Analysis of the genome sequence of the flowering plant Arabidopsis thaliana

Nature

Volumn 408, Issue 6814, 2000, Pages 796-815

  Kaul, Samir ^a   Koo, Hean L ^a   Jenkins, Jennifer ^a   Rizzo, Michael ^a   Rooney, Timothy ^a   Tallon, Luke J ^a   Feldblyum, Tamara ^a   Nierman, William ^a   Benito, Maria Ines ^a   Lin, Xiaoying ^a   Town, Christopher D ^a   Venter, J Craig ^a   Fraser, Claire M ^a   Tabata, Satoshi ^b   Nakamura, Yasukazu ^b   Kaneko, Takakazu ^b   Sato, Shusei ^b   Asamizu, Erika ^b   Kato, Tomohiko ^b   Kotani, Hirokazu ^b   Sasamoto, Shigemi ^b   Ecker, Joseph R ^c,f   Theologis, Athanasios ^d   Federspiel, Nancy A ^e,f,g   Palm, Curtis J ^e,e   Osborne, Brian I ^d   Shinn, Paul ^c   Dewar, Ken ^c   Kim, Christopher J ^c,d   Buehler, Eugen ^c,d   Dunn, Patrick ^c   Chao, Qimin ^c   Chen, Huaming ^c,c   Vysotskaia, Valentina S ^d   Lenz, Catherine A ^d   Hansen, Nancy F ^d,e   Liu, Shirley X ^d   Alta, Hootan ^e   Sakano, Hitomi ^d   Lam, Bao ^e   Pham, Paul K ^d   Nguyen, Michelle ^e   Yu, Guixia ^d   Southwick, Audrey ^e   Lee, Jeong Mi ^d   Miranda, Molly ^e   Toriumi, Mitsue J ^d   Davis, Ronald W ^e   Conway, Aaron B ^e   Conn, Lane ^e   Hootan, Altafi ^e   Wambutt, R ^h   Murphy, G ⁱ   Dusterhoft A ^j   Stiekema, W ^k   Pohl, T ^l   Entian, K D ^m   Terryn, N ⁿ   Volckaert, G ^o   Salanoubat, M ^p   Choisne, N ^p   Artiguenave, F ^p   Weissenbach, J ^p   Quetier, F ^p,ab   Rieger, M ^q   Ansorge, W ^r   Unseld, M ^s   Fartmann, B ^t   Valle, G ^u   Wilson, Richard K ^v   Sekhon, M ^v   Pepin, K ^v   Murray, J ^v   Johnson, D ^v   Hillier, L ^v   de la Bastide, Melissa ^w   Huang, Emily ^w   Spiegel, Lori ^w   Gnoj, Lidia ^w   Habermann, Kristina ^w   Dedhia, Neilay ^w   Parnell, Larry ^w   Preston, Raymond ^w   Marra, M ^w   McCombie, W Richard ^w   Chen, Ellson ^x   Martienssen, Robert ^w   Mayer, Klaus ^y   Lemcke, Kai ^y   Haas, Brian ^y   Haase, Dirk ^y   Rudd, Stephen ^y   Schoof, Heiko ^y   Frishman, Dimitrij ^y   Morgenstern, Burkhard ^y   Zaccaria, Paulo ^y   Mewes, Hans Werner ^y   White, Owen ^a   Creasy, Todd H ^a   Bielke, Cord ^a   Maiti, Rama ^a   Peterson, Jeremy ^a   Ermolaeva, Maria ^a   Pertea, Mihaela ^a   Quackenbush, John ^a   Volfovsky, Natalia ^a   Wu, Dongying ^a   Salzberg, Steven L ^a   Bevan, Michael ⁱ   Lowe, Todd M ^e   Rounsley, S ^z   Bush, D ^z   Subramaniam, S ^z   Levin, I ^z   Norris, S ^z   Schmidt, R ^aa   Acarkan, A ^aa   Bancroft, I ⁱ   Brennicke, A ^ac   Eisen, J A ^a   Bureau, T ^ad   Legault, B A ^ad   Le, Q H ^ad   Agrawal, N ^ad   Yu, Z ^ad   Copenhaver, G P ^ae   Luo, S ^ae   Preuss, D ^ae   Pikaard, C S ^af   Paulsen, I T ^a   Sussman, M ^ag   Britt, A B ^ah   Selinger, D A ^ai   Pandey, R ^ai   Chandler, V L ^ai   Jorgensen, R A ^ai   Mount, D W ^aj   Pikaard, C ^af   Juergens, G ^ak   Meyerowitz, E M ^al   Dangl, J ^am   Jones, J D G ^an   Chen, M ^ao   Chory, J ^ao   Somerville, C ^ap   more..

