Syntenic relationships between Medicago truncatula and Arabidopsis reveal extensive divergence of genome organization

Plant Physiology

Volumn 131, Issue 3, 2003, Pages 1018-1026

  Zhu, Hongyan ^a   Kim, Dong Jin ^a   Baek, Jong Min ^a   Choi, Hong Kyu ^a   Ellis, Leland C ^b   Küester, Helge ^c   McCombie, W Richard ^d   Peng, Hui Mei ^b   Cook, Douglas R ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b TEXAS A AND M UNIVERSITY   (United States)

^c BIELEFELD UNIVERSITY   (Germany)

^d Howard Hughes Medical Institute Cold Spring Harbor Laboratory Cold Spring Harbor   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BACTERIA; BIODIVERSITY; GENES; MAPPING;

ARABIDOPSIS;

PLANT CELL CULTURE;

ARABIDOPSIS; BACTERIA (MICROORGANISMS); EMBRYOPHYTA; MEDICAGO; MEDICAGO TRUNCATULA; ROSIDAE;

EID: 0037355428     PISSN: 00320889     EISSN: None     Source Type: Journal    
DOI: 10.1104/pp.102.016436     Document Type: Article

References (42)

1. Acarkan A, Rossberg M, Koch M, Schmidt R (2000) Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella. Plant J 23: 55-62
2. 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
3. Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796-815
4. Bancroft I (2001) Duplicate and diverge: the evolution of plant genome microstructure. Trends Genet 17: 89-93
5. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12: 1021-1029
6. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12: 1093-1101
7. Burge C, Karlin S (1997) Prediction of complete gene structures in human genomic DNA. J Mol Biol 268: 78-94
8. Cook DR (1999) Medicago truncatula: a model in the making! Curr Opin Plant Biol 2: 301-304
9. Devos KM, Beales J, Nagamura Y, Sasaki T (1999) Arabidopsis-rice: Will colinearity allow gene prediction across the eudicot-monocot divide? Genome Res 9: 825-829
10. Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12: 636-646
11. Endre G, Kereszt A, Kevei Z, Mihacea S, Kalo P, Kiss GB (2002) A receptor kinase gene regulating symbiotic nodule development. Nature 417: 962-966
12. Bwing B, Hillier L, Wendl MC, Green P (1998) Base-calling of automated sequencer traces using phred: I. Accuracy assessment. Genome Res 8: 175-185
13. Foster-Hartnett D, Mudge J, Larsen D, Yan H, Denny R, Penuela S, Young ND (2002) Comparative genomic analysis of sequences sampled from a small region on soybean (Glycine max) molecular linkage group G. Genome 45: 634-645
14. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95: 1971-1974
15. Gamas P, Nieble FC, Lescure N, Cullimore J (1996) Use of a subtractive hybridization approach to identify new Medicago truncatula genes induced during root nodule development. Mol Plant-Microbe Interact 9: 233-242
16. Gordon D, Abajian (2, Green P (1998) Consed: a graphical tool for sequence finishing. Genome Res 8: 195-202
17. Grant D, Cregan P, Shoemaker RC (2000) Genome organization in dicots: genome duplication in Arabidopsis and synteny between soybean and Arabidopsis. Proc Natl Acad Sci USA 97: 4168-4173
18. Kowalski SP, Lan T-H, Feldmann KA, Paterson AH (1994) Comparative mapping of Arabidopsis thaliana and Brassica oleracea chromosomes reveals islands of conserved organization. Genetics 138: 499-510
19. Ku H-M, 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
20. Kumar S, Tamura K, Jakobsen IB, Nei M (2001) MEGA2: molecular evolutionary genetic analysis software. Bioinformatics 17: 1244-1245
21. Lagercrantz U (1998) Comparative mapping between Arabidopsis thaliana and Brassica napus indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusion and frequent rearrangements. Genetics 150: 1217-1228
