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

详细信息    查看全文

• 作者：Chuan Jiang (1) (2)
  Chao Chen (1) (2)
  Ziyue Huang (1)
  Renyi Liu (1)
  Jerome Verdier (1)
  
  1. Shanghai Center for Plant Stress Biology ; Shanghai Institutes for Biological Sciences ; Chinese Academy of Sciences ; Shanghai ; 201602 ; China
  2. University of Chinese Academy of Sciences ; Beijing ; 100039 ; China
  
• 关键词：Transposable elements ; Insertion sites ; ITIS ; Forward genetics ; Tnt1 ; Medicago truncatula
• 刊名：BMC Bioinformatics
• 出版年：2015
• 出版时间：December 2015
• 年：2015
• 卷：16
• 期：1
• 全文大小：923 KB
• 参考文献：1. Slotkin, RK, Martienssen, R (2007) Transposable elements and the epigenetic regulation of the genome. Nat Rev Genet 8: pp. 272-285 CrossRef
  2. Carlson, CM, Dupuy, AJ, Fritz, S, Roberg-Perez, KJ, Fletcher, CF, Largaespada, DA (2003) Transposon mutagenesis of the mouse germline. Genetics 165: pp. 243-256
  3. Ross-Macdonald, P, Coelho, PS, Roemer, T, Agarwal, S, Kumar, A, Jansen, R (1999) Large-scale analysis of the yeast genome by transposon tagging and gene disruption. Nature 402: pp. 413-418 CrossRef
  4. Bazopoulou, D, Tavernarakis, N (2009) The NemaGENETAG initiative: large scale transposon insertion gene-tagging in Caenorhabditis elegans. Genetica 137: pp. 39-46 CrossRef
  5. Thibault, ST, Singer, MA, Miyazaki, WY, Milash, B, Dompe, NA, Singh, CM (2004) A complementary transposon tool kit for Drosophila melanogaster using P and piggyBac. Nat Genet 36: pp. 283-287 CrossRef
  6. Rosso, MG, Li, Y, Strizhov, N, Reiss, B, Dekker, K, Weisshaar, B (2003) An Arabidopsis thaliana T-DNA mutagenized population (GABI-Kat) for flanking sequence tag-based reverse genetics. Plant Mol Biol 53: pp. 247-259 CrossRef
  7. Tadege, M, Wen, J, He, J, Tu, H, Kwak, Y, Eschstruth, A (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 54: pp. 335-347 CrossRef
  8. Verdier, J, Kakar, K, Gallardo, K, Signor, C, Aubert, G, Schlereth, A (2008) Gene expression profiling of M. truncatula transcription factors identifies putative regulators of grain legume seed filling. Plant Mol Biol 67: pp. 567-580 CrossRef
  9. Verdier, J, Lalanne, D, Pelletier, S, Torres-Jerez, I, Righetti, K, Bandyopadhyay, K (2013) A regulatory network-based approach dissects late maturation processes related to the acquisition of desiccation tolerance and longevity of Medicago truncatula seeds. Plant Physiol 163: pp. 757-774 CrossRef
  10. Zhang, F, Wang, YW, Li, GF, Tang, YH, Kramer, EM, Tadege, M (2014) STENOFOLIA Recruits TOPLESS to Repress ASYMMETRIC LEAVES2 at the Leaf Margin and Promote Leaf Blade Outgrowth in Medicago truncatula. Plant Cell 26: pp. 650-664 CrossRef
  11. Ge, L, Peng, J, Berbel, A, Madueno, F, Chen, R (2014) Regulation of compound leaf development by PHANTASTICA in Medicago truncatula. Plant Physiol 164: pp. 216-228 CrossRef
  12. Murray, JD, Muni, RRD, Torres-Jerez, I, Tang, Y, Allen, S, Andriankaja, M (2011) 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 65: pp. 244-252 CrossRef
  13. Sinharoy, S, Torres-Jerez, I, Bandyopadhyay, K, Kereszt, A, Pislariu, CI, Nakashima, J (2013) 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 25: pp. 3584-3601 CrossRef
  14. Verdier, J, Zhao, J, Torres-Jerez, I, Ge, SJ, Liu, CG, He, XZ (2012) MtPAR MYB transcription factor acts as an on switch for proanthocyanidin biosynthesis in Medicago truncatula. Proc Natl Acad Sci U S A 109: pp. 1766-1771 CrossRef
  15. Zhang, JY, Cruz, DECMH, Torres-Jerez, I, Kang, Y, Allen, SN, Huhman, DV (2014) Global reprogramming of transcription and metabolism in Medicago truncatula during progressive drought and after rewatering. Plant Cell Environ 37: pp. 2553-2576 CrossRef
  16. Uppalapati, SR, Ishiga, Y, Doraiswamy, V, Bedair, M, Mittal, S, Chen, J (2012) 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 24: pp. 353-370 CrossRef
  17. Young, ND, Debelle, F, Oldroyd, GED, Geurts, R, Cannon, SB, Udvardi, MK (2011) The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature 480: pp. 520-524
  18. Tang, H, Krishnakumar, V, Bidwell, S, Rosen, B, Chan, A, Zhou, S (2014) An improved genome release (version Mt4.0) for the model legume Medicago truncatula. BMC Genomics 15: pp. 312 CrossRef
  19. d鈥橢rfurth, I, Cosson, V, Eschstruth, A, Lucas, H, Kondorosi, A, Ratet, P (2003) Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J 34: pp. 95-106 CrossRef
  20. Lucas, H, Feuerbach, F, Kunert, K, Grandbastien, M, Caboche, M (1995) RNA-mediated transposition of the tobacco retrotransposon Tntl in Arabidopsis thaliana. EMBO J 14: pp. 2364-2373
  21. Cheng, X, Wang, M, Lee, HK, Tadege, M, Ratet, P, Udvardi, M (2014) An efficient reverse genetics platform in the model legume Medicago truncatula. New Phytol 201: pp. 1065-1076 CrossRef
  22. Nelson, M, Bergman, C (2013) A review of methods for detecting non-reference transposable element insertions from high throughput genome resequencing data. Cold Spring Harbor Laboratory Regional Meeting on Mobile Genetic Elements.
  23. Kofler, R, Betancourt, AJ, Schlotterer, C (2012) Sequencing of pooled DNA samples (Pool-Seq) uncovers complex dynamics of transposable element insertions in Drosophila melanogaster. PLoS Genet 8: pp. e1002487 CrossRef
  24. Platzer, A, Nizhynska, V, Long, Q (2012) TE-Locate: A Tool to Locate and Group Transposable Element Occurrences Using Paired-End Next-Generation Sequencing Data. Biology 1: pp. 395-410 CrossRef
  25. Keane, TM, Wong, K, Adams, DJ (2013) RetroSeq: transposable element discovery from next-generation sequencing data. Bioinformatics 29: pp. 389-390 CrossRef
  26. Zhuang, J, Wang, J, Theurkauf, W, Weng, Z (2014) TEMP: a computational method for analyzing transposable element polymorphism in populations. Nucleic Acids Res 42: pp. 6826-6838 CrossRef
  27. Robb, SM, Lu, L, Valencia, E, Burnette, JM, Okumoto, Y, Wessler, SR (2013) The use of RelocaTE and unassembled short reads to produce high-resolution snapshots of transposable element generated diversity in rice. G3 3: pp. 949-957 CrossRef
  28. Nakagome, M, Solovieva, E, Takahashi, A, Yasue, H, Hirochika, H, Miyao, A (2014) Transposon Insertion Finder (TIF): a novel program for detection of de novo transpositions of transposable elements. BMC Bioinformatics 15: pp. 71 CrossRef
  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 (2012) pIRS: Profile-based Illumina pair-end reads simulator. Bioinformatics 28: pp. 1533-1535 CrossRef
  31. Cui, Y, Barampuram, S, Stacey, MG, Hancock, CN, Findley, SD, Mathieu, M, Zhang, Z, Parrott, W, Stacey, G (2012) Tnt1 Retrotransposon Mutagenesis: A Tool for Soybean [Glycine max (L.) Merr.] Functional Genomics. Plant Physiol 161: pp. 36-47 CrossRef
  32. Duangpan, S, Zhang, W, Wu, Y, Jansky, SH, Jiang, J (2013) Insertional Mutagenesis Using Tnt1 Retrotransposon in Potato. Plant Physiol 163: pp. 21-29 CrossRef
  33. Medicago truncatula Mutant Database [http://bioinfo4.noble.org/mutant/]
  34. Cox, MP, Peterson, DA, Biggs, PJ, Solexa, QA (2010) At-a-glance quality assessment of Illumina second-generation sequencing data. BMC Bioinformatics 11: pp. 485 CrossRef
  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]
  
