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The Sequence of the Arabidopsis Genome as a Tool for Comparative Structural Genomics in Brassicaceae

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Brassicas and Legumes From Genome Structure to Breeding

Part of the book series: Biotechnology in Agriculture and Forestry ((AGRICULTURE,volume 52))

Abstract

Comparative structural genomics aims to describe the differences in genome organization seen among diverse organisms and ultimately to unravel the molecular and genetic mechanisms accounting for these changes. Comparisons can be undertaken at different levels of resolution.

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References

  • 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

    Article  PubMed  CAS  Google Scholar 

  • Alonso-Bianco C, Peeters AJ, Koornneef M, Lister C, Dean C, van den Bosch N, Pot J, Kuiper MT (1998) Development of an AFLP based linkage map of Ler, Col and Cvi Arabidopsis thaliana ecotypes and construction of a Ler/Cvi recombinant inbred line population. Plant J 14:259–271

    Article  Google Scholar 

  • Altschul SF, Gish W, Miller W, Myers EW, Lipman D (1990) Basic local alignment search tool. J Mol Biol 215:403–410

    PubMed  CAS  Google Scholar 

  • Arumuganathan K, Earle ED (1991) Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9:208–218

    Article  CAS  Google Scholar 

  • Bell CJ, Ecker JR (1994) Assignment of 30 microsatellite loci to the linkage map of Arabidopsis. Genomics 19:137–144

    Article  PubMed  CAS  Google Scholar 

  • Bennett MD (1998) Plant genome values: how much do we know? Proc Natl Acad Sci USA 95:2011–2016

    Article  PubMed  CAS  Google Scholar 

  • Bennetzen JL (2000) Comparative sequence analysis of plant nuclear genomes: microcollinearity and its many exceptions. Plant Cell 12:1021–1029

    PubMed  CAS  Google Scholar 

  • Blanc G, Barakat A, Guyot R, Cooke R, Delseny M (2000) Extensive duplication and reshuffling in the Arabidopsis genome. Plant Cell 12:1093–1101

    PubMed  CAS  Google Scholar 

  • Bohuon EJR, Keith DJ, Parkin IAP, Sharpe AG, Lydiate DJ (1996) Alignment of the conserved C genome of Brassica oleracea and Brassica napus. Theor Appl Genet 93:833–839

    Article  CAS  Google Scholar 

  • Camilleri C, Lafleuriel J, Macadre C, Varoquaux F, Parmentier Y, Picard G, Caboche M, Bouchez D (1998) A YAC contig map of Arabidopsis thaliana chromosome 3. Plant J 14:633–642

    Article  PubMed  CAS  Google Scholar 

  • Cavell AC, Lydiate DJ, Parkin IAP, Dean C, Trick M (1998) Collinearity between a 30-centimor-gan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome. Genome 41:62–69

    PubMed  CAS  Google Scholar 

  • Chang C, Bowman JL, DeJohn AW, Lander ES, Meyerowitz EM (1988) Restriction fragment length polymorphism linkage map for Arabidopsis thaliana. Proc Natl Acad Sci USA 85: 6856–6860

    Article  PubMed  CAS  Google Scholar 

  • Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ (1999) Genome-wide mapping with biallelic markers in Arabidopsis thaliana. Nat Genet 23:203–207

    Article  PubMed  CAS  Google Scholar 

  • Choi S, Creelman RA, Mullet JE, Wing RA (1995) Construction and characterization of a bacterial artificial chromosome library of Arabidopsis thaliana. Plant Mol Biol Rep 13:124–128

    Article  Google Scholar 

  • Creusot F, Fouilloux E, Dron M, Lafleuriel J, Picard G, Billault A, Le Paslier D, Cohen D, Chabouté M-E, Durr A, Fleck J, Gigot C, Camilleri C, Bellini C, Caboche M, Bouchez D (1995) The CIC library: a large insert YAC library for genome mapping in Arabidopsis thaliana. Plant J 8: 763–770

    Article  PubMed  CAS  Google Scholar 

  • Ecker JR (1990) PFGE and YAC analysis of the Arabidopsis genome. Methods 1:186–194