22. Lagercrantz U, Lydiate DJ (1996) Comparative genome mapping in Brassica. Genetics 144: 1903-1910
23. Lee Y, Sultana R, Pertea G, Cho J, Karamycheva S, Tsai J, Parvizi B, Cheung F, Antonescu V, White J et al. (2002) Cross-referencing eukaryotic genomes: TIGR orthologous gene alignments (TOGA). Genome Res 12: 493-502
24. Leister D, Kurth J, Laurie DA, Yano M, Sasaki T, Devos K, Graner A, Schulze-Lefert P (1998) Rapid reorganization of resistance gene homologues in cereal genomes. Proc Natl Acad Sci USA 95: 370-375
25. Liu H, Sachidanandam R, Stein L (2001) Comparative genomics between rice and Arabidopsis shows scant collinearity in gene order. Genome Res 11: 2020-2026
26. Lukashin AV, Borodovsky M (1998) GeneMark. hmm: new solutions for gene finding. Nucleic Acids Res 26: 1107-1115
27. Mayer K, Murphy G, Tarchini R, Wambutt R, Volckaert G, Pohl T, Dusterhoft A, Stiekema W, Entian KD, Terryn N et al. (2001) Conservation of microstructure between a sequenced region of the genome of rice and multiple segments of the genome of Arabidopsis thaliana. Genome Res 11: 1167-1174
28. Menacio-Hautea D, Fatokum CA, Kumar L, Danesh D, Young ND (1993) Comparative genome analysis of mungbean (Vigna radiata L. Wilczek) and cowpea (V. unguiculata) using RFLP analysis. Theor Appl Genet 86: 797-810
29. Nam Y, Penmetsa RV, Endre G, Uribe P, Kim D, Cook DR (1999) Construction of a bacterial artificial chromosome library of Medicago truncatula and identification of clones containing ethylene-response genes. Theor Appl Genet 98: 638-646
30. O'Neill CM, Bancroft I (2000) Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homeologous to sequenced regions of chromosomes 4 and 5 of Arabfdopsis thaliana. Plant J 23: 233-243
31. Parniske M, Hammond-Kosack KE, Golstein C, Thomas CM, Jones DA, Harrison K, Wulff BB, Jones JD (1997) Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus of tomato. Cell 91: 821-832
32. Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang CX, Katsar CS, Lan TH, Lin YR, Ming R et al. (2000) Comparative genomics of plant chromosomes. Plant Cell 12: 1523-1540
33. Paterson AH, Lan TH, Reischmann KP, Chang C, Lin YR, Liu SC, Burow MD, Kowalski SP, Katsar CS, DelMonte TA et al. (1996) Toward a unified genetic map of higher plants, transcending the monocot-dicot divergence. Nat Genet 14: 380-382
34. Paterson AH, Lin Y-R, Li Z, Scherta KF, Doebley JF, Pinson SRM, Liu S-C, Stensel JW, Irvine JE (1995) Convergent domestication of cereal crops by independent mutations at corresponding genetic loci. Science 269: 1714-1717
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. Stracke S, Kistner C, Yoshida S, Mulder L, Sato S, Kaneko T, Tabata S, Sandal N, Stougaard J, Szczyglowski K et al. (2002) A plant receptor-like kinase required for both bacterial and fungal symbiosis. Nature 417: 959-962
37. Tanksley SD, Ganal MW, Prince JP, de Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132: 1141-1160
38. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence aligmnent aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882
39. Tortes AM, Weeden NF, Martin A (1993) Linkage among isozyme, RFLP, and RAPD markers in Vicia faba. Theor Appl Genet 85: 937-945
40. van Dodeweerd AM, Hall CR, Bent EG, Johnson SJ, Bevan MW, Bancroft I (1999) Identification and analysis of homoeologous segments of the genomes of rice and Arabidopsis thaliana. Genome 42: 887-892
41. Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117
42. Weeden NL, Muehlbauer FJ, Ladizinsky G (1992) Extensive conservation of linkage relationships between pea and lentil genetic maps. J Hered 83: 123-129