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Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
Published on Jan 1, 2000in Nature 41.58
· DOI :10.1038/35048692
Arabidopsis Genome Initiative1
Estimated H-index: 1
Abstract
The flowering plant Arabidopsis thaliana is an important model system for identifying genes and determining their functions. Here we report the analysis of the genomic sequence of Arabidopsis. The sequenced regions cover 115.4 megabases of the 125-megabase genome and extend into centromeric regions. The evolution of Arabidopsis involved a whole-genome duplication, followed by subsequent gene loss and extensive local gene duplications, giving rise to a dynamic genome enriched by lateral gene transfer from a cyanobacterial-like ancestor of the plastid. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of Drosophila and Caenorhabditis elegans - the other sequenced multicellular eukaryotes. Arabidopsis has many families of new proteins but also lacks several common protein families, indicating that the sets of common proteins have undergone differential expansion and contraction in the three multicellular eukaryotes. This is the first complete genome sequence of a plant and provides the foundations for more comprehensive comparison of conserved processes in all eukaryotes, identifying a wide range of plant-specific gene functions and establishing rapid systematic ways to identify genes for crop improvement.
  • References (118)
  • Cited By (6700)
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References118
Published on Dec 1, 1999in Mutation Research-dna Repair
Jonathan A. Eisen80
Estimated H-index: 80
(Stanford University),
Philip C. Hanawalt75
Estimated H-index: 75
(Stanford University)
The ability to recognize and repair abnormal DNA structures is common to all forms of life. Studies in a variety of species have identified an incredible diversity of DNA repair pathways. Documenting and characterizing the similarities and differences in repair between species has important value for understanding the origin and evolution of repair pathways as well as for improving our understanding of phenotypes affected by repair (e.g., mutation rates, lifespan, tumorigenesis, survival in extr...
354 Citations Source Cite
Published on Jul 1, 1999in Nature Genetics 27.13
Marco A. Marra114
Estimated H-index: 114
(University of Washington),
Tamara A. Kucaba19
Estimated H-index: 19
(University of Washington)
+ 17 AuthorsC. Gund1
Estimated H-index: 1
(University of Washington)
Arabidopsis thaliana has emerged as a model system for studies of plant genetics and development, and its genome has been targeted for sequencing by an international consortium (the Arabidopsis Genome Initiative; http://genome-www.stanford.edu/Arabidopsis/agi.html). To support the genome- sequencing effort, we fingerprinted more than 20,000 BACs (ref. 2) from two high-quality publicly available libraries, generating an estimated 17-fold redundant coverage of the genome, and used the fingerprints...
117 Citations Source Cite
Published on Jul 1, 1999in Nature Genetics 27.13
Teresa Mozo1
Estimated H-index: 1
,
Ken Dewar35
Estimated H-index: 35
+ 8 AuthorsSebastian Meier-Ewert9
Estimated H-index: 9
Arabidopsis thaliana is a small flowering plant that serves as the major model system in plant molecular genetics'. The efforts of many scientists have produced genetic maps that provide extensive coverage of the genome (http://genome-www.stanford.edulArabidopsis/maps.html). Recently, detailed YAC, BAG, P1 and cosmid-based physical maps (that is, representations of genomic regions as sets of overlapping clones of corresponding libraries) have been established that extend over wide genomic areas ...
139 Citations Source Cite
Published on Jan 30, 1998in Science 41.06
Nicholas C. Carpita59
Estimated H-index: 59
(Purdue University),
Claudia E. Vergara7
Estimated H-index: 7
(Purdue University)
Cellulose, polymers of glucose organized into long fibrils, forms the bulk of the world's biomass. But the identity of the enzyme that makes this critical substance has been uncertain. In this week's issue, [ Arioli et al .][1] report the first confirmation that the gene CelA is indeed a cellulose synthase, and Carpita and Vergara, in their research commentary, explain why this result has been so long in coming and what we now know about how cellulose is made. [1]: http://www.sciencemag.org/cgi/...
67 Citations Source Cite
Published on Apr 1, 2000in Nature 41.58
Sarah J. Liljegren9
Estimated H-index: 9
(University of California, San Diego),
Gary S. Ditta35
Estimated H-index: 35
(University of California, San Diego)
+ 3 AuthorsMartin F. Yanofsky64
Estimated H-index: 64
(University of California, San Diego)
The fruit, which mediates the maturation and dispersal of seeds, is a complex structure unique to flowering plants. Seed dispersal in plants such as Arabidopsis occurs by a process called fruit dehiscence, or pod shatter. Few studies 1-3 have focused on identifying genes that regulate this process, in spite of the agronomic value of controlling seed dispersal in crop plants such as canola 4,5 . Here we show that the closely related SHATTERPROOF (SHP1) and SHATTERPROOF2 (SHP2) MADS-box genes are ...