    Article  CAS  Google Scholar 

  • Fabri C, Schäffner A (1994) An Arabidopsis thaliana RFLP mapping set to localize mutations to chromosomal regions. Plant J 5:149–156

    Article  CAS  Google Scholar 

  • Feinberg AP, Vogelstein B (1983) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Anal Biochem 132:6–13

    Article  PubMed  CAS  Google Scholar 

  • Feinberg AP, Vogelstein B (1984) A technique for radiolabelling DNA restriction endonuclease fragments to high specific activity. Addendum. Anal Biochem 137:266–267

    Article  PubMed  CAS  Google Scholar 

  • Flavell R (1980) The molecular characterization and organization of plant chromosomal DNA sequences. Annu Rev Plant Phys 31:569–596

    Article  CAS  Google Scholar 

  • Flavell RB, Bennett MD, Smith JB, Smith DB (1974) Genome size and the proportion of repeated nucleotide sequence DNA in plants. Biochem Genet 12:257–269

    Article  PubMed  CAS  Google Scholar 

  • Höfte H, Desprez T, Amselem J, Chiapello H, Rouzé P, Caboche M, Moison A, Jourjon M-F, Charpenteau J-L, Berthomieu P, Guerrier D, Giraudat J, Quigley F, Thomas F, Yu D-Y, Mache R, Raynal M, Cooke R, Grellet F, Delseny M, Parmentier Y, de Marcillac G, Gigot C, Fleck J, Philipps G, Axelos M, Bardet C, Tremousaygue D, Lescure B (1993) An inventory of 1152 expressed sequence tags obtained by partial sequencing of cDNAs from Arabidopsis thaliana. Plant J 4:1051–1061

    Article  PubMed  Google Scholar 

  • Konieczny A, Ausubel F (1993) A procedure for quick mapping of Arabidopsis mutants using ecotype specific markers. Plant J 4:403–410

    Article  PubMed  CAS  Google Scholar 

  • Kotani H, Sato S, Fukami M, Hosouchi T, Nakazaki N, Okumura S, Wada T, Liu YG, Shibata D, Tabata S (1997) A fine physical map of Arabidopsis thaliana chromosome 5: construction of a sequence-ready contig map. DNA Res 4:371–378

    Article  PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • 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

    PubMed  CAS  Google Scholar 

  • Lagercrantz U, Lydiate D (1996) Comparative genome mapping in Brassica. Genetics 144:1903–1910

    PubMed  CAS  Google Scholar 

  • Lagercrantz U, Putterill J, Coupland G, Lydiate D (1996) Comparative mapping in Arabidopsis and Brassica, fine scale genome collinearity and congruence of genes controlling flowering time. Plant J 9:13–20

    Article  PubMed  CAS  Google Scholar 

  • Lander ES, Green P, Abrahamson J, Barlow A, Daly MJ, Lincoln SE, Newburg L (1987) Map Maker: an interactive computer package for constructing primary genetic linkage maps of experimental and natural populations. Genomics 1:174–181

    Article  PubMed  CAS  Google Scholar 

  • Leitch IJ, Chase MW, Bennett MD (1998) Phylogenetic analysis of DNA C-values provides evidence for a small ancestral genome size in flowering plants. Ann Bot 82(Suppl A):85–94

    Article  CAS  Google Scholar 

  • Liu Y-G, Mitsukawa N, Lister C, Dean C, Whittier RF (1996) Isolation and mapping of a new set of 129 RFLP markers in Arabidopsis thaliana recombinant inbred lines. Plant J 10:733–736

    Article  PubMed  CAS  Google Scholar 

  • Marra M, Kucaba T, Sekhon M, Hillier L, Martienssen R, Chinwalla A, Crockett J, Fedele J, Grover H, Gund C, McCombie WR, McDonald K, McPherson J, Mudd N, Parnell L, Schein J, Seim R, Shelby P, Waterston R, Wilson R (1999) A map for sequence analysis of the Arabidopsis thaliana genome. Nat Genet 22:265–270

    Article  PubMed  CAS  Google Scholar 

  • Mozo T, Fischer S, Shizuya H, Altmann T (1998) Construction and characterization of the IGF Arabidopsis BAC library. Mol Gen Genet 258:562–570