^a J CRAIG VENTER INSTITUTE   (United States)

^b KAZUSA DNA RESEARCH INSTITUTE   (Japan)

^c UNIVERSITY OF PENNSYLVANIA   (United States)

^d PLANT GENE EXPRESSION CENTER   (United States)

^e STANFORD UNIVERSITY SCHOOL OF MEDICINE   (United States)

^f SALK INSTITUTE FOR BIOLOGICAL STUDIES   (United States)

^g EXELIXIS INC   (United States)

^h AGOWA GmbH   (Germany)

ⁱ JOHN INNES CENTRE   (United Kingdom)

^j QIAGEN GMBH   (Germany)

^k WAGENINGEN UNIVERSITY   (Netherlands)

^l GATC GmbH   (Germany)

^m SRD GmbH   (Germany)

ⁿ GHENT UNIVERSITY   (Belgium)

^o LABORATORY OF GENE TECHNOLOGY   (Belgium)

^p Genoscope   (France)

^q Genotype GmbH   (Germany)

^r EUROPEAN MOLECULAR BIOLOGY LABORATORY   (Germany)

^s Axaron Bioscience AG   (Germany)

^t MWG Biotech AG   (Germany)

^u UNIVERSITY OF PADOVA   (Italy)

^v WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

^w Simons Center for Quantitative Biology   (United States)

^x CELERA   (United States)

^y MAX PLANCK INSTITUTE OF BIOCHEMISTRY   (Germany)

^z Cereon Genomics   (United States)

^aa Max Delbruck Laboratorium der Max Planck Gesellschaft   (Germany)

^ab CENTRE NATIONAL DE SÉQUENÇAGE   (France)

^ac UNIVERSITY OF ULM   (Germany)

^ad MCGILL UNIVERSITY   (Canada)

^ae UNIVERSITY OF CHICAGO   (United States)

^af WASHINGTON UNIVERSITY   (United States)

^ag UNIVERSITY OF WISCONSIN MADISON   (United States)

^ah UNIVERSITY OF CALIFORNIA   (United States)

^ai UNIVERSITY OF ARIZONA   (United States)

^aj The University of Arizona   (United States)

^ak Entwicklungsgenetik   (Germany)

^al CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^am UNIVERSITY OF NORTH CAROLINA   (United States)

^an SAINSBURY LABORATORY   (United Kingdom)

^ao HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^ap GEOPHYSICAL LABORATORY   (United States)

more..

Author keywords

[No Author keywords available]

Indexed keywords

ARABIDOPSIS; ARTICLE; CROP; EUKARYOTE; EVOLUTION; GENE DUPLICATION; GENE FUNCTION; GENE LOSS; GENE SEQUENCE; GENE TRANSFER; GENETIC ANALYSIS; GENETIC CODE; GENOME; PRIORITY JOURNAL; PROTEIN EXPRESSION;

ANIMALS; ARABIDOPSIS; BIOLOGICAL TRANSPORT; CELL MEMBRANE; CELL NUCLEUS; CENTROMERE; CHLOROPLASTS; CHROMOSOME MAPPING; DNA REPAIR; DNA TRANSPOSABLE ELEMENTS; DNA, PLANT; DNA, RIBOSOMAL; GENE DUPLICATION; GENE EXPRESSION REGULATION, PLANT; GENOME, PLANT; HUMANS; LIGHT; MITOCHONDRIA; PHOTOSYNTHESIS; PLANT DISEASES; PROTEOME; RECOMBINATION, GENETIC; REPETITIVE SEQUENCES, NUCLEIC ACID; SEQUENCE ANALYSIS, DNA; SIGNAL TRANSDUCTION; SPECIES SPECIFICITY; TELOMERE;

EID: 0034649566     PISSN: 00280836     EISSN: None     Source Type: Journal    
DOI: 10.1038/35048692     Document Type: Article

References (122)