• 刊物主题：Bioinformatics; Microarrays; Computational Biology/Bioinformatics; Computer Appl. in Life Sciences; Combinatorial Libraries; Algorithms;
• 出版者：BioMed Central
• ISSN：1471-2105

文摘

Background Transposable elements constitute an important part of the genome and are essential in adaptive mechanisms. Transposition events associated with phenotypic changes occur naturally or are induced in insertional mutant populations. Transposon mutagenesis results in multiple random insertions and recovery of most/all the insertions is critical for forward genetics study. Using genome next-generation sequencing data and appropriate bioinformatics tool, it is plausible to accurately identify transposon insertion sites, which could provide candidate causal mutations for desired phenotypes for further functional validation. Results We developed a novel bioinformatics tool, ITIS (Identification of Transposon Insertion Sites), for localizing transposon insertion sites within a genome. It takes next-generation genome re-sequencing data (NGS data), transposon sequence, and reference genome sequence as input, and generates a list of highly reliable candidate insertion sites as well as zygosity information of each insertion. Using a simulated dataset and a case study based on an insertional mutant line from Medicago truncatula, we showed that ITIS performed better in terms of sensitivity and specificity than other similar algorithms such as RelocaTE, RetroSeq, TEMP and TIF. With the case study data, we demonstrated the efficiency of ITIS by validating the presence and zygosity of predicted insertion sites of the Tnt1 transposon within a complex plant system, M. truncatula. Conclusion This study showed that ITIS is a robust and powerful tool for forward genetic studies in identifying transposable element insertions causing phenotypes. ITIS is suitable in various systems such as cell culture, bacteria, yeast, insect, mammal and plant.