Complex organization and evolution of the tomato pericentromeric region at the FER gene locus

Plant Physiology

Volumn 138, Issue 3, 2005, Pages 1205-1215

  Guyot, Romain ^a   Cheng, Xudong ^b   Su, Yan ^b   Cheng, Zhukuan ^b   Schlagenhauf, Edith ^a   Keller, Beat ^a   Ling, Hong Qing ^a,b  

^a UNIVERSITY OF ZURICH   (Switzerland)

^b INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

CROPS; GENES; MOLECULAR BIOLOGY; MOLECULAR STRUCTURE;

GENOME DUPLICATION; GENOME SEQUENCING; TRANSPOSABLE ELEMENTS (TE);

PLANTS (BOTANY);

GENES; MOLECULAR STRUCTURE; PLANTS;

ARABIDOPSIS; ARABIDOPSIS THALIANA; LYCOPERSICON ESCULENTUM; TRITICEAE; UNCLASSIFIED ORGANISMS; ZEA MAYS;

VEGETABLE PROTEIN;

ARTICLE; CENTROMERE; CHROMOSOME MAP; FLUORESCENCE IN SITU HYBRIDIZATION; GENE; GENETICS; GENOME; METHODOLOGY; MOLECULAR EVOLUTION; PLANT CHROMOSOME; PSEUDOGENE; TOMATO;

CENTROMERE; CHROMOSOME MAPPING; CHROMOSOMES, PLANT; EVOLUTION, MOLECULAR; GENES, PLANT; GENOME, PLANT; IN SITU HYBRIDIZATION, FLUORESCENCE; LYCOPERSICON ESCULENTUM; PLANT PROTEINS; PSEUDOGENES;

EID: 27244458110     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.104.058099     Document Type: Article

References (55)

