Haplotype divergence in Beta vulgaris and microsynteny with sequenced plant genomes

Plant Journal

Volumn 57, Issue 1, 2009, Pages 14-26

  Dohm, Juliane C ^b   Lange, Cornelia ^b   Reinhardt, Richard ^b   Himmelbauer, Heinz ^a,b  

^a CENTRE FOR GENOMIC REGULATION CRG   (Spain)

^b MAX PLANCK INSTITUTE FOR MOLECULAR GENETICS   (Germany)

Author keywords

Comparative plant genomics; Genomic sequencing; Haplotype divergence; Microsynteny; Repeat detection; Transposable elements

Indexed keywords

PLANT DNA;

ARTICLE; BACTERIAL ARTIFICIAL CHROMOSOME; BEET; COMPARATIVE STUDY; DNA BASE COMPOSITION; DNA SEQUENCE; GENE LIBRARY; GENE ORDER; GENETIC POLYMORPHISM; GENETICS; GENOTYPE; HAPLOTYPE; PLANT CHROMOSOME; PLANT GENE; PLANT GENOME; SEQUENCE ALIGNMENT; SYNTENY;

BASE COMPOSITION; BETA VULGARIS; CHROMOSOMES, ARTIFICIAL, BACTERIAL; CHROMOSOMES, PLANT; DNA, PLANT; GENE LIBRARY; GENE ORDER; GENES, PLANT; GENOME, PLANT; GENOTYPE; HAPLOTYPES; POLYMORPHISM, GENETIC; SEQUENCE ALIGNMENT; SEQUENCE ANALYSIS, DNA; SYNTENY;

ARABIDOPSIS; BACTERIA (MICROORGANISMS); BETA VULGARIS; BETA VULGARIS SUBSP. VULGARIS; MEDICAGO; VITACEAE; VITIS;

EID: 58149105394     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2008.03665.x     Document Type: Article