1. Sequence and analysis of the genome of C. elegans
2. The genome sequence of Drosophila melanogaster
3. Arabidopsis thaliana: A model plant for genome analysis
4. Sequence and analysis of chromosome 2 of the plant Arabidopsis thaliana
5. Sequence and analysis of chromsome 4 of the plant Arabidopsis thaliana
6. Sequence and analysis of chromosome 1 of the plant Arabidopsis thaliana
7. Sequence and analysis of chromosome 3 of the plant Arabidopsis thaliana
8. Sequence and analysis of chromosome 5 of the plant Arabidopsis thaliana
9. Construction and characterisation of a bacterial artificial chromosome library from Arabidopsis thaliana
10. Construction and characterization of the IGF Arabidopsis BAC library
11. Generation of a high-quality P1 library of Arabidopsis suitable for chromosome walking
12. Complementation of plant mutants with large genomic DNA fragments by a transformation-competent artificial chromosome vector accelerates positional cloning
13. A map or sequence analysis of the Arabidopsis thaliana genome
14. A complete BAC-based physical map of the Arabidopsis thaliana genome
15. Structural analysis of Arabidopsis thaliana chromosome 5. I. Sequence features of the 1.6 Mb regions covered by twenty physically assigned P1 clones
16. BAC representation of two low-copy regions of the genome of Arabidopsis thaliana
17. Genetic definition and sequence analysis of Arabidopsis centromeres
18. tRNAscan-SE: A program for improved detection of transfer RNA genes in genomic sequence
19. Evaluation of gene prediction software using a genomic data set: Application to Arabidopsis thaliana sequences
20. Overview of the yeast genome
21. Functional and structural genomics using PEDANT
22. The complete genome sequence of Escherichia coli K-12
23. Lessons from the sequencing of the genome of a unicellular cyanobacterium, Synechocystis SP. PCC6803
24. RPS2 of Arabidopsis thaliana a leucine-rich repeat class of plant disease resistance genes
25. F box proteins are receptors that recruit phsphorylated substrates to the SCF ubiquitin-ligase complex
26. RING finger proteins: Mediators of ubiquitin ligase activity
27. Comparative genomics of the eukaryotes
28. Alignment of whole genomes
29. Extensive duplication and reshuffling in the Arabidopsis genome
30. Genome evolution in polyploids
31. DNA sequence evidence for the segmental allotetraploid origin of maize
32. Comparing sequenced segments of the tomato and Arabidopsis genomes: Large-scale duplication followed by selective gene loss creates a network of synteny
33. Pronounced intraspecific haplotype divergence at the RPP5 complex disease resistance locus of Arabidopsis
34. Structure, function, and evolution of plant disease resistance genes
35. High density molecular linkage maps of the tomato and potato genomes
36. Grasses, line up and form a circle
37. Comparative genome analysis reveals extensive conservation of genome organisation for Arabidopsis thaliana and Capsella rubella
38. A 30 centimorgan segment of Arabidopsis thaliana chromosome 4 has six collinear homologues within the Brassica napus genome
39. Comparative physical mapping of segments of the genome of Brassica oleracea var alboglabra that are homologous to sequenced regions of the chromosomes 4 and 5 of Arabidopsis thaliana
40. Date of the monocot-dicot divergence estimated from the chloroplast DNA sequence data
41. Identification and analysis of homologous segments of the genomes of rice and Arabidopsis thaliana
42. Sequence level analysis of homologous segments of the genomes of rice and Arabidopsis thaliana
43. Complete structure of the chloroplast genome of Arabidopsis thaliana
44. The mitochondrial genome in Arabidopsis thaliana contains 57 genes in 366,924 nucleotides
45. Dynamic evolution of plant mitochondrial genomes: Mobile genes and introns and highly variable mutation rates
46. Transposon diversity in Arabidopsis thaliana
47. Mutator-like elements (MULEs) in Arabidopsis thaliana: Structure, diversity and evolution
48. Evidence that a family of miniature inverted-repeat transposable elements (MITEs) from the Arabidopsis thaliana genome has arisen from a pogo-like DNA transposon
49. Transposons, DNA methylation and gene control
50. Robertson's Mutator transposons in Arabidopsis are regulated by the chromatin-remodeling gene Decrease in DNA Methylation (DDM1)
51. Nested retrotransposons in the intergenic regions of the maize genome
52. Two-dimensional RFLP analyses reveal megabase-sized dusters of rRNA gene variants in Arabidopsis thaliana, suggesting local spreading of variants as the mode for gene homogenization during concerted evolution
53. Cytogenetics for the model system Arabidopsis thaliana
54. Isolation of a higher eukarotic telomere from Arabidopsis thaliana
55. Arabidopsis thaliana centromere regions: Genetic map positions and repetitive DNA structure
56. The complete sequence of a heterochromatic island from a higher eukaryote
57. Integrated cytogenetic map of chromosome arm 4S of A. thaliana: Structural organization of heterochromatic knob and centromere region
