Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

Nature

Volumn 402, Issue 6763, 1999, Pages 769-777

  Correction Mayer, K ^a   Schuller C ^a,aj   Wambutt, R ^b   Murphy, G ^c   Volckaert, G ^d   Pohl, T ^e   Dusterhoft A ^f   Stiekema, W ^g   Entian, K D ^h   Terryn, N ⁱ   Harris, B ^j   Ansorge, W ^k   Brandt, P ^l,o   Grivell, L ^m   Rieger, M ⁿ   Weichselgartner, M ^o   De Simone, V ^p   Obermaier, B ^q   Mache, R ^r   Muller M ^s   Kreis, M ^t   Delseny, M ^u   Puigdomenech, P ^v   Watson, M ^w   Schmidtheini, T ^x   Reichert, B ^y   Portatelle, D ^z   Perez Alonso, M ^aa   Boutry, M ^ab   Bancroft, I ^c   Vos, P ^ac   Hoheisel, J ^ad   Zimmermann, W ^b   Wedler, H ^b   Ridley, P ^c   Langham, S A ^c   McCullagh, B ^c   Bilham, L ^c   Robben, J ^d   Van Der Schueren, J ^d   Grymonprez, B ^d   Chuang, Y J ^d   Vandenbussche, F ^d   Braeken, M ^d   Weltjens, I ^d   Voet, M ^d   Bastiaens, I ^d   Aert, R ^d   Defoor, E ^d   Weitzenegger, T ^e   Bothe, G ^e   Ramsperger, U ^f   Hilbert, H ^f   Braun, M ^f   Holzer, E ^f   Brandt, A ^f   Peters, S ^g   Van Staveren, M ^g   Dirkse, W ^g   Mooijman, P ^g   Klein Lankhorst, R ^g   Rose, M ^h   Hauf, J ^h   Kotter P ^h   Berneiser, S ^h   Hempel, S ^h   Feldpausch, M ^h   Lamberth, S ^h   Van Den Daele, H ⁱ   De Keyser, A ⁱ   Buysshaert, C ⁱ   Gielen, J ⁱ   Villarroel, R ⁱ   De Clercq, R ⁱ   Van Montagu, M ⁱ   Rogers, J ^j   Cronin, A ^j   Quail, M ^j   Bray Allen, S ^j   Clark, L ^j   Doggett, J ^j   Hall, S ^j   Kay, M ^j   Lennard, N ^j   McLay, K ^j   Mayes, R ^j   Pettett, A ^j   Rajandream, M A ^j   Lyne, M ^j   Benes, V ^k   Rechmann, S ^k   Borkova, D ^k   Blocker H ^l   Scharfe, M ^l   Grimm, M ^l   Lohnert T H ^l   Dose, S ^l   De Haan, M ^m   Maarse, A ^m   Schafer M ⁿ   Muller Auer S ⁿ   Gabel, C ⁿ   Fuchs, M ⁿ   Fartmann, B ^o   Granderath, K ^o   Dauner, D ^o   Herzl, A ^o   Neumann, S ^o   Argiriou, A ^p   Vitale, D ^p   Liguori, R ^p   Piravandi, E ^q   Massenet, O ^r   Quigley, F ^r   Clabauld, G ^r   Mundlein A ^s   Felber, R ^s   Schnabl, S ^s   Hiller, R ^s   Schmidt, W ^s   Lecharny, A ^t   Aubourg, S ^t   Chefdor, F ^t   Cooke, R ^u   Berger, C ^u   Montfort, A ^u   Casacuberta, E ^u   Gibbons, T ^w   Weber, N ^x   Vandenbol, M ^z   Bargues, M ^aa   Terol, J ^aa   Torres, A ^aa   Perez Perez, A ^aa,ai   Purnelle, B ^ab   Bent, E ^c   Johnson, S ^c   Tacon, D ^c   Jesse, T ^ac   Heijnen, L ^ac   Schwarz, S ^ad   Scholler, P ^ad   Heber, S ^ad   Francs, P ^ae   Bielke, C ^a   Frishman, D ^a   Haase, D ^a   Lemcke, K ^a   Mewes, H W ^a   Stocker, S ^a   Zaccaria, P ^a   Bevan, M ^c   Wilson, R K ^af   De La Bastide, M ^ag   Habermann, K ^ag   Parnell, L ^ag   Dedhia, N ^ag   Gnoj, L ^ag   Schutz, K ^ag   Huang, E ^ag   Spiegel, L ^ag   Sehkon, M ^af   Murray, J ^af   Sheet, P ^af   Cordes, M ^af   Abu Threideh, J ^af   Stoneking, T ^af   Kalicki, J ^af   Graves, T ^af   Harmon, G ^af   Edwards, J ^af   Latreille, P ^af   Courtney, L ^af   Cloud, J ^af   Abbott, A ^af   Scott, K ^af   Johnson, D ^af   Minx, P ^af   Bentley, D ^af   Fulton, B ^af   Miller, N ^af   Greco, T ^af   Kemp, K ^af   Kramer, J ^af   Fulton, L ^af   Mardis, E ^af   Dante, M ^af   Pepin, K ^af   Hillier, L ^af   Nelson, J ^af   Spieth, J ^af   Ryan, E ^ag   Andrews, S ^af   Geisel, C ^af   Layman, D ^af   Du, H ^af   Ali, J ^af   Berghoff, A ^ag   Jones, K ^ag   Drone, K ^ag   Cotton, M ^ag   Joshu, C ^ag   Antonoiu, B ^ag   Zidanic, M ^ag   Strong, C ^ag   Sun, H ^ag   Lamar, B ^ag   Yordan, C ^ag   Ma, P ^ah,am   Zhong, J ^ah,am   Preston, R ^ag   Vil, D ^ag   Shekher, M ^ag   Matero, A ^ag   Shah, R ^ag   Swaby, I'K ^ag   O'Shaughnessy, A ^ag   Rodriguez, M ^ag   Hoffman, J ^ag   Till, S ^ag   Granat, S ^ag   Shohdy, N ^ag   Hasegawa, A ^ag   Hameed, A ^ag   Lodhi, M ^ag,ak   Johnson, A ^ag,al   Chen, E ^ah,am   Marra, M ^ag   Martienssen, R ^ag   McCombie, W R ^ag   more..