References (48)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. Lipman, D.J. (1990) Basic local alignment search tool. J. Mol. Biol. 215, 403 410.
2. Arumuganathan, K. Earle, E.D. (1991) Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9, 208 211.
3. Birney, E. Durbin, R. (2000) Using GeneWise in the Drosophila annotation experiment. Genome Res. 10, 547 548.
4. Blanc, G., Hokamp, K. Wolfe, K.H. (2003) A recent polyploidy superimposed on older large-scale duplications in the Arabidopsis genome. Genome Res. 13, 137 144.
5. Bray, N. Pachter, L. (2004) MAVID constrained ancestral alignment of multiple sequences. Genome Res. 14, 693 699.
6. Brunner, S., Fengler, K., Morgante, M., Tingey, S. Rafalski, A. (2005) Evolution of DNA sequence nonhomologies among maize inbreds. Plant Cell, 17, 343 360.
7. Burge, C. Karlin, S. (1997) Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78 94.
8. Cannon, S.B., Sterck, L., Rombauts, S. et al. (2006) Legume genome evolution viewed through the Medicago truncatula and Lotus japonicus genomes. Proc. Natl Acad. Sci. USA, 103, 14959 14964.
9. Ching, A., Caldwell, K.S., Jung, M., Dolan, M., Smith, O.S., Tingey, S., Morgante, M. Rafalski, A.J. (2002) SNP frequency, haplotype structure and linkage disequilibrium in elite maize inbred lines. BMC Genet. 3, 19.
10. Church, G.M. Gilbert, W. (1984) Genomic sequencing. Proc. Natl Acad. Sci. USA, 81, 1991 1995.
11. Cogan, N.O., Ponting, R.C., Vecchies, A.C. et al. (2006) Gene-associated single nucleotide polymorphism discovery in perennial ryegrass (Lolium perenne L.). Mol. Genet. Genomics, 276, 101 112.
12. Deleu, W., González, V., Monfort, A., Bendahmane, A., Puigdomènech, P., Arús, P. Garcia-Mas, J. (2007) Structure of two melon regions reveals high microsynteny with sequenced plant species. Mol. Genet. Genomics, 278, 611 622.
13. Dominguez, I., Graziano, E., Gebhardt, C., Barakat, A., Berry, S., Arús, P., Delseny, M. Barnes, S. (2003) Plant genome archaeology evidence for conserved ancestral chromosome segments in dicotyledonous plant species. Plant Biotechnol. J. 1, 91 99.
14. Ewing, B., Hillier, L., Wendl, M.C. Green, P. (1998) Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8, 175 185.
15. Fénart, S., Arnaud, J.F., De Cauwer, I. Cuguen, J. (2008) Nuclear and cytoplasmic genetic diversity in weed beet and sugar beet accessions compared to wild relatives: new insights into the genetic relationships within the Beta vulgaris complex species. Theor. Appl. Genet. 116, 1063 1077.
16. Feng, Q., Zhang, Y., Hao, P. et al. (2002) Sequence and analysis of rice chromosome 4. Nature, 420, 316 320.
17. Fischer, H.E. (1989) Origin of the 'Weisse Schlesische Rübe' (white Silesian beet) and resynthesis of sugar beet. Euphytica, 41, 75 80.
18. Fu, H. Dooner, H.K. (2002) Intraspecific violation of genetic colinearity and its implications in maize. Proc. Natl Acad. Sci. USA, 99, 9573 9578.
19. Galtier, N., Gouy, M. Gautier, C. (1996) SeaView and Phylo_win, two graphic tools for sequence alignment and molecular phylogeny. Comput. Appl. Biosci. 12, 543 548.
20. Gindullis, F., Dechyeva, D. Schmidt, T. (2001) Construction and characterization of a BAC library for the molecular dissection of a single wild beet centromere and sugar beet (Beta vulgaris) genome analysis. Genome, 44, 846 855.
21. Herwig, R., Schulz, B., Weisshaar, B. et al. (2002) Construction of a 'unigene' cDNA clone set by oligonucleotide fingerprinting allows access to 25 000 potential sugar beet genes. Plant J. 32, 845 857.
22. Hohmann, U., Jacobs, G., Telgmann, A., Gaafar, R.M., Alam, S. Jung, C. (2003) A bacterial artificial chromosome (BAC) library of sugar beet and a physical map of the region encompassing the bolting gene B. Mol. Genet. Genomics, 269, 126 136.
23. Huang, X. Madan, A. (1999) CAP3 A DNA sequence assembly program. Genome Res. 9, 868 877.
24. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature, 436, 793 800.
25. Jaillon, O., Aury, J.M., Noel, B. et al. (2007) The grapevine genome sequence suggests ancestral hexaploidization in major angiosperm phyla. Nature, 449, 463 467.
