Genome-wide analysis of the "cut-and-paste" transposons of grapevine

PLoS ONE

Volumn 3, Issue 9, 2008, Pages

  Benjak, Andrej ^a,b   Forneck, Astrid ^b   Casacuberta, Josep M ^a  

^a CENTRE FOR RESEARCH IN AGRICULTURAL GENOMICS CRAG   (Spain)

^b UNIVERSITY OF NATURAL RESOURCES AND LIFE SCIENCES   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

GENE PRODUCT; PROTEIN CACTA; PROTEIN CACTAVINE 10; PROTEIN CACTAVINE 11; PROTEIN CACTAVINE 12; PROTEIN CACTAVINE 13; PROTEIN CACTAVINE 2; PROTEIN CACTAVINE 3; PROTEIN CACTAVINE 4; PROTEIN CACTAVINE 5; PROTEIN CACTAVINE 6; PROTEIN CACTAVINE 7; PROTEIN CACTAVINE 8; PROTEIN CACTAVINE 9; PROTEIN HAT; PROTEIN HATVINE 6; PROTEIN HOP; PROTEIN JITTERY; PROTEIN MUTATOR; PROTEIN MUTAVINE 1; PROTEIN MUTAVINE 18; PROTEIN MUTAVINE 2; PROTEIN MUTAVINE 3; PROTEIN MUTAVINE 4; PROTEIN MUTAVINE 5; PROTEIN MUTAVINE 6; PROTEIN PIF; PROTEIN PIFVINE 3; TRANSPOSASE; UNCLASSIFIED DRUG;

ARTICLE; CELL FUNCTION; DOMESTICATED PLANT; EXPRESSED SEQUENCE TAG; GENE AMPLIFICATION; GENE DUPLICATION; GENE SEQUENCE; GENE STRUCTURE; GENETIC TRANSCRIPTION; GENETIC VARIABILITY; GENOME ANALYSIS; GRAPE; NONHUMAN; NUCLEOTIDE SEQUENCE; PLANT GENETICS; PROTEIN FAMILY; TRANSPOSON; UNINDEXED SEQUENCE; BIOLOGICAL MODEL; CROSS BREEDING; GENETIC POLYMORPHISM; MUTATION; NUCLEOTIDE REPEAT; PHYLOGENY; PHYSIOLOGY; PLANT GENE; PLANT GENOME; POLYMERASE CHAIN REACTION; STATISTICAL MODEL;

VITIS;

CROSSES, GENETIC; DNA TRANSPOSABLE ELEMENTS; EXPRESSED SEQUENCE TAGS; GENES, PLANT; GENETIC VARIATION; GENOME, PLANT; LIKELIHOOD FUNCTIONS; MODELS, GENETIC; MUTATION; PHYLOGENY; POLYMERASE CHAIN REACTION; POLYMORPHISM, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; VITIS;

EID: 52349120967     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0003107     Document Type: Article

References (56)