^a MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^b AGOWA GmbH   (Germany)

^c JOHN INNES CENTRE   (United Kingdom)

^d LABORATORY OF GENE TECHNOLOGY   (Belgium)

^e GATC GmbH   (Germany)

^f QIAGEN GMBH   (Germany)

^g WAGENINGEN UNIVERSITY   (Netherlands)

^h SRD GmbH   (Germany)

ⁱ GHENT UNIVERSITY   (Belgium)

^j WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^k EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^l HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^m UNIVERSITY OF AMSTERDAM   (Netherlands)

ⁿ Genotype GmbH   (Germany)

^o MWG AG Biotech   (Germany)

^p UNIVERSITY OF NAPLES FEDERICO II   (Italy)

^q Medigenomix   (Germany)

^r UNIV GRENOBLE ALPES   (France)

^s Vienna Biocenter   (Austria)

^t INSTITUTE OF PLANT SCIENCES PARIS SACLAY IPS2   (France)

^u UNIVERSITÉ DE PERPIGNAN   (France)

^v INSTITUT DE BIOLOGIA MOLECULAR DE BARCELONA   (Spain)

^w DURHAM UNIVERSITY   (United Kingdom)

^x MICROSYNTH AG   (Switzerland)

^y BaseClear BV   (Netherlands)

^z UNIVERSITY OF LIÈGE   (Belgium)

^aa UNIVERSITY OF VALENCIA   (Spain)

^ab UNIVERSITÉ CATHOLIQUE DE LOUVAIN   (Belgium)

^ac KEYGENE N V   (Netherlands)

^ad GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^ae LEIBNIZ INSTITUTE OF PLANT GENETICS AND CROP PLANT RESEARCH IPK   (Germany)

^af WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

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

^ah APPLIED BIOSYSTEMS   (United States)

^ai Sistemas Genomicos SL   (Spain)

^aj Biomax Informatics AG   (Germany)

^ak Axys Pharmaceuticals Inc   (United States)

^al NORTH CAROLINA STATE UNIVERSITY   (United States)

^am CELERA   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

DNA;

ARABIDOPSIS; ARTICLE; CAENORHABDITIS ELEGANS; CHROMOSOME 2; CHROMOSOME 4; CHROMOSOME ANALYSIS; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; NONHUMAN; PRIORITY JOURNAL; SACCHAROMYCES CEREVISIAE; SEQUENCE HOMOLOGY;

ARABIDOPSIS; ARABIDOPSIS THALIANA; CAENORHABDITIS ELEGANS; EMBRYOPHYTA; ESCHERICHIA COLI; SACCHAROMYCES CEREVISIAE;

EID: 0343621499     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/47134     Document Type: Article

References (50)