26. Jansen, R.K., Kaittanis, C., Saski, C., Lee, S.B., Tomkins, J., Alverson, A.J. Daniell, H. (2006) Phylogenetic analyses of Vitis (Vitaceae) based on complete chloroplast genome sequences effects of taxon sampling and phylogenetic methods on resolving relationships among rosids. BMC Evol. Biol. 6, 32.
27. Kelleher, C.T., Chiu, R., Shin, H. et al. (2007) A physical map of the highly heterozygous Populus genome integration with the genome sequence and genetic map and analysis of haplotype variation. Plant J. 50, 1063 1078.
28. Ku, H.M., Vision, T., Liu, J. Tanksley, S.D. (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.
29. Kubis, S.E., Heslop-Harrison, J.S., Desel, C. Schmidt, T. (1998) The genomic organization of non-LTR retrotransposons (LINEs) from three Beta species and five other angiosperms. Plant Mol. Biol. 36, 821 831.
30. Kuhl, J.C., Cheung, F., Yuan, Q. et al. (2004) A unique set of 11,008 onion expressed sequence tags reveals expressed sequence and genomic differences between the monocot orders Asparagales and Poales. Plant Cell, 16, 114 125.
31. Laurent, V., Devaux, P., Thiel, T., Viard, F., Mielordt, S., Touzet, P. Quillet, M.C. (2007) Comparative effectiveness of sugar beet microsatellite markers isolated from genomic libraries and GenBank ESTs to map the sugar beet genome. Theor. Appl. Genet. 115, 793 805.
32. Lewis, S.E., Searle, S.M., Harris, N. et al. (2002) Apollo a sequence annotation editor. Genome Biol. 3, Research 0082.1-0082.14.
33. Mao, L., Begum, D., Goff, S.A. Wing, R.A. (2001) Sequence and analysis of the tomato JOINTLESS locus. Plant Physiol. 126, 1331 1340.
34. McGrath, M.J., Shaw, R.S., De Los Reyes, B.G. Weiland, J.J. (2004) Construction of a sugar beet BAC library from a hybrid with diverse traits. Plant Mol. Biol. Rep. 22, 23 28.
35. Menzel, G., Dechyeva, D., Keller, H., Lange, C., Himmelbauer, H. Schmidt, T. (2006) Mobilization and evolutionary history of miniature inverted-repeat transposable elements (MITEs) in Beta vulgaris L. Chromosome Res. 14, 831 844.
36. Ming, R., Hou, S., Feng, Y. et al. (2008) The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature, 452, 991 996.
37. Nagamine, T., Catty, J.P. Ford-Lloyd, B.V. (1989) Phenotypic polymorphism and allele differentiation of isozymes in fodder beet, multigerm sugar beet and monogerm sugar beet. Theor. Appl. Genet. 77, 711 720.
38. Rice, P., Longden, I. Bleasby, A. (2000) EMBOSS The European Molecular Biology Open Software Suite. Trends Genet. 16, 276 277.
39. Schmid, K.J., Rosleff Soerensen, T., Stracke, R., Torjek, O., Altmann, T., Mitchell-Olds, T. Weisshaar, B. (2003) Large-scale identification and analysis of genome-wide single-nucleotide polymorphisms for mapping in Arabidopsis thaliana. Genome Res. 13, 1250 1257.
40. Schneider, K., Kulosa, D., Rosleff Soerensen, T. et al. (2007) Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes. Theor. Appl. Genet. 115, 601 615.
41. Schumacher, K., Schondelmaier, J., Barzen, E., Steinrücken, G., Borchardt, D., Weber, W.E., Jung, C. Salamini, F. (1997) Combining different linkage maps in sugar beet (Beta vulgaris L.) to make one map. Plant Breed. 116, 23 38.
42. Sonnhammer, E.L. Durbin, R. (1994) A workbench for large scale sequence homology analysis. Comput. Appl. Biosci. 10, 301 307.
43. The Angiosperm Phylogeny Group (2003) An update of the Angiosperm Phylogeny Group classification for the orders and families of flowering plants AGP II. Bot. J. Linn. Soc. 141, 399 436.
44. The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature, 408, 796 815.
45. Thompson, J.D., Gibson, T.J., Plewniak, F., Jeanmougin, F. Higgins, D.G. (1997) The ClustalX windows interface flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 24, 4876 4882.
46. Tuskan, G.A., Difazio, S., Jansson, S. et al. (2006) The genome of black cottonwood, Populus trichocarpa (Torr. & Gray). Science, 313, 1596 1604.
47. Wu, C.A., Lowry, D.B., Cooley, A.M., Wright, K.M., Lee, Y.W. Willis, J.H. (2008) Mimulus is an emerging model system for the integration of ecological and genomic studies. Heredity, 100, 220 230.
48. Young, N.D., Cannon, S.B., Sato, S., Kim, D., Cook, D.R., Town, C.D., Roe, B.A. Tabata, S. (2005) Sequencing the genespaces of Medicago truncatula and Lotus japonicus. Plant Physiol. 137, 1174 1181.