1. Levadoux L (1956) Les populations sauvages el cultivées de Vitis vinifera L. Ann Amélior Plant 6: 59-117.
2. Arroyo-Garcia R, Ruiz-Garcia L, Bolling L, Ocete R, Lopez MA, et al. (2006) Multiple origins of cultivated grapevine (Vitis vinifera L. ssp. saliva) based on chloroplast DNA polymorphisms. Molecular Ecology 15: 3707-3714.
3. This P, Lacombe T, Thomas MR (2006) Historical origins and genetic diversity of wine grapes. Trends in Genetics 22: 511-519.
4. Forneck A (2005) Plant Breeding: Clonality - A concept for stability and variability during vegetative propagation. In: Esser ULK, Beyschlag W, Murata J, eds. Progress in Botany. Heidelberg, Germany: Springer Berlin, pp 165-183.
5. Franks T, Botta R, Thomas MR, Franks J (2002) Chimerism in grapevines: implications for cultivar identity, ancestry and genetic improvement TAG Theoretical and Applied Genetics 104: 192-199.
6. Le Q, Melayah D, Bonnivard E, Petit M, Grandbastien M (2007) Distribution dynamics of the Tntl retrotransposon in tobacco. Molecular Genetics and Genomics 278: 1617-4615.
7. Kobayashi S, Goto-Yamamoto N, Hirochika H (2004) Retrotransposon-Induced Mutations in Grape Skin Color. Science 304: 982-.
8. Lijavetzky D, Ruiz-García L, Cabezas J, De Andrés M, Bravo G, et al. (2006) Molecular genetics of berry colour variation in table grape. Molecular Genetics and Genomics 276: 427-435.
9. Walker A, Lee E, Bogs J, McDavid D, Thomas M, et al. (2007) White grapes arose through the mutation of two similar and adjacent regulatory genes. The Plant Journal 49: 772-785.
10. Pelsy F, Merdinoglu D (2002) Complete sequence of Tvvl, a family of Tyl copia-like retrotransposons of Vitis vinifera L, reconstituted by chromosome walking. TAG Theoretical and Applied Genetics 105: 614-621.
11. Verriès C, Bes C, This P, Tesnière C (2000) Cloning and characterization of Vine-1, a LTR-retrotransposon-like element in Vitis vinifera L., and other Vitis species. Genome 43: 366-376.
12. Jaillon O, Aury JM, Noel B, Policriti A, Clepet C, et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature 449: 463-467.
13. Velasco R, Zharkikh A, Troggio M, Cartwright D, Cestaro A, et al. (2007) A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety. PLoS ONE 2: e1326.
14. Feschotte C, Pritham EJ (2007) DNA Transposons and the Evolution of Eukaryotic Genomes. Annual Review of Genetics 41: 331-368.
15. Guynet C, Hickman AB, Barabas O, Dyda F, Chandler M, et al. (2008) In Vitro Reconstitution of a Single-Stranded Transposition Mechanism of IS608. Molecular Cell 29: 302-312.
16. Barabas O, Ronning DR, Guynet C, Hickman AB, Ton-Hoang B, et al. (2008) Mechanism of IS200/IS605 Family DNA Transposases: Activation and Transposon-Directed Target Site Selection. Cell 132: 208-220.
17. Wicker T, Sabol F, Hua-Van A, Bennetzen JL, Capy P, et al. (2007) A unified classification system for eukaryotic transposable elements. Nat Rev Genet 8: 973-982.
18. Feschotte C, Osterlund MT, Peeler R, Wessler SR (2005) DNA-binding specificity of rice mariner-like transposases and interactions with Stowaway MITEs. Nucl Acids Res 33: 2153-2165.
19. Rubin E, Lithwick G, Levy AA (2001) Structure and Evolution of the hAT Transposon Superfamily. Genetics 158: 949-957.
20. Zhang X, Wessler SR (2004) Genome-wide comparative analysis of the transposable elements in the related species Arabidopsis thaliana and Brassica oleracea. Proceedings of the National Academy of Sciences 101: 5589-5594.
21. Wicker T, Guyot R, Yahiaoui N, Keller B (2003) CACTA Transposons in Triticeae. A Diverse Family of High-Copy Repetitive Elements. Plant Physiol 132: 52-63.
22. Miura A, Kato M, Watanabe K, Kawabe A, Kotani H, et al. (2004) Genomic localization of endogenous mobile CACTA family transposons in natural variants of Arabidopsis thaliana. Molecular Genetics and Genomics 270: 524-532.
23. Robertson D (1978) Characterization of a mutator system in maize. Mutant Research 51: 21-28.
24. Lisch D (2002) Mutator transposons. Trends in Plant Science 7: 498-504.
25. Holligan D, Zhang X, Jiang N, Pritham EJ, Wessler SR (2006) The Transposable Element Landscape of the Model Legume Lotus japonicus. Genetics 174: 2215-2228.
26. Juretic N, Hoen DR, Huynh ML, Harrison PM, Bureau TE (2005) The evolutionary fate of MULE-medialed duplications of host gene fragments in rice. Genome Res 15: 1292-1297.
27. Turcotte K, Srinivasan S, Bureau T (2001) Survey of transposable elements from rice genomic sequences. The Plant Journal 25: 169-179.