606 Citations Source Cite
Published on May 1, 1998in Genetics 4.08
Steven Henikoff98
Estimated H-index: 98
(Fred Hutchinson Cancer Research Center),
Luca Comai58
Estimated H-index: 58
(University of Washington)
Chromodomains are thought to mediate protein-protein interactions between chromatin components. We have detected a chromodomain embedded within the catalytic region of a predicted Arabidopsis DNA methyltransferase that is diverged from other eukaryotic enzymes. The 791 residue "chromomethylase" (CMT1) is encoded by a floral transcript that is spliced from 20 exons and is present at only approximately 1/10(-7) of total mRNA. Genomic sequencing reveals an ancient haplotype split at CMT1 between Co...
165 Citations
Published on Nov 1, 1997in Genome Research 10.10
Elaine K. Round1
Estimated H-index: 1
,
Susan K. Flowers4
Estimated H-index: 4
,
Eric J. Richards37
Estimated H-index: 37
The genetic positions of the five Arabidopsis thaliana centromere regions have been identified by mapping size polymorphisms in the centromeric 180-bp repeat arrays. Structural and genetic analysis indicates that 180-bp repeat arrays of up to 1000 kb are found in the centromere region of each chromosome. The genetic behavior of the centromeric arrays suggests that recombination within the arrays is suppressed. These results indicate that the centromere regions of A. thaliana resemble human centr...
146 Citations Source Cite
Published on Aug 1, 2000in Journal of Molecular Biology 4.89
Ian T. Paulsen53
Estimated H-index: 53
(University of California, San Diego),
Lily Nguyen1
Estimated H-index: 1
(University of California, San Diego)
+ 2 AuthorsMilton H. Saier91
Estimated H-index: 91
(University of California, San Diego)
Abstract Here, we present a comprehensive analysis of solute transport systems encoded within the completely sequenced genomes of 18 prokaryotic organisms. These organisms include four Gram-positive bacteria, seven Gram-negative bacteria, two spirochetes, one cyanobacterium and four archaea. Membrane proteins are analyzed in terms of putative membrane topology, and the recognized transport systems are classified into 76 families, including four families of channel proteins, four families of prim...
225 Citations Source Cite
Kuo-Chen Yeh21
Estimated H-index: 21
,
Lagarias Jc1
Estimated H-index: 1
The discovery of cyanobacterial phytochrome histidine kinases, together with the evidence that phytochromes from higher plants display protein kinase activity, bind ATP analogs, and possess C-terminal domains similar to bacterial histidine kinases, has fueled the controversial hypothesis that the eukaryotic phytochrome family of photoreceptors are light-regulated enzymes. Here we demonstrate that purified recombinant phytochromes from a higher plant and a green alga exhibit serine/threonine kina...
333 Citations Source Cite
Published on Jun 1, 2000in Microscopy Research and Technique 1.09
Jean Canaday15
Estimated H-index: 15
(Centre national de la recherche scientifique),
Virginie Stoppin-Mellet13
Estimated H-index: 13
(Centre national de la recherche scientifique)
+ 2 AuthorsAnne-Catherine Schmit20
Estimated H-index: 20
(Centre national de la recherche scientifique)
The assembly of the higher plant cytoskeleton poses several fundamental ques- tions. Since different microtubule arrays are successively assembled during the cell cycle in the absence of centrosomes, we can ask how these arrays are assembled and spatially organized. Two hypotheses are under debate. Either multiple nucleation sites are responsible for the assembly and organization of microtubule arrays or microtubule nucleation takes place at one site, the nuclear surface. In the latter case, mic...
51 Citations Source Cite
Cited By6700
Published on Jan 1, 2002
Yukio Kawamura14
Estimated H-index: 14
(Iwate University),
Matsuo Uemura35
Estimated H-index: 35
(Iwate University)
Many plant species have obtained the capability to resist freezing and/or low temperatures and have thus extended their geographical distribution into regions with cold climates. A number of studies have been carried out to try to determine how these plants acclimate to low temperatures and survive under freezing conditions, and the results of those studies have indicated that irreversible damage in the plasma membrane that occurs during freeze-induced dehydration is the primary cause of freezin...