58. Microbial genome analyses: Comparative transport capabilities in eighteen prokaryotes
59. Unified inventory of established and putative transporters encoded within the complete genome of Saccharomyces cerevisiae
60. A role for the AKT1 potassium channel in plant nutrition
61. Depolarization of the plasma membrane of Neurospora during active transport of glucose: Evidence for a proton-dependent cotransport system
62. Systemin: A polypeptide signal for plant defensive genes
63. A phylogenomic study of DNA repair genes, proteins, and processes
64. Structure and function of transcription-repair coupling factor. Structural domains and binding properties
65. Molecular genetics of DNA repair in higher plants
66. Second family of histone deacetylases
67. Conserved plant genes with similarity to mammalian de novo DNA methyltransferases
68. A DNA methyltransferase homologue with a chromodomain exists in multiple polymorphic forms in Arabidopsis
69. Drosophila proteins related to vertebrate DNA (5-cytosine) methyltransferases
70. An RNA-dependent-RNA polymerase in Arabidopsis is required for post transcriptional gene silencing mediated by a transgene but not by a virus - The truth
71. A genomic perspective on plant transcription factors
72. SHATTERPROOF MADS-box genes control seed dispersal in Arabidopsis
73. B and C floral organ identity functions require SEPALLATA MADS-box genes
74. Higher plant cells: Gamma-tubulin and microtubule nucleation in the absence of centrosomes
75. Unique features of the plant vacuolar sorting machinery
76. The Rrop GTPase switch turns on polar growth in pollen
77. Triggering the cell cycle in plants
78. Cytokinesis in flowering plants: Cellular process and developmental integration
79. Plants, animals, and the logic of development
80. Divergence time estimates for the early history of animal phyla and the origin of plants, animals and fungi
81. Receptor kinase activation and signal transduction in plants: An emerging picture
82. Eukaryotic phytochromes: Light-regulated serine/threonine protein kinases with histidine kinase ancestry
83. Conservation and innovation in plant signaling pathways
84. Molecular cloning of cDNAs from maize and Arabidopsis encoding a G protein beta subunit
85. Cyclic GMP and calcium mediate phytochrome phototransduction
86. Ethylene signaling: From mutants to molecules
87. Two-component systems in plant signal transduction
88. Genes encoding pseudo-response regulators: Insight into His-to-Asp phosphorelay and circadian rhythm in Arabidopsis thaliana
89. Phosphorelay signal transduction: The emerging family of plant response regulators
90. Cloning of the Arabidopsis clock gene TOC1, an autoregulatory response regulator homologue
91. Plant-pathogen arms races at the molecular level
92. Signal transduction in the plant innate immune response
93. Plant disease-resistance proteins and the gene-for-gene concept
94. A conserved signaling pathway: The Drosophila toll-dorsal pathway
95. Identification of paracaspases and metacaspases: Two ancient families of caspase-like proteins, one of which plays a key rote in MALT lymphoma
96. Light control of plant development
97. Blue-light photoreceptors in higher plants
98. LOV (light, oxygen, or voltage) domains of the blue-light photoreceptor phototropin (nph1): Binding sites for the chromophore flavin mononucleotide
99. Structure and function of photosystem I
100. Complete sequence of the maize chloroplast genome: Gene content, hotspots of divergence and fine tuning of genetic information by transcript editing
101. Toward a functional catalog of the plant genome. A survey of genes for lipid biosynthesis
102. Photorespiration deficient mutants of Arabidopsis thaliana lacking mitochrondrial serine transhydroxymethylase activity
103. The cellulose synthase superfamily
104. A recipe for cellulose
105. Sur la loi de disjonction des hybrides
106. Naturally occurring variation in Arabidopsis: An underexploited resource for plant genetics
107. Functional genomics and the virtual plant. A blueprint for understanding how plants are built and how to improve them
108. Prediction of complete gene structures in human genomic DNA
109. GeneMark.hmm: New solutions for gene finding
110. Locating protein-coding regions in human DNA sequences by a multiple sensor-neural network approach
111. Interpolated Markov models for eukaryotic gene finding
112. Splice site prediction in Arabidopsis thaliana DNA by combining local and global sequence information
113. Prediction of locally optimal splice sites in plant pre-mRNA with applications to gene identification in Arabidopsis thaliana genomic DNA
114. The TIGR gene indices: Reconstruction and representation of expressed gene sequences
115. A tool for analyzing and annotating genomic sequences
116. Basic local alignment search tool
117. DIALIGN2: Improvement of the segment-to-segment approach to multiple sequence alignment
118. SCOP: A structural classification of proteins database for the investigation of sequences and structures
119. Predicting subcellular localization of proteins based on their N-terminal amino acid sequence