Estimates of conserved microsynteny among the genomes of Glycine max, Medicago truncatula and Arabidopsis thaliana

Theoretical and Applied Genetics

Volumn 106, Issue 7, 2003, Pages 1256-1265

  Yan, H H ^a   Mudge, J ^a   Kim, D J ^b   Larsen, D ^a   Shoemaker, R C ^c   Cook, D R ^b   Young, N D ^a  

^a UNIVERSITY OF MINNESOTA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c IOWA STATE UNIVERSITY   (United States)

Author keywords

Evolution; Genome duplication; Glycine max; Medicago truncatula; Microsynteny

Indexed keywords

BACTERIA; CHROMOSOMES; GENES; PROBES;

HYBRIDIZATION;

GENETIC ENGINEERING;

ARABIDOPSIS; ARABIDOPSIS THALIANA; BACTERIA (MICROORGANISMS); EMBRYOPHYTA; GLYCINE MAX; MEDICAGO TRUNCATULA; STAPHYLOCOCCUS PHAGE 187;

EID: 0037777806     PISSN: 00405752     EISSN: None     Source Type: Journal    
DOI: 10.1007/s00122-002-1183-y     Document Type: Article

References (34)

1. Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcolinearity and its many exceptions. Plant Cell 12:1021-1029
2. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12:1093-1101
3. Burr B, Burr R, Thompson K, Albertson M, Stuber C (1988) Gene mapping with recombinant inbreds in maize. Genetics 118:519-526
4. Cavell AC, Lydiate DJ, Parkin IAP, Dean C, Trick M (1998) Colinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome 41:62-69
5. Chen M, SanMiguel P, de Oliveira AC, Woo S-S, Zhang H, Wing RA, Bennetzen JL (1997) Microcolinearity in sh2-homologous regions of the maize, rice and sorghum genomes. Proc Natl Acad Sci USA 94:3431-3435
6. Chen M, SanMiguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/ a1-homologous regions of sorghum and rice. Genetics 148:435-443
7. Cook DR (1999) Medicago truncatula - a model in the making. Curr Opin Plant Biol 2:301-304
8. Cook DR, VandenBosch K, de Bruijn FJ, Huguet T (1997) Model legumes get the nod. Plant Cell 9:275-280
9. Danesh D, Penuela S, Mudge J, Denny RL, Nordstrom H, Martinez JP, Young ND (1998) A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistance gene. Theor Appl Genet 96:196-202
10. Devos KM, Gale MD (2000) Genome relationships: the grass model in current research. Plant Cell 12:637-646
11. 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
12. Endre G, Kereszt A, Kevei Z, Mihacea S, Kaló P, Kiss GB (2002) A receptor kinase gene regulating symbiotic nodule development. Nature 417:962-966
13. Gale MD, Devos KM (1998) Plant comparative genetics after 10 years. Science 282:656-659
14. Gualtieri G, Kulikova O, Limpens E, Kim DJ, Cook DR, Bisseling T, Geurts R (2002) Microsynteny between pea and Medicago truncatula in the SYM2 region. Plant Mol Biol 50:225-235
15. Gaut BS, Doebley JF (1997) DNA sequence evidence for the segmental allotetraploid origin of maize. Proc Natl Acad Sci USA 94:6809-6814
16. 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
17. Jackson SA, Cheng Z, Wang ML, Goodman HM, Jiang J (2000) Comparative fluorescence in situ hybridization mapping of a 431-kb Arabidopsis thaliana bacterial artificial chromosome contig reveals the role of chromosomal duplications in the expansion of the Brassica rapa genome. Genetics 156:833-838
18. Keim P, Diers B, Olson T, Shoemaker RC (1990) RFLP mapping in soybean: association between marker loci and variation in quantitative traits. Genetics 126:735-742
19. Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5:246-251
20. 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 systeny. Proc Natl Acad Sci USA 97:9121-9126
21. Kulikova O, Gualtieri G, Geurts R, Kim DJ, Cook DR, 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
22. Lagercrantz U (1998) Comparative mapping between Arabidopsis thaliana and Brassica nigra indicates that Brassica genomes have evolved through extensive genome replication accompanied by chromosome fusions and frequent rearrangements. Genetics 150:1217-1228
23. Marek LF, Shoemaker RC (1997) BAC contig development by fingerprint analysis in soybean. Genome 40:420-427
24. Marek LF, Mudge J, Darnielle L, Grant D, Hanson N, Paz M, Yan H, Denny R, Larson K, Foster-Hartnett D, Cooper A, Danesh D, Larsen D, Schmidt T, Staggs R, Crow JA, Retzel E, Young ND, Shoemaker RC (2001) Soybean genomic survey: BAC-end sequences near RFLP and SSR markers. Genome 44:572-581
25. Marra MA, Kucaba TA, Dietrich NL, Green ED, Brownstein B, Wilson RK, McDonald KM, Hillier LW, McPherson JD, Waterston RH (1997) High throughput fingerprint analysis of large-insert clones. Genome Res 7:1072-1084
26. Mayer K, Murphy G, Tarchini R, Wambutt R, Volckaert G, Pohl T, Dusterhoft A, Stiekema W, Entian KD, Terryn N, Lemcke K, Haase D, Hall CR, van Dodeweerd AM, Tingey SV, Mewes HW, Bevan MW, Bancroft I (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
27. Nam Y-W, 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
28. Shoemaker RC, Polzin K, Labate J, Specht J, Brummer EC, Olson T, Young N, Concibido V, Wilcox J, Tamulonis JP, Kochert G, Boerma HR (1996) Genome duplication in soybean (Glycine subgenus soja). Genetics 144:329-338
29. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A (2000) The complete sequence of 340 kb of DNA around the rice adh1-adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12:381-391
30. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796-815
31. Tikhonov AP, SanMiguel PJ, Nakajima Y, Gorenstein NM, Bennetzen JL, Avramova Z (1999) Colinearity and its exceptions in orthologous adh regions of maize and sorghum. Proc Natl Acad Sci USA 96:7409-7414
32. Van Dodeweerd A-M, 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
33. Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290:2114-2117
34. Wong GKS, Yu J, Thayer EC, Olson MV (1997) Multiple-complete-digest restriction fragment mapping: generating sequence-ready maps for large-scale DNA sequencing. Proc Natl Acad Sci USA 94:5225-5230