Genome organization of the tomato sun locus and characterization of the unusual retrotransposon Rider

Plant Journal

Volumn 60, Issue 1, 2009, Pages 181-193

  Jiang, Ning ^a   Gao, Dongying ^a,c   Xiao, Han ^b   Van Der Knaap, Esther ^b  

^a MICHIGAN STATE UNIVERSITY   (United States)

^b OHIO STATE UNIVERSITY   (United States)

^c Purdue University ^*  (United States)

Author keywords

Evolution; Genome structure; Rider; Tomato; Transposons

Indexed keywords

PLANT DNA;

ARTICLE; COMPARATIVE GENOMIC HYBRIDIZATION; DNA BASE COMPOSITION; DNA SEQUENCE; GENETIC POLYMORPHISM; GENETICS; MOLECULAR EVOLUTION; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; PLANT GENE; PLANT GENOME; RETROPOSON; SEQUENCE ALIGNMENT; TOMATO;

BASE COMPOSITION; BASE SEQUENCE; COMPARATIVE GENOMIC HYBRIDIZATION; CONSERVED SEQUENCE; DNA, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; LYCOPERSICON ESCULENTUM; MOLECULAR SEQUENCE DATA; POLYMORPHISM, GENETIC; RETROELEMENTS; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA;

LYCOPERSICON; LYCOPERSICON ESCULENTUM; SOLANUM;

EID: 70349515979     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2009.03946.x     Document Type: Article

References (44)