7 Citations Source Cite
Published on Jan 1, 2004
Yasuko Kamisugi15
Estimated H-index: 15
(University of Leeds),
Andrew C. Cuming24
Estimated H-index: 24
(University of Leeds)
The massive investment in genome sequencing in recent years has provided an ever-increasing resource of information for biologists. Comparative analysis of gene sequences reveals the evolutionary relatedness of organisms and predicts functions for hitherto unknown genes. Among the bryophytes, the moss Physcomitrella patens has been the focus of intensive gene discovery (EST) programmes in both the public and private sectors. Using simple bioinformatic tools combined with powerful PCR amplificati...
2 Citations Source Cite
Published on Jan 1, 2008
S. Sherman-Broyles1
Estimated H-index: 1
(Cornell University),
J. B. Nasrallah1
Estimated H-index: 1
(Cornell University)
Genetically determined self-incompatibility (SI) systems ensure high rates of out-crossing because they allow the pistil to recognise and reject genetically identical pollen. As such, SI systems are thought to be advantageous because populations with high levels of polymorphism have the genetic variability required for withstanding a wide range of environmental challenges. Nevertheless, SI has repeatedly been lost in plant lineages, and it has been noted that the most frequently travelled path i...
15 Citations Source Cite
Published on Feb 1, 2003in Genomics, Proteomics & Bioinformatics
Yin Long Qiu1
Estimated H-index: 1
(University of Michigan),
Jun Yu66
Estimated H-index: 66
(Beijing Genomics Institute)
Abstract The aquatic ferns of the genus Azolla are nitrogen-fixing plants that have great potentials in agricultural production and environmental conservation. Azolla in many aspects is qualified to serve as a model organism for genomic studies because of its importance in agriculture, its unique position in plant evolution, its symbiotic relationship with the N 2 -fixing cyanobacterium, Anabaena azollae , and its moderate-sized genome. The goals of this genome project are not only to understand...
7 Citations Source Cite
Published on May 15, 2010
Genomics is a young scientific discipline, the development of which has considerably facilitated the study of metabolic pathways in living organisms. The aim of this work was to present the fields of genomics and post-genomics, and to explain their principles and use in biochemistry in order to understand the metabolism of an organic entity.
Published on Apr 30, 2007in Molecules and Cells 3.08
Jin A Kim10
Estimated H-index: 10
,
Tae-Jin Yang25
Estimated H-index: 25
+ 11 AuthorsChoi Bs1
Estimated H-index: 1
Elucidation of the roles of circadian associated factors requires a better understanding of the molecular mechanisms of circadian rhythms, control of flowering time through photoperiodic pathways, and photosensory signal transduction. In Arabidopsis, the APRR1 quintet, APRRs 1, 3, 5, 7, and 9, are known as central oscillator genes. Other plants may share the molecular mechanism underlying the circadian rhythm. To identify and characterize these circadian response genes in Brassica crops whose ge...
23 Citations
Published on Jan 1, 2008
Cell walls are a distinct feature of plants and their chemical constituents, cellulose, hemicelluloses and lignin, are economically valuable. Plant fibres rich in cellulose, which mainly resides in ...
Published on Jan 1, 2010
Khalid Meksem3
Estimated H-index: 3
,
Günter Kahl3
Estimated H-index: 3
INDUCED MUTATIONS Physically induced mutagenesis: Ion beam mutagenesis (Magori, Tanaka, Kawaguchi) Ds transposon mutant lines for saturation mutagenesis of the Arabidopsis genome (Kuromori, Hirayama) Use of mutants from T-DNA insertion populations generated by high-throughput screening (Stracke, Huep, Weisshaar) Making mutations is an active process: Examining DNA polymerase errors (Eckert, Gestl) Tnt1 induced mutations in Medicago: Characterisation and Applications (Ratet, Cosson, Wen, Tadege, ...
15 Citations
Published on Apr 1, 2013in Physiological and Molecular Plant Pathology 1.40
Todd A. Naumann8
Estimated H-index: 8
,
Donald T. Wicklow34
Estimated H-index: 34
Abstract Chitinase modifying proteins, cmps, are secreted fungal proteases that truncate specific plant class IV chitinases by cleaving peptide bonds in their amino termini. We recently identified a cmp from the Zea mays (maize) pathogen Fusarium verticillioides and found that it is a member of the fungalysin class of proteases. We also found that Alternaria brassicae , a pathogen of the mustard plant family Brassicaceae, secretes a protease with the same activity. To determine which pathogens o...
8 Citations Source Cite
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