In silico comparative analysis reveals a mosaic conservation of genes within a novel colinear region in wheat chromosome 1AS and rice chromosome 5S

Functional and Integrative Genomics

Volumn 4, Issue 1, 2004, Pages 47-58

  Guyot, Romain ^a   Yahiaoui, Nabila ^a   Feuillet, Catherine ^a   Keller, Beat ^a  

^a Institute of Plant Biology   (Switzerland)

Author keywords

Colinearity; Genome evolution; Rice; Wheat

Indexed keywords

ARTICLE; CHROMOSOME 1; CHROMOSOME 1AS; CHROMOSOME 5; CHROMOSOME 5S; CHROMOSOME ANALYSIS; CHROMOSOME INVERSION; COMPARATIVE GENE MAPPING; COMPUTER MODEL; EXPRESSED SEQUENCE TAG; GENE AMPLIFICATION; GENE DELETION; GENE DISRUPTION; GENETIC CONSERVATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORTHOLOGY; PLANT GENETICS; PRIORITY JOURNAL; BIOLOGY; CHROMOSOME ABERRATION; GENETICS; GENOME; MOLECULAR EVOLUTION; MOSAICISM; PLANT CHROMOSOME; RICE; WHEAT;

POACEAE; TRITICUM AESTIVUM;

CHROMOSOME ABERRATIONS; CHROMOSOMES, PLANT; COMPUTATIONAL BIOLOGY; EVOLUTION, MOLECULAR; GENOME, PLANT; MOSAICISM; ORYZA SATIVA; TRITICUM;

EID: 4143116005     PISSN: 1438793X     EISSN: None     Source Type: Journal    
DOI: 10.1007/s10142-004-0103-4     Document Type: Article

References (47)