28. Xu Z, Yan X, Maurais S, Fu H, O'Brien DG, et al. (2004) Jittery, a Mutator Distant Relative with a Paradoxical Mobile Behavior: Excision without Reinsertion. Plant Cell 16: 1105-1114.
29. Chalvet F, Grimaldi C, Kaper F, Langin T, Daboussi M-J (2003) Hop, an Active Mutator-like Element in the Genome of the Fungus Fusarium oxysporum. Mol Biol Evol 20: 1362-1375.
30. Le QH, Wright S, Yu Z, Bureau T (2000) Transposon diversity in Arabidopsis thaliana. Proceedings of the National Academy of Sciences 97: 7376-7381.
31. Hoen DR, Park KC, Elrouby N, Yu Z, Mohabir N, et al. (2006) Transposon-Mediated Expansion and Diversification of a Family of ULP-like Genes. Mol Biol Evol, 23: 1254-1268.
32. Zhang X, Jiang N, Feschotte C, Wessler SR (2004) PIF- and Pong-Like Transposable Elements: Distribution, Evolution and Relationship With Tourist-Like Miniature Inverted-Repeat Transposable Elements. Genetics 166: 971-986.
33. Casola C, Lawing AM, Betran E, Feschotte C (2007) PIF-like Transposons are Common in Drosophila and Have Been Repeatedly Domesticated to Generate New Host Genes. Mol Biol Evol 24: 1872-1888.
34. Kapitonov W, Jurka J (2004) Harbinger Transposons and an Ancient HARBI1 Gene Derived from a Transposase. DNA and Cell Biology 23: 311-324.
35. Zabala G, Vodkin L (2007) Novel exon combinations generated by alternative splicing Of gene fragments mobilized by a CACTA transposon in Glycine max. BMC Plant Biology 7: 38.
36. Jiang N, Bao Z, Zhang X, Eddy SR, Wessler SR (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature 431: 569-573.
37. Yu Z, Wright SI, Bureau TE (2000) Mutalor-like Elements in Arabidopsis thaliana: Structure, Diversity and Evolution, Genetics 156: 2019-2031.
38. van Leeuwen H, Monfort A, Puigdomenech P (2007) Mutator -like elements identified in melon, Arabidopsis and rice contain ULP1 protease domains. Molecular Genetics and Genomics 277: 357-364.
39. Kawasaki S, Nitasaka E (2004) Characterization of Tpn1 Family in the Japanese Morning Glory: En/Spm-related Transposable Elements Capturing Host Genes. Plant Cell Physiol 45: 933-944.
40. Zabala G, Vodkin LO (2005) The wp Mutation of Glycine max Carries a Gene-Fragment-Rich Transposon of the CACTA Superfamily. Plant Cell 17: 2619-2632.
41. Volff J-N (2006) Turning junk into gold: domestication of transposable elements and the creation of new genes in eukaryotes. BioEssays 28: 913-922.
42. Hudson ME, Lisch DR, Quail PH (2003) The FHY3 and FAR1 genes encode transposase-related proteins involved in regulation of gene expression by the phytochrome A-signaling pathway. The Plant Journal 34: 453-471.
43. Lin R, Ding L, Casola C, Ripoll DR, Feschotte C, et al. (2007) Transposase-Derived Transcription Factors Regulate Light Signaling in Arabidopsis. Science 318: 1302-1305.
44. Bundock P, Hooykaas P (2005) An Arabidopsis hAT-like transposase is essential for plant development. Nature 436: 282-284.
45. Cowan RK, Hoen DR, Schoen DJ, Bureau TE (2005) MUSTANG Is a Novel Family of Domesticated Transposase Genes Found in Diverse Angiosperms. Mol Biol Evol 22: 2084-2089.
46. Muehlbauer G, Bhau B, Syed N, Heinen S, Cho S, et al. (2006) A hAT superfamily transposase recruited by the cereal grass genome. Molecular Genetics and Genomics 275: 553-563.
47. Saccaro JNL, Van Sluys M-A, de Mello Varani A, Rossi M (2007) MudrA-like sequences from rice and sugarcane cluster as two bona fide transposon clades and two domesticated transposases. Gene 392: 117-125.
48. Altschul SF GW, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
49. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
50. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucl Acids Symp Ser 41: 95-98.
51. Guindon S, Lethiec F, Duroux P, Gascuel O (2005) PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucl Acids Res 33: W557-559.
52. Kempken F, Windhofer F (2001) The hAT family: a versatile transposon group common to plants, fungi, animals, and man. Chromosoma 110: 1-9.
53. Jurka J (2005) MuDR2_OS: MuDR-type DNA transposon from rice. Repbase Reports 5: 201-201.
54. Kapilonov V, Jurka J (1999) Molecular paleontology of transposable elements from Arabidopsis thaliana. Genetica 107: 27-37.
55. Jurka J (2005) OSHOOTER: EnSpm-type DNA transposon from rice. Repbase Reports 5: 205.
56. Kumar S, Tamura K, Nei M (2004) MEGA3: Integrated software for Molecular Evolutionary Genetics Analysis and sequence alignment. Briefings in Bioinformatics 5: 150-163.