1. Bennetzen, J.L. (1996) The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol. 4, 347 353.
2. Bernatzky, R. Tanksley, S.D. (1986) Toward a saturated linkage map in tomato based on isozymes and random cDNA sequences. Genetics, 112, 887 898.
3. Bureau, T.E., White, S.E. Wessler, S.R. (1994) Transduction of a cellular gene by a plant retroelement. Cell, 77, 479 480.
4. Casa, A.M., Brouwer, C., Nagel, A., Wang, L., Zhang, Q., Kresovich, S. Wessler, S.R. (2000) Inaugural article: the MITE family heartbreaker (Hbr): molecular markers in maize. Proc. Natl Acad. Sci. USA, 97, 10083 10089.
5. Cheng, X., Zhang, D., Cheng, Z., Keller, B. Ling, H.-Q. (2009) A new family of Ty1-copia-like retrotransposon originated in the tomato genomes by a recent horizontal transfer event. Genetics, 181, 1183 1193.
6. Datema, E., Mueller, L.A., Buels, R., Giovannoni, J.J., Visser, R.G., Stiekema, W.J. van Ham, R.C. (2008) Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato. BMC Plant Biol. 8, 34.
7. Doebley, J., Stec, A. Hubbard, L. (1997) The evolution of apical dominance in maize. Nature, 386, 485 488.
8. Feschotte, C., Jiang, N. Wessler, S.R. (2002) Plant transposable elements: where genetics meets genomics. Nat. Rev. Genet. 3, 329 341.
9. Frary, A., Nesbitt, T.C., Grandillo, S., van der Knaap, E., Cong, B., Liu, J., Meller, J., Elber, R., Alpert, K.B. Tanksley, S.D. (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science, 289, 85 88.
10. Fray, R.G. Grierson, D. (1993) Identification and genetic analysis of normal and mutant phytoene synthase genes of tomato by sequencing, complementation and co-suppression. Plant Mol. Biol. 22, 589 602.
11. Fridman, E., Carrari, F., Liu, Y.S., Fernie, A.R. Zamir, D. (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science, 305, 1786 1789.
12. Fu, H. Dooner, H.K. (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl Acad. Sci. USA, 99, 9573 9578.
13. Fulton, T.M., Chunwongse, J. Tanksley, S.D. (1995) Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Mol. Biol. Rep. 13, 207 209.
14. Grandbastien, M.A., Spielmann, A. Caboche, M. (1989) Tnt1, a mobile retroviral-like transposable element of tobacco isolated by plant cell genetics. Nature, 337, 376 380.
15. Hirochika, H., Sugimoto, K., Otsuki, Y., Tsugawa, H. Kanda, M. (1996) Retrotransposons of rice involved in mutations induced by tissue culture. Proc. Natl Acad. Sci. USA, 93, 7783 7788.
16. Huang, X., Lu, G., Zhao, Q., Liu, X. Han, B. (2008) Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice. Plant Physiol. 148, 25 40.
17. Jiang, N., Bao, Z., Zhang, X., Eddy, S.R. Wessler, S.R. (2004) Pack-MULE transposable elements mediate gene evolution in plants. Nature, 431, 569 573.
18. Jin, Y.K. Bennetzen, J.L. (1994) Integration and nonrandom mutation of a plasma membrane proton ATPase gene fragment within the Bs1 retroelement of maize. Plant Cell, 6, 1177 1186.
19. Juretic, N., Hoen, D.R., Huynh, M.L., Harrison, P.M. Bureau, T.E. (2005) The evolutionary fate of MULE-mediated duplications of host gene fragments in rice. Genome Res. 15, 1292 1297.
20. Kidd, J.M., Cooper, G.M., Donahue, W.F. et al. (2008) Mapping and sequencing of structural variation from eight human genomes. Nature, 453, 56 64.
21. Lewin, B. (2008) Genes IX, 9th edn. Sudbury, MA : Jones and Bartlett Publishers.
22. Ling, H.Q., Bauer, P., Bereczky, Z., Keller, B. Ganal, M. (2002) The tomato fer gene encoding a bHLH protein controls iron-uptake responses in roots. Proc. Natl Acad. Sci. USA, 99, 13938 13943.
23. Liu, J., Van Eck, J., Cong, B. Tanksley, S.D. (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc. Natl Acad. Sci. USA, 99, 13302 13306.
24. Ma, J., Devos, K.M. Bennetzen, J.L. (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res. 14, 860 869.
25. McCarroll, S.A. Altshuler, D.M. (2007) Copy-number variation and association studies of human disease. Nat. Genet. 39, S37 S42.
26. Miyao, A., Tanaka, K., Murata, K., Sawaki, H., Takeda, S., Abe, K., Shinozuka, Y., Onosato, K. Hirochika, H. (2003) Target site specificity of the Tos17 retrotransposon shows a preference for insertion within genes and against insertion in retrotransposon-rich regions of the genome. Plant Cell, 15, 1771 1780.
27. Morgante, M., Brunner, S., Pea, G., Fengler, K., Zuccolo, A. Rafalski, A. (2005) Gene duplication and exon shuffling by helitron-like transposons generate intraspecies diversity in maize. Nat. Genet. 37, 997 1002.
28. Muse, S.V. (2000) Examining rates and patterns of nucleotide substitution in plants. Plant Mol. Biol. 42, 25 43.
29. Nesbitt, T.C. Tanksley, S.D. (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics, 162, 365 379.
30. Paran, I. van der Knaap, E. (2007) Genetic and molecular regulation of fruit and plant domestication traits in tomato and pepper. J. Exp. Bot. 58, 3841 3852.
31. Pickersgill, B. (2007) Domestication of plants in the Americas: insights from Mendelian and molecular genetics. Ann. Bot. 100, 925 940.
32. SanMiguel, P., Gaut, B.S., Tikhonov, A., Nakajima, Y. Bennetzen, J.L. (1998) The paleontology of intergene retrotransposons of maize. Nat. Genet. 20, 43 45.
33. Tam, S.M., Mhiri, C., Vogelaar, A., Kerkveld, M., Pearce, S.R. Grandbastien, M.A. (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor. Appl. Genet. 110, 819 831.
34. Temin, H.M. (1981) Structure, variation and synthesis of retrovirus long terminal repeat. Cell, 27, 1 3.
35. Van den Broeck, D., Maes, T., Sauer, M., Zethof, J., De Keukeleire, P., D'Hauw, M., Van Montagu, M. Gerats, T. (1998) Transposon display identifies individual transposable elements in high copy number lines. Plant J. 13, 121 129.
36. Van der Knaap, E., Sanyal, A., Jackson, S.A. Tanksley, S.D. (2004) High-resolution fine mapping and fluorescence in situ hybridization analysis of sun, a locus controlling tomato fruit shape, reveals a region of the tomato genome prone to DNA rearrangements. Genetics, 168, 2127 2140.
37. Wang, Y., van der Hoeven, R.S., Nielsen, R., Mueller, L.A. Tanksley, S.D. (2005) Characteristics of the tomato nuclear genome as determined by sequencing undermethylated EcoRI digested fragments. Theor. Appl. Genet. 112, 72 84.
38. Wang, W., Zheng, H., Fan, C. et al. (2006a) High rate of chimeric gene origination by retroposition in plant genomes. Plant Cell, 18, 1791 1802.
39. Wang, Y., Tang, X., Cheng, Z., Mueller, L., Giovannoni, J. Tanksley, S.D. (2006b) Euchromatin and pericentromeric heterochromatin: comparative composition in the tomato genome. Genetics, 172, 2529 2540.
40. Wang, Y., Diehl, A., Wu, F., Vrebalov, J., Giovannoni, J., Siepel, A. Tanksley, S.D. (2008) Sequencing and comparative analysis of a conserved syntenic segment in the Solanaceae. Genetics, 180, 391 408.
41. Wikstrom, N., Savolainen, V. Chase, M.W. (2001) Evolution of the angiosperms: calibrating the family tree. Proc. Biol. Sci. 268, 2211 2220.
42. Wu, F., Mueller, L.A., Crouzillat, D., Petiard, V. Tanksley, S.D. (2006) Combining bioinformatics and phylogenetics to identify large sets of single-copy orthologous genes (COSII) for comparative, evolutionary and systematic studies: a test case in the euasterid plant clade. Genetics, 174, 1407 1420.
43. Xiao, H., Jiang, N., Schaffner, E.K., Stockinger, E.J. Van der Knaap, E. (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science, 319, 1527 1530.
44. Zhu, W., Ouyang, S., Iovene, M., O'Brien, K., Vuong, H., Jiang, J. Buell, C.R. (2008) Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition. BMC Genomics, 9, 286.