1. Ahn S, Anderson JA, Sorrells ME, Tanksley SD (1993) Homoeologous relationships of rice, wheat and maize chromosomes. Mol Gen Genet 241:483-490 1:CAS:528:DyaK2cXkt1yhuro%3D
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 9254694
3. Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208-218 1:CAS:528:DyaK38XhslSjurY%3D
4. Bennetzen JL, Ramakrishna W (2002) Numerous small rearrangements of gene content, order and orientation differentiate grass genomes. Plant Mol Biol 48:821-827 10.1023/A:1014841515249
5. Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12:1093-1101 1:CAS:528:DC%2BD3cXlslygtL0%3D
6. Brunner S, Keller B, Feuillet C (2003) A large rearrangement involving genes and low-copy DNA interrupts the microcolinearity between rice and barley at the Rph7 locus. Genetics 164:673-683 1:CAS:528:DC%2BD3sXlvFaisLY%3D
7. Cenci A, Chantret N, Kong X, Gu Y, Anderson OD, Fahima T, Distelfeld A, Dubcovsky J (2003) Construction and characterization of a half million clone BAC library of durum wheat (Triticum turgidum ssp. durum). Theor Appl Genet 107:931-939 10.1007/s00122-003-1331-z
8. Chen M, SanMiguel P, de Oliveira AC, Woo SS, 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 1:CAS:528:DyaK2sXisVKns7Y%3D
9. Chen M, SanMiguel P, Bennetzen JL (1998) Sequence organization and conservation in sh2/a1 -homologous regions of sorghum and rice. Genetics 148:435-443 1:CAS:528:DyaK1cXptVWjsg%3D%3D
10. m of Triticum monococcum and its recognition by the wheat Ph1 locus. Proc Natl Acad Sci USA 92:6645-6649 1:CAS:528:DyaK2MXmslOjsLY%3D
11. Dubcovsky J, Ramakrishna W, SanMiguel PJ, Busso CS, Yan L, Shiloff BA, Bennetzen JL (2001) Comparative sequence analysis of colinear barley and rice bacterial artificial chromosomes. Plant Physiol 125:1342-1353 1:CAS:528:DC%2BD3MXitFWrtLg%3D
12. Endo TR, Gill BS (1996) The deletion stocks of common wheat. J Hered 87:295-307 1:CAS:528:DyaK28Xls1Clt7s%3D
13. Feuillet C, Keller B (1999) High gene density is conserved at syntenic loci of small and large grass genomes. Proc Natl Acad Sci USA 96:8265-8270 1:CAS:528:DyaK1MXltVOrtr4%3D
14. Feuillet C, Keller B (2002) Comparative genomics in the grass family: molecular characterization of grass genome structure and evolution. Ann Bot (Lond) 89:3-10
15. Gale MD, Devos KM (1998) Comparative genetics in the grasses. Proc Natl Acad Sci USA 95:1971-1974 1:CAS:528:DyaK1cXhslejsLk%3D
16. Gallego F, Feuillet C, Messmer M, Penger A, Graner A, Yano M, Sasaki T, Keller B (1998) Comparative mapping of the two wheat leaf rust resistance loci Lr1 and Lr10 in rice and barley. Genome 41:328-336 10.1139/gen-41-3-328
17. Gaut BS (2002) Evolutionary dynamics of grass genomes. New Phytol 154:15-28 10.1046/j.1469-8137.2002.00352.x
18. Gill KS, Gill BS, Endo TR, Taylor T (1996) Identification and high-density mapping of gene-rich regions in chromosome group 1 of wheat. Genetics 144:1883-1891 1:CAS:528:DyaK2sXkslylsw%3D%3D
19. Goff SA, Ricke D, Lan TH, Presting G, Wang R et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. japonica). Science 296:92-100 1:CAS:528:DC%2BD38XivVSqtrw%3D
20. Keller B, Feuillet C (2000) Colinearity and gene density in grass genomes. Trends Plant Sci 5:246-251 1:STN:280:DC%2BD3czpsVahtA%3D%3D
21. Kishimoto N, Higi H, Abe K, Arai S, Saito A, Higo K (1994) Identification of the duplicated segments in rice chromosome 1 and 5 by linkage analysis of cDNA markers of known functions. Theor Appl Genet 88:722-726 1:CAS:528:DyaK2MXitVWrs7w%3D
22. Klein PE, Klein RR, Vrebalov J, Mullet JE (2003) Sequence-based alignment of sorghum chromosome 3 and rice chromosome 1 reveals extensive conservation of gene order and one major chromosomal rearrangement. Plant J 34:605-621 10.1046/j.1365-313X.2003.01751.x
23. Kurata N, Moore G, Nagamura Y, Foote T, Yano M, Minobe Y, Gale M (1994) Conservation of genome structure between rice and wheat. Bio-Technology 12:276-278
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 1:CAS:528:DyaK1cXjtl2gsg%3D%3D