1. Meinke, D. W., Cherry, J. M., Dean, C. D., Rounsley, S. & Koornneef, M. Arabidopsis thaliana: a model plant for genome analysis. Science 282, 662-682 (1998).
2. Copenhaver, G. C. & Pikaard, C. S. Two dimensional RFLP analyses reveal megabase-sized clusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution. Plant J. 9, 273-282 (1996).
3. Lister, C. & Dean, C. Recombinant inbred lines for mapping RFLP and phenotypic markers in Arabidopsis thaliana. Plant J. 4, 745-750 (1993).
4. Bevan, M. et al. Analysis of 1.9 Mb of contiguous sequence from chromosome 4 of Arabidopsis thaliana. Nature 391, 485-488 (1998).
5. Kotani, H., Nakamura, Y., Sato, S., Kaneko, T., Asamizu, E. et al. Structural analysis of Arabidopsis thaliana chromosome 5. II. Sequence features of 1,044,062 bp covered by thirteen physically-assigned P1 clones. DNA Res. 4, 291-300 (1997).
6. The C. elegans Sequencing Consortium. Genome sequence of the nematode C. elegans: a platform for investigating biology. Science 282, 2012-2018 (1999).
7. Gardner, M. J. et al. Chromosome 2 sequence of the human malarial parasite Plasmodium falciparum. Science 282, 1126-1132 (1998).
8. Bowman, S. et al. The complete nucleotide sequence of chromosome 3 of Plasmodium falciparum. Nature 400, 532-538 (1999).
9. Richards, E. J. & Ausubel, F. M. Isolation of a higher eukaryotic telomere from Arabidopsis thaliana. Cell 53, 127-136 (1988).
10. Copenhaver, G. C. & Pikaard, C. S. RFLP and physical mapping with an rDNA-specific endonuclease reveals that nucleolus organiser regions of Arabidopsis thaliana adjoin the telomeres on chromosomes 2 and 4. Plant J. 9, 259-272 (1996).
11. Richards, E. J., Goodman, H. M. & Ausubel, F. M. The centromeric region of Arabidopsis thaliana chromosome 1 contains telomere-similar sequences. Nucleic Acids Res. 19, 3351-3357 (1991).
12. Mewes, H. W. et al. MIPS: a database for genomes and protein sequences. Nucleic Acids Res. 27, 44-48 (1999).
13. Hubbard, T. J. P., Ailey, B., Brenner, S. E., Murzin, A. G. & Chothia, C. SCOP: a structural classification database of proteins. Nucleic Acids Res. 27, 254-256 (1999).
14. Gerstein, M. A structural census of genomes: comparing bacterial, eukaryotic and archeal genomes in terms of protein structure. J. Mol. Biol. 274, 562-576 (1997).
15. Mizutani, M., Ward, E. & Ohta, D. Cytochrome P-450 superfamily in Arabidopsis thaliana: isolation of cDNAS, differential expression, and RFLP mapping of multiple cytochromes P-450. Plant Mol. Biology 37, 39-52 (1998).
16. Joazeiro, C. A. P. et al. The tyrosine kinase negative regulator c-Cbl as a RING-type, E2-dependent ubiquitin-protein ligase. Science 286, 309-312 (1999).
17. Jensen, R. B., Jensen, K. L., Jespersen, H. M. & Skriver, K. Widespread occurrence of a highly conserved RING-H2 zinc finger motif in the model plant Arabidopsis thaliana. FEBS Lett. 436, 283-287 (1998).
18. Moncrief, N. D., Kretsinger, R. H. & Goodman, M. Evolution of EF-hand calcium-modulated proteins 2. Domains of several sub-families have diverse evolutionary history. J. Mol. Evol. 30, 522-562 (1991).
19. 2+signaling systems. Trends Plant Sci. 3, 32-36 (1998).
20. Douglas, S. E. Plastid evolution: origins, diversity, trends. Curr. Opin. Genet. Dev. 8, 655-661 (1998).
21. Emanuelsson, O., Nielsen, H. & von Heijne, G. ChloroP, a neural network-based method for predicting chloroplast transit peptides and their cleavage sites. Protein Sci. 8, 978-984 (1999).
22. Gamas, P., de Carvalho Niebel, R. Lescure, N. & Cullimore, J. V. Use of a subtractive hybridisation approach to identify new Medicago truncatula genes induced during nodule development. Mol. Plant Microbe Interaction 9, 233-242 (1996).
23. Parniske, M. et al. Novel disease resistance specificities result from sequence exchange between tandemly repeated genes at the Cf-4/9 locus in tomato. Cell 9, 821-832 (1997).
24. Mewes, H.-W. et al. Nature 387 (Suppl.) 7-8 (1997).
