Spy: A new group of eukaryotic DNA transposons without target site duplications

Genome Biology and Evolution

Volumn 6, Issue 7, 2014, Pages 1748-1757

  Han, Min Jin ^a   Xu, Hong En ^b   Zhang, Hua Hao ^a,c   Feschotte, Cédric ^d   Zhang, Ze ^a  

^a CHONGQING UNIVERSITY   (China)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c JIUJIANG UNIVERSITY   (China)

^d UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

Author keywords

DNA transposon; Spy; Target site duplication; Transposition

Indexed keywords

TRANSPOSON;

ANIMAL; BOMBYX; EUKARYOTE; GENE DUPLICATION; GENETICS; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PHYLOGENY; SEQUENCE ALIGNMENT; TRANSPOSON;

ANIMALS; BASE SEQUENCE; BOMBYX; DNA TRANSPOSABLE ELEMENTS; EUKARYOTA; GENE DUPLICATION; MOLECULAR SEQUENCE DATA; PHYLOGENY; SEQUENCE ALIGNMENT;

EID: 84926131704     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evu140     Document Type: Article

References (38)

1. BaoWD, Jurka J (2013) DNA transposons from the Pacific oyster genome. Repbase Rep. 13: 578-580.
2. Bryson K, et al (2005) Protein structure prediction servers at University College London. Nucleic Acids Res. 33: W36-W38.
3. Chandler M, Mahillon J (2002) Insertion sequences revisited, in mobile DNA II. Washington (DC): American Society for Microbiology
4. Craig NL, Craigie R, Gellert M, Lambowitz AM (2002) Mobile DNA II. Washington (DC): American Society for Microbiology Press.
5. Craigie R,Mizuuchi K (1985) Mechanism of transposition of bacteriophage Mu: structure of a transposition intermediate. Cell 41: 867-876.
6. Darriba D, Taboada GL, Doallo R, Posada D (2011) ProtTest 3: fast selection of best-fit models of protein evolution. Bioinformatics 27: 1164-1165.
7. de Koning AP, GuW, Castoe TA, Batzer MA, Pollock DD (2011) Repetitive elements may comprise over two-thirds of the human genome. PLoS Genet. 7: e1002384.
8. Dodd IB, Egan BJ (1990) Improved detection of helix-turn-helix DNA-binding motifs in protein sequences. Nucleic Acids Res. 18: 5019-5026.
9. Feschotte C, Jiang N, Wessler SR (2002) Plant transposable elements: where genetics meets genomics. Nat Rev Genet. 3: 329-341.
10. Feschotte C, Pritham EJ (2007) DNA transposons and the evolution of eukaryotic genomes. Annu Rev Genet. 41: 331-368.
11. Feschotte C, Zhang X, Wessler SR (2002) Miniature inverted-repeat transposable elements (MITEs) and their relationship with established DNA transposons, in mobile DNA II. Washington (DC): American Society of Microbiology Press.
12. Finnegan DJ (1989) Eukaryotic transposable elements and genome evolution. Trends Genet. 5: 103-107.
13. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program forWindows 95/98/NT. Nucleic Acids Symp Ser. 41: 95-98.
14. Holt RA, et al (2002) The genome sequence of the malaria mosquito Anopheles gambiae. Science 298: 129-149.
15. International Silkworm Genome Consortium. 2008) The genome of a lepidopteran model insect, the silkworm Bombyx mori. Insect Biochem Mol Biol. 38: 1036-1045.
16. Jurka J, et al (2005) Repbase update, a database of eukaryotic repetitive elements. Cytogenet Genome Res. 110: 462-467.
17. Kapitonov VV, Jurka J (2001) Rolling-circle transposons in eukaryotes. Proc Natl Acad Sci U S A. 98: 8714-8719.
18. Kapitonov VV, Jurka J (2003) Molecular paleontology of transposable elements in the Drosophila melanogaster genome. Proc Natl Acad Sci U S A (100: 6569-6574.
19. Kempken F, Windhofer F (2001) The hAT family: a versatile transposon group common to plants, fungi, animals, and man. Chromosoma 110: 1-9.
20. Kichenaradja P, Siguier P, Pérochon J, Chandler M (2010) ISbrowser: an extension of ISfinder for visualizing insertion sequences in prokaryotic genomes. Nucleic Acids Res. 38: D62-D68.
21. Kidwell MG (2002) Transposable elements and the evolution of genome size in eukaryotes. Genetica 115: 49-63.
22. Lander ES, et al (2001) Initial sequencing and analysis of the human genome. Nature 409: 860-921.
23. Lisch D (2002) Mutator transposons. Trends Plant Sci. 7: 498-504.
24. Marquez CP, Pritham EJ (2010) Phantom, a new subclass of mutator DNA transposons found in insect viruses and widely distributed in animals. Genetics 185: 1507-1517.
25. Mitra R, Fain-Thornton J, Craig NL (2008) piggyBac can bypass DNA synthesis during cut and paste transposition. EMBO J (27: 1097-1109.
26. Nagaraja GM, Nagaraju J (1995) Genome fingerprinting of the silkworm, Bombyx mori, using random arbitrary primers. Electrophoresis 16: 1633-1638.
27. Nene V, et al (2007) Genome sequence of Aedes aegypti, a major arbovirus vector. Science 316: 1718-1723.Rice P, Longden I, Bleasby A (2000) EMBOSS: The European molecular biology open software suite. Trends Genet. 16: 276-277.
28. Rice P, Longden I, Bleasby A (2000) EMBOSS: The European molecular biology open software suite. Trends Genet. 16: 276-277.
29. Ronquist F, Huelsenbeck JP (2003) MrBayes 3: Bayesian phylogenetic inference under mixed models. Bioinformatics 19: 1572-1574.
30. Sarkar A, et al (2003) Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences. Mol Genet Genomics. 270: 173-180.
31. Shao H, Tu Z (2001) Expanding the diversity of the IS630-Tc1-mariner superfamily: discovery of a unique DD37E transposon and reclassification of the DD37D and DD39D transposons. Genetics 159: 1103-1115.
32. Sinzelle L, et al (2008) Transposition of a reconstructed Harbinger element in human cells and functional homology with two transposon-derived cellular genes. Proc Natl Acad Sci U S A (105: 4715-4720.
33. Waterston RH, et al (2002) Initial sequencing and comparative analysis of the mouse genome. Nature 420: 520-562.
34. Wicker T, et al (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet. 8: 973-982.
35. Xu HE, et al (2013) BmTEdb: a collective database of transposable elements in the silkworm genome. Database (Oxford) 2013: bat055.Yuan YW, Wessler SR (2011) The catalytic domain of all eukaryotic cutand-paste transposase superfamilies. Proc Natl Acad Sci U S A (108: 7884-7889.
36. Yuan YW, Wessler SR (2011) The catalytic domain of all eukaryotic cutand-paste transposase superfamilies. Proc Natl Acad Sci U S A (108: 7884-7889.
37. Zhang X, Jiang N, Feschotte C, Wessler SR (2004) PIF-and Pong-like transposable elements: distribution, evolution and relationships with Tourist-like MITEs. Genetics 166: 971-986.
38. Zhang X, et al (2001) P instability factor: an active maize transposon system associated with the amplification of Tourist-like MITEs and a new superfamily of transposases. Proc Natl Acad Sci U S A. 98: 12572-12577.