASYMMETRIC LEAVES2 at the Leaf Margin and Promote Leaf Blade Outgrowth in Medicago truncatula. Plant Cell. 2014;26(2):650-64.
11. Ge L, Peng J, Berbel A, Madueno F, Chen R. Regulation of compound leaf development by PHANTASTICA in Medicago truncatula. Plant Physiol. 2014;164(1):216-28.
12. Murray JD, Muni RRD, Torres-Jerez I, Tang Y, Allen S, Andriankaja M, et al. Vapyrin, a gene essential for intracellular progression of arbuscular mycorrhizal symbiosis, is also essential for infection by rhizobia in the nodule symbiosis of Medicago truncatula. Plant J. 2011;65(2):244-52.
13. Sinharoy S, Torres-Jerez I, Bandyopadhyay K, Kereszt A, Pislariu CI, Nakashima J, et al. The C2H2 transcription factor regulator of symbiosome differentiation represses transcription of the secretory pathway gene VAMP721a and promotes symbiosome development in Medicago truncatula. Plant Cell. 2013;25(9):3584-601.
14. Verdier J, Zhao J, Torres-Jerez I, Ge SJ, Liu CG, He XZ, et al. MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula. Proc Natl Acad Sci U S A. 2012;109(5):1766-71.
15. Zhang JY, Cruz DECMH, Torres-Jerez I, Kang Y, Allen SN, Huhman DV, et al. Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after rewatering. Plant Cell Environ. 2014;37(11):2553-76.
16. Uppalapati SR, Ishiga Y, Doraiswamy V, Bedair M, Mittal S, Chen J, et al. Loss of abaxial leaf epicuticular wax in Medicago truncatula irg1/palm1 mutants results in reduced spore differentiation of anthracnose and nonhost rust pathogens. Plant Cell. 2012;24(1):353-70.
17. Young ND, Debelle F, Oldroyd GED, Geurts R, Cannon SB, Udvardi MK, et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature. 2011;480(7378):520-4.
18. Tang H, Krishnakumar V, Bidwell S, Rosen B, Chan A, Zhou S, et al. An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics. 2014;15:312.
19. d'Erfurth I, Cosson V, Eschstruth A, Lucas H, Kondorosi A, Ratet P. Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J. 2003;34(1):95-106.
20. Lucas H, Feuerbach F, Kunert K, Grandbastien M, Caboche M. RNA-mediated transposition of the tobacco retrotransposon Tntl in Arabidopsis thaliana. EMBO J. 1995;14:2364-73.
21. Cheng X, Wang M, Lee HK, Tadege M, Ratet P, Udvardi M, et al. An efficient reverse genetics platform in the model legume Medicago truncatula. New Phytol. 2014;201(3):1065-76.
22. Nelson M, Bergman C. A review of methods for detecting non-reference transposable element insertions from high throughput genome resequencing data. In: Cold Spring Harbor Laboratory Regional Meeting on Mobile Genetic Elements. 2013.
23. Kofler R, Betancourt AJ, Schlotterer C. Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet. 2012;8(1):e1002487.
24. Platzer A, Nizhynska V, Long Q. TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data. Biology. 2012;1(2):395-410.
25. Keane TM, Wong K, Adams DJ. RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics. 2013;29(3):389-90.
26. Zhuang J, Wang J, Theurkauf W, Weng Z. TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res. 2014;42(11):6826-38.
27. Robb SM, Lu L, Valencia E, Burnette 3rd JM, Okumoto Y, Wessler SR, et al. The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. G3. 2013;3(6):949-57.
28. Nakagome M, Solovieva E, Takahashi A, Yasue H, Hirochika H, Miyao A. Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements. BMC Bioinformatics. 2014;15:71.
29. Li H. Aligning sequence reads, clone sequences and assembly contigs with BWA-MEM. ArXiv:q-bio.GN/1303.3997. 2013. http://arxiv.org/abs/1303.3997v2 .
30. Hu X, Yuan J, Shi Y, Lu J, Liu B, Li Z, et al. pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics. 2012;28(11):1533-5.
31. Cui Y, Barampuram S, Stacey MG, Hancock CN, Findley SD, Mathieu M, et al. Tnt1 Retrotransposon Mutagenesis: A Tool for Soybean [Glycine max (L.) Merr.] Functional Genomics. Plant Physiol. 2012;161:36-47.
32. Duangpan S, Zhang W, Wu Y, Jansky SH, Jiang J. Insertional Mutagenesis Using Tnt1 Retrotransposon in Potato. Plant Physiol. 2013;163(1):21-9.
33. Medicago truncatula Mutant Database [http://bioinfo4.noble.org/mutant/]
34. Cox MP, Peterson DA, Biggs PJ, Solexa QA. At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics. 2010;11(1):485.
35. Martin M: Cutadapt removes adapter sequences from high-throughput sequencing reads. EMBO J 2011, 17:10-12. Medicago Truncatula Genome Project [http://www.jcvi.org/medicago/index.php]