    Article  PubMed  CAS  Google Scholar 

  • Mozo T, Dewar K, Dunn P, Ecker JR, Fischer S, Kloska S, Lehrach H, Marra M, Martienssen R, Meier-Ewert S, Altmann T (1999) A complete BAC-based physical map of the Arabidopsis thaliana genome. Nat Genet 22:271–275

    Article  PubMed  CAS  Google Scholar 

  • Nam H-G, Giraudat J, den Boer B, Moonan F, Loos WDB, Hauge BM, Goodman H (1989) Restriction fragment length polymorphism linkage map of Arabidopsis thaliana. Plant Cell 1:699–705

    PubMed  CAS  Google Scholar 

  • Newman T, de Bruijn FJ, Green P, Keegstra K, Kende H, Mcintosh L, Ohlrogge J, Raikhel N, Somerville S, Thomashow M, Retzel E, Somerville C (1994) Genes galore: a summary of methods for accessing results from large-scale partial sequencing of anonymous Arabidopsis cDNA clones. Plant Physiol 106:1241–1255

    Article  PubMed  CAS  Google Scholar 

  • Noël L, Moores TL, van der Biezen EA, Parniske M, Daniels MJ, Parker JE, Jones JDG (1999) Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis. Plant Cell 11:2099–2111

    PubMed  Google Scholar 

  • O’Neill CM, Bancroft I (2000) Comparative physical mapping of segments of the genome of Brassica oleracea var. alboglabra that are homoeologous to sequenced regions of chromosomes 4 and 5 of Arabidopsis thaliana. Plant J 23:233–243

    Article  PubMed  Google Scholar 

  • Paterson AH, Bowers JE, Burow MD, Draye X, Elsik CG, Jiang C-X, Katsar CS, Lan T-H, Lin Y-R, Ming R, Wright RJ (2000) Comparative genomics of plant chromosomes. Plant Cell 12:1523–1539

    PubMed  CAS  Google Scholar 

  • Price RA, Palmer JD, Al-Shebaz IA (1994) Systematic relationships of Arabidopsis: a molecular and morphological perspective. In: Meyerowitz EM, Somerville CR (eds) Arabidopsis. Cold Spring Harbor Lab Press, Cold Spring Harbor, NY, pp 7–19

    Google Scholar 

  • Quackenbush J, Liang F, Holt I, Pertea G, Upton J (2000) The TIGR gene indices: reconstruction and representation of expressed gene sequences. Nucleic Acids Res 28:141–145

    Article  PubMed  CAS  Google Scholar 

  • Quackenbush J, Cho J, Lee D, Liang F, Holt I, Karamycheva S, Parvizi B, Pertea G, Sultana R, White J (2001) The TIGR gene indices: analysis of gene transcript sequences in highly sampled eukaryotic species. Nucleic Acids Res 29:159–164

    Article  PubMed  CAS  Google Scholar 

  • Reiter RS, Williams JGK, Feldmann KA, Rafalski JA, Tingey SV, Scolnik PA (1992) Global and local genome mapping in Arabidopsis thaliana by using recombinant inbred lines and random amplified polymorphic DNAs. Proc Natl Acad Sci USA 89:1477–1481

    Article  PubMed  CAS  Google Scholar 

  • Rossberg M, Theres K, Acarkan A, Herrero R, Schmitt T, Schumacher K, Schmitz G, Schmidt R (2001) Comparative sequence analysis reveals extensive microcollinearity in the Lateral suppressor regions of the tomato, Arabidopsis and Capsella genomes. Plant Cell 13:979–988

    PubMed  CAS  Google Scholar 

  • Rounsley SD, Glodek A, Sutton G, Adams MD, Somerville CR, Venter JC, Kerlavage AR (1996) The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification. Plant Physiol 112:1177–1183

    Article  PubMed  CAS  Google Scholar 

  • Ryder CD, Smith LB, Teakle GR, King GJ (2001) Contrasting genome organisation: two regions of the Brassica oleracea genome compared with collinear regions of the Arabidopsis thaliana genome. Genome 44:808–817