25. Round, E., Flowers, S. K. & Richards, E. J. Arabidopsis thaliana centromere regions: genetic map positions and repetitive DNA structure. Genome Res. 7, 1045-1054 (1997).
26. Fransz, P. F. et al. Cytogenetics for the model system Arabidopsis thaliana. Plant J. 13, 867-876 (1998).
27. Richards, E. J. & Dawe, R. K. Plant centromeres: structure and control. Curr. Opin. Plant Biol. 1, 130-135 (1998).
28. Murphy, T. D. & Karpen, G. H. Localization of centromere function in a Drosophila minichromosome. Cell 82, 599-609 (1995).
29. Henning, K. A. et al. Human artificial chromosomes generated by modification of a yeast artificial chromosome containing both human alpha satellite and single-copy sequences. Proc. Natl Acad. Sci. USA 96, 592-597 (1999).
30. Copenhaver, G. P., Browne, W. E. & Preuss, D. Assaying genome-wide recombination and centromere functions with Arabidopsis tetrads. Proc. Natl Acad. Sci. USA 95, 247-252 (1998).
31. Grewal, S. I. S. & Klar, A. J. S. A recombinationally repressed region between mat2 and mat3 loci shares homology to centromeric repeats and regulates directionality of mating type switching in fission yeast. Genetics 146, 1221-1238 (1997).
32. Allshire, R. C., Nimmo, E. R., Ekwall, K., Javerzat, J.-P. & Cranston, G. Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9, 218-233 (1995).
33. Xu, X. J., Hsai, A.-P., Zhang, L., Nikolau, B. J. & Schnable, P. S. Meiotic recombination breakpoints resolve at high rates at the 5′ end of a maize coding sequence. Plant Cell 7, 2151-2161 (1995).
34. Lin, X. et al. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana. Nature 402, 761-768 (1999).
35. Choi, S. D., Creelman, R., Mullet, J. & Wing, R. A. Construction and characterisation of a bacterial artificial chromosome library from Arabidopsis thaliana. Weeds World 2, 17-20 (1995).
36. Mozo, T. et al. A complete BAC-based physical map of the Arabidopsis thaliana genome. Nature Genet. 22, 271-275 (1999).
37. Marra, M. et al. A map or sequence analysis of the Arabidopsis thaliana genome. Nature Genet. 22, 265-270 (1999).
38. Bent, E., Johnson, S. & Bancroft, I. BAC representation of two low-copy regions of the genome of Arabidopsis thaliana. Plant J. 13, 849-855 (1998).
39. Vos, P. et al. AFLP, a new technique for DNA fingerprinting. Nucleic Acids Res. 23, 4407-4414 (1995).
40. Borodovsky, M. & Peresetsky, A. Deriving non-homogeneous DNA Markov chain models by cluster analysis algorithm minimizing multiple alignment entropy. Comput. Chem. 18, 259-267 (1994).
41. Uberbacher, E. C. & Mural, R. J. Locating protein coding regions in human DNA sequences by a multiple sensor-neural network approach. Proc. Natl Acad. Sci. 88, 1261-1265 (1991).
42. Burge, C. & Karlin, S. Prediction of complete gene structures in human genomic DNA. J. Mol. Biol. 268, 78-94 (1997).
43. Hebsgaard, S. M. et al. Splice site prediction in Arabidopsis thaliana pre-mRNA by combining local and global sequence information. Nucleic Acids Res. 24, 3439-3452 (1996).
44. Altschul, S. F. et al. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 25, 3389-3402 (1997).
45. Fichant, G. A. & Burks, C. Identifying potential tRNA genes in genomic DNA sequences. J. Mol. Biol. 220, 659-671 (1991).
46. Wootton, J. C. & Federhen, S. Statistics of local complexity in amino acid sequences and sequence databases. Comput. Chem. 17, 149-163 (1993).
47. Lupas, A. N., van Dyke, M. & Stock, J. Predicting coiled coils from protein sequences. Science 252, 1162-1164 (1991).
48. Klein, P., Kanehisa, M. & DeLisi, C. The detection and classification of membrane-spanning proteins. Biochim. Biophys. Acta 815, 468-476 (1985).
49. Schäffer, A. A. et al. IMPALA: Software to match a protein sequence against a collection of PSI-BLAST-constructed position-specific score matrices. Bioinformatics, in the press.
50. Pearson, W. R. & Lipman, D. J. Improved tools for biological sequence comparison. Proc. Natl Acad. Sci. 85, 2444-2448 (1988).