1. Altschul SF, Madden TL, Schaffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389-3402
2. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208-218
3. Barton DW (1950) Pachytene morphology of the tomato chromosome complement. Am J Bot 37: 639-643
4. Blanc G, Hokamp K, Wolfe KH (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res 13: 137-144
5. Brown SW (1949) The structure and meiotic behavior of the differentiated chromosomes of tomato. Genetics 34: 437-461
6. Budiman MA, Chang SB, Lee S, Yang TJ, Zhang HB, de Jong H, Wing RA (2004) Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theor Appl Genet 108: 190-196
7. Budiman MA, Mao L, Wood TC, Wing RA (2000) A deep-coverage tomato BAC library and prospects toward development of an STC framework for genome sequencing. Genome Res 10: 129-136
8. Cannon SB, Kozik A, Chan B, Michelmore R, Young ND (2003) Diag-Hunter and GenoPix2D: programs for genomic comparisons, large-scale homology discovery and visualization. Genome Biol 4: R68
9. Copenhaver GP, Nickel K, Kuromori T, Benito MI, Kaul S, Lin X, Bevan M, Murphy G, Harris B, Parnell LD, et al (1999) Genetic definition and sequence analysis of Arabidopsis centromeres. Science 286: 2468-2474
10. Devos KM, Brown JK, Bennetzen JL (2002) Genome size reduction through illegitimate recombination counteracts genome expansion in Arabidopsis. Genome Res 12: 1075-1079
11. Ewing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 8: 175-185
12. Feschotte C, Mouches C (2000) Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon. Mol Biol Evol 17: 730-737
13. Hoskins RA, Smith CD, Carlson JW, Carvalho AB, Halpern A, Kaminker JS, Kennedy C, Mungall CJ, Sullivan BA, Sutton GG, et al (2002) Heterochromatic sequences in a Drosophila whole-genome shotgun assembly. Genome Biol 3: RESEARCH0085
14. Jiang J, Gill BS, Wang GL, Ronald PC, Ward DC (1995) Metaphase and interphase fluorescence in situ hybridization mapping of the rice genome with bacterial artificial chromosomes. Proc Natl Acad Sci USA 92: 4487-4491
15. Ku HM, Vision T, Liu J, Tanksley SD (2000) Comparing sequenced segments of the tomato and Arabidopsis genomes: large-scale duplication followed by selective gene loss creates a network of synteny. Proc Natl Acad Sci USA 97: 9121-9126
16. Kulikova O, Gualtieri G, Geurts R, Kim DJ, Cook D, Huguet T, de Jong JH, Fransz PF, Bisseling T (2001) Integration of the FISH pachytene and genetic maps of Medicago truncatula. Plant J 27: 49-58
17. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532
18. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetics analysis software. Bioinformatics 17: 1244-1245
19. Li L, Cheng X, Ling H-Q (2004) Isolation and characterization of Fe(III)-chelate reductase gene LeFRO1 in tomato. Plant Mol Biol 54: 125-136
20. 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
21. Ling H-Q, Pich A, Scholz G, Ganal MW (1996) Genetic analysis of two tomato mutants affected in the regulation of iron metabolism. Mol Gen Genet 252: 87-92
22. Ma J, Devos KM, Bennetzen JL (2004) Analyses of LTR-retrotransposon structures reveal recent and rapid genomic DNA loss in rice. Genome Res 14: 860-869
23. Mao L, Begum D, Goff SA, Wing RA (2001) Sequence and analysis of the tomato JOINTLESS locus. Plant Physiol 126: 1331-1340
24. Messeguer R, Ganal MW, Steffens JC, Tanksley SD (1991) Characterization of the level, target sites and inheritance of cytosine methylation in tomato nuclear DNA. Plant Mol Biol 16: 753-770
25. Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P, Williamson VM (1998) The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell 10: 1307-1319
26. Moniz de Sa M, Drouin G (1996) Phylogeny and substitution rates of angiosperm actin genes. Mol Biol Evol 13: 1198-1212
27. Motoyoshi F, Ohmori T, Murata M (1996) Molecular characterization of heterochromatic regions around the Tm-2 locus in chromosome 9 of tomato. Symp Soc Exp Biol 50: 65-70
28. Nagaki K, Cheng Z, Ouyang S, Talbert PB, Kim M, Jones KM, Henikoff S, Buell CR, Jiang J (2004) Sequencing of a rice centromere uncovers active genes. Nat Genet 6: 138-145
29. Oosumi T, Belknap WR (1997) Characterization of the Sol3 family of nonautonomous transposable elements in tomato and potato. J Mol Evol 45: 137-144
30. Oosumi T, Garlick B, Belknap WR (1995) Identification and characterization of putative transposable DNA elements in solanaceous plants and Caenorhabditis elegans. Proc Natl Acad Sci USA 92: 8886-8890
31. Peterson DG, Pearson WR, Stack SM (1998) Characterization of the tomato (Lycopersicon esculentum) genome using in vitro and in situ DNA reassociation. Genome 41: 346-356
32. Peterson DG, Price HJ, Johnston JS, Stack SM (1996) DNA of content of heterochromatin and euchromatin in tomato (Lycopersicon esculentum) pachytene chromosomes. Genome 39: 77-82
33. Pozueta-Romero J, Houlne G, Schantz R (1996) Nonautonomous inverted repeat Alien transposable elements are associated with genes of both monocotyledonous and dicotyledonous plants. Gene 171: 147-153
34. Rice P, Longden I, Bleasby A (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277
35. Rossberg M, Theres K, Acarkan A, Herrero R, Schmitt T, Schumacher K, Schmitz G, Schmidt R (2001) Comparative sequence analysis reveals extensive microcolinearity in the lateral suppressor regions of the tomato, Arabidopsis, and capsella genomes. Plant Cell 13: 979-988
36. Rubin E, Lithwick G, Levy AA (2001) Structure and evolution of the hAT transposon superfamily. Genetics 158: 949-957
37. Rutherford K, Parkhill J, Crook J, Horsnell T, Rice P, Rajandream MA, Barrell B (2000) Artemis: sequence visualization and annotation. Bioinformatics 16: 944-945
38. SanMiguel P, Gaut BS, Tikhonov A, Nakajima Y, Bennetzen JL (1998) The paleontology of intergene retrotransposons of maize. Nat Genet 20: 43-45
39. Shiu OY, Oetiker JH, Yip WK, Yang SF (1998) Promoter of LE-ACS7 an early flooding-induced 1-aminocyclopropane-1-carboxylate synthase gene of the tomato is tagged by a Sol3 transposon. Proc Natl Acad Sci USA 95: 10334-10339
40. Simillion C, Vandepoele K, Van Montagu MC, Zabeau M, Van de Peer Y (2002) The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 99: 13627-13632
41. Sonnhammer EL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167: GC1-10
42. Su PY, Brown TA (1997) Ty3/gypsy-like retrotransposon sequences in tomato. Plasmid 38: 148-157
43. Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB, et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160
44. van Daelen RA, Gerbens F, van Ruissen F, Aarts J, Hontelez J, Zabel P (1993) Long-range physical maps of two loci (Aps-1 and GP79) flanking the root-knot nematode resistance gene (Mi) near the centromere of tomato chromosome 6. Plant Mol Biol 23: 185-192
45. Van der Hoeven R, Ronning C, Giovannoni J, Martin G, Tanksley S (2002) Deductions about the number, organization, and evolution of genes in the tomato genome based on analysis of a large expressed sequence tag collection and selective genomic sequencing. Plant Cell 14: 1441-1456
46. Vicient CM, Suoniemi A, Anamthawat-Jonsson K, Tanskanen J, Beharav A, Nevo E, Schulman AH (1999) Retrotransposon BARE-1 and its role in genome evolution in the genus Hordeum. Plant Cell 11: 1769-1784
47. Weiler KS, Wakimoto BT (1995) Heterochromatin and gene expression in Drosophila. Annu Rev Genet 29: 577-605
48. Wessler SR (1998) Transposable elements associated with normal plant genes. Physiol Plant 103: 581-586
49. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (T. monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26: 307-316
50. Wicker T, Yahiaoui N, Guyot R, Schlagenhauf E, Liu ZD, Dubcovsky J, Keller B (2003) Rapid genome divergence at orthologous low molecular weight glutenin loci of the A and Am genomes of wheat. Plant Cell 15: 1186-1197
51. Witte CP, Le QH, Bureau T, Kumar A (2001) Terminal-repeat retrotransposons in miniature (TRIM) are involved in restructuring plant genomes. Proc Natl Acad Sci USA 98: 13778-13783
52. Wu HK (1967) Note on the preparing of pachytene chromosomes by double mordant. Scientific Agriculture 15: 40-44
53. Wu J, Yamagata H, Hayashi-Tsugane M, Hijishita S, Fujisawa M, Shibata M, Ho Y, Nakamura M, Sakaguchi M, Yoshihara R, et al (2004) Composition and structure of the centromeric region of rice chromosome 8. Plant Cell 16: 967-976
54. Yanez M, Verdugo I, Rodriguez M, Prat S, Ruiz-Lara S (1998) Highly heterogeneous families of Ty1/copia retrotransposons in the Lycopersicon chilense genome. Gene 222: 223-228
55. Zhang Y, Huang Y, Zhang L, Li Y, Lu T, Lu Y, Feng Q, Zhao Q, Cheng Z, Xue Y, et al (2004) Structural features of the rice chromosome 4 centromere. Nucleic Acids Res 32: 2023-2030