    PubMed  CAS  Google Scholar 

  • Sambrook J, Fritsch EF, Maniatis T (1989) Molecular cloning: a laboratory manual, 2nd edn. Cold Spring Harbor Lab Press, Cold Spring Harbor, NY

    Google Scholar 

  • Sanguinetti CJ, Neto ED, Simpson AJG (1994) Rapid silver staining and recovery of PCR products separated on Polyacrylamide gels. BioTechniques 17:915–919

    Google Scholar 

  • Sato S, Kotani H, Hayashi R, Liu YG, Shibata D, Tabata S (1998) A physical map of Arabidopsis thaliana chromosome 3 represented by two contigs of CIC YAC, PI, TAC and BAC clones. DNA Res 5:163–168

    Article  PubMed  CAS  Google Scholar 

  • Schmidt R (2000) Synteny: recent advances and future prospects. Curr Opin Plant Biol 3:97–102

    Article  PubMed  CAS  Google Scholar 

  • Schmidt R (2002) Plant genome evolution: lessons from comparative genomics at the DNA level. Plant Mol Biol 48:21–37

    Article  PubMed  CAS  Google Scholar 

  • Schmidt R, West J, Love K, Lenehan Z, Lister C, Thompson H, Bouchez D, Dean C (1995) Physical map and organization of Arabidopsis thaliana chromosome 4. Science 270:480–483

    Article  PubMed  CAS  Google Scholar 

  • Schmidt R, Acarkan A, Koch M, Rossberg M (1999) A strategy for comparative physical mapping in cruciferous plants. In: van Raamsdonk LWD, den Nijs JCM (eds) Plant evolution in man-made habitats. Proceedings of the VIIth Symposium of the International Organization of Plant Biosystematics. Hugo de Vries Lab, University of Amsterdam, Amsterdam, ppl83–196

    Google Scholar 

  • Schwarzacher T (1994) Mapping in plants: progress and prospects. Curr Opin Genet Dev 4:868–874

    Article  PubMed  CAS  Google Scholar 

  • Slabaugh MB, Huestis GM, Leonard J, Holloway JL, Rosato C, Hongtrakul V, Martini N, Toepfer R, Voetz M, Schell J, Knapp SJ (1997) Sequence-based genetic markers for genes and gene families: single-strand conformational polymorphisms for the fatty acid synthesis genes of Cuphea. Theor Appl Genet 94:400–408

    Article  CAS  Google Scholar 

  • Terryn N, Heijnen L, De Keyser A, Van Asseldonck M, De Clercq R, Verbakel H, Gielen J, Zabeau M, Villarroel R, Jesse T, Neyt P, Hogers R, Van Den Daele H, Ardiles W, Schueller C, Mayer K, Déhais P, Rombauts S, Van Montagu M, Rouzé P, Vos P (1999) Evidence for an ancient chromosomal duplication in Arabidopsis thaliana by sequencing and analyzing a 400-kb contig at the Apetala2 locus on chromosome 4. FEBS Lett 445:237–245

    Article  PubMed  CAS  Google Scholar 

  • The Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408:796–815

    Article  Google Scholar 

  • Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42:225–249

    Article  PubMed  CAS  Google Scholar 

  • Zachgo EA, Wang ML, Dewdney J, Bouchez D, Camilleri C, Belmonte S, Huang L, Dolan M, Goodman HM (1996) A physical map of chromosome 2 of Arabidopsis thaliana. Genome Res 6:19–25

    Article  PubMed  CAS  Google Scholar 

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Schmidt, R., Acarkan, A., Boivin, K., Clarenz, O., Rossberg, M. (2003). The Sequence of the Arabidopsis Genome as a Tool for Comparative Structural Genomics in Brassicaceae. In: Nagata, T., Tabata, S. (eds) Brassicas and Legumes From Genome Structure to Breeding. Biotechnology in Agriculture and Forestry, vol 52. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-662-05036-1_3

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  • DOI: https://doi.org/10.1007/978-3-662-05036-1_3

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-07662-6

  • Online ISBN: 978-3-662-05036-1

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