25. Lijavetzky D, Muzzi G, Wicker T, Keller B, Wing R, Dubcovsky J (1999) Construction and characterization of a bacterial artificial chromosome (BAC) library for the A genome of wheat. Genome 42:1176-1182 10.1139/ gen-42-6-1176
26. Ma Z, Weining S, Sharp PJ, Liu C (2000) Non-gridded library: A new approach for BAC (bacterial artificial chromosome) exploitation in hexaploid wheat (Triticum aestivum). Nucleic Acids Res 28:E106 10.1093/ nar/28.24.e106
27. Moullet O, Zhang HB, Lagudah ES (1999) Construction and characterization of a large DNA insert library from the D genome of wheat. Theor Appl Genet 99:305-313 10.1007/s001220051237
28. Qi L, Echalier B, Friebe B, Gill BS (2003) Molecular characterization of a set of wheat deletion stocks for use in chromosome bin mapping of ESTs. Funct Integr Genom 3:39-55 1:CAS:528:DC%2BD3sXht1CktLo%3D
29. Rice P, Longden I, Bleasby A (2000) EMBOSS: The European Molecular Biology Open Software Suite. Trends Genetics 16:276-277 10.1016/ S0168-9525(00)02024-2
30. Sandhu D, Gill KS (2002) Structural and functional organization of the "1S0.8 gene-rich region" in the Triticeae. Plant Mol Biol 48:791-804 10.1023/A:1014876409166
31. Sandhu D, Champoux JA, Bondareva SN, Gill KS (2001) Identification and physical localization of useful genes and markers to a major gene-rich region on wheat group 1S chromosomes. Genetics 157:1735-1747 1:CAS:528:DC%2BD3MXjsFemtbw%3D
32. m. Funct Integr Genom 2:70-80 12021852
33. Sasaki T, Matsumoto T, Yamamoto K, Sakata K et al (2002) The genome sequence and structure of rice chromosome 1. Nature 420:312-316 10.1038/ nature01184
34. Sears ER (1966) Nullisomic-tetrasomic combinations in hexaploid wheat. In: Riley R, Lewis KR (eds) Chromosome manipulations and plant genetics. Oliver and Boyd, Edinburgh, pp 29-45
35. Song R, Llaca V, Messing J (2002) Mosaic organization of orthologous sequences in grass genomes. Genome Res 12:1549-1555 10.1101/gr.268302
36. Sonnhammer EL, Durbin R (1995) A dot-matrix program with dynamic threshold control suited for genomic DNA and protein sequence analysis. Gene 167:GC1-GC10 1:STN:280:BymC2cvjtVA%3D
37. Sorrells ME, La Rota M, Bermudez-Kandianis CE, Greene RA et al (2003) Comparative DNA sequence analysis of wheat and rice genomes. Genome Res 13:1818-1827 1:CAS:528:DC%2BD3sXmsVWqt7c%3D
38. Stein N, Feuillet C, Wicker T, Schlagenhauf E, Keller B (2000) Subgenome chromosome walking in wheat: A 450-kb physical contig in Triticum monococcum L. spans the Lr10 resistance locus in hexaploid wheat (Triticum aestivum L.). Proc Natl Acad Sci USA 97:13436-13441 1:CAS:528:DC%2BD3cXosVOjsLY%3D
39. 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 1:CAS:528:DC%2BD3cXktFWju78%3D
40. 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 1:CAS:528:DyaK1MXltVOqsrg%3D
41. Van Deynze AE, Dubcovsky J, Gill, KS, Nelson JC, Sorrells ME, Dvorak J, Gill BS, Lagudah ES, McCouch SR, Appels R (1995a) Molecular-genetic maps of group 1 chromosomes of Triticeae species and their relations to chromosomes in rice and oat. Genome 38:45-59
42. Van Deynze AE, Nelson JC, Yglesias ES, Harrington SE, Braga DP, McCouch SR, Sorrells ME (1995b) Comparative mapping in grasses. Wheat relationships. Mol Gen Genet 248:744-754 7476878
43. Wicker T, Stein N, Albar L, Feuillet C, Schlagenhauf E, Keller B (2001) Analysis of a contiguous 211 kb sequence in diploid wheat (Triticum monococcum L.) reveals multiple mechanisms of genome evolution. Plant J 26:307-316 10.1046/j.1365-313X.2001.01028.x
44. m genomes of wheat. Plant Cell 15:1186-1197 10.1105/tpc.011023
45. Wolfe KH, Gouy M, Yang YW, Sharp PM, Li WH (1989) Date of the monocot-dicot divergence estimated from chloroplast DNA sequence data. Proc Natl Acad Sci USA 86:6201-6205 1:CAS:528:DyaL1MXltlSqsLY%3D
46. Wu J, Kurata N, Tanoue H, Shimokawa T, Umehara Y, Yano M, Sasaki T (1998) Physical mapping of duplicated genomic regions of two chromosome ends in rice. Genetics 150:1595-1603 1:CAS:528:DyaK1MXitVeksg%3D%3D
47. Yu J, Hu S, Wang J, Wong GK, Li S et al (2002) A draft sequence of the rice genome (Oryza sativa L. ssp. indica). Science 296:79-92 1:CAS:528:DC%2BD38XivVSqtr8%3D