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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)
  • Citations (6776)
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References118
Newest
Published on Jan 1, 2001in Bioinformatics 5.48
Dmitrij Frishman49
Estimated H-index: 49
(Biomax Informatics AG),
Kaj Albermann13
Estimated H-index: 13
(Biomax Informatics AG)
+ 4 AuthorsHans-Werner Mewes8
Estimated H-index: 8
(Biomax Informatics AG)
Motivation: Enormous demand for fast and accurate analysis of biological sequences is fuelled by the pace of genome analysis efforts. There is also an acute need in reliable up-to-date genomic databases integrating both functional and structural information. Here we describe the current status of the PEDANT software system for highthroughput analysis of large biological sequence sets and the genome analysis server associated with it. Results: The principal features of PEDANT are: (i) completely ...
183 Citations Source Cite
Published on Dec 1, 2000in Nature 41.58
Athanasios Theologis41
Estimated H-index: 41
(University of California, Berkeley),
Joseph R. Ecker121
Estimated H-index: 121
(University of Pennsylvania)
+ 86 AuthorsCheryl L. Bowman7
Estimated H-index: 7
The genome of the flowering plant Arabidopsis thaliana has five chromosomes1,2. Here we report the sequence of the largest, chromosome 1, in two contigs of around 14.2 and 14.6 megabases. The contigs extend from the telomeres to the centromeric borders, regions rich in transposons, retrotransposons and repetitive elements such as the 180-base-pair repeat. The chromosome represents 25% of the genome and contains about 6,850 open reading frames, 236 transfer RNAs (tRNAs) and 12 small nuclear RNAs....
211 Citations Source Cite
Published on Oct 1, 2000in Current Opinion in Plant Biology 7.35
Keiko U. Torii37
Estimated H-index: 37
(University of Washington)
Abstract Plant receptor kinases play key roles in the cell–cell recognition process during development, defense against pathogens, and self incompatibility. Recent identification of potential ligand molecules and downstream signaling components, together with biochemical studies on receptor-complex formation, have revealed an emerging picture of receptor-kinase activation and signal transduction in plants.
118 Citations Source Cite
Published on Oct 1, 2000in Current Opinion in Plant Biology 7.35
Anna N. Stepanova16
Estimated H-index: 16
(Salk Institute for Biological Studies),
Joseph R. Ecker121
Estimated H-index: 121
(Salk Institute for Biological Studies)
Abstract The past decade has been incredibly productive for ethylene researchers. Major components in the ethylene signaling pathway in plants have been identified and characterized. The past year’s contributions include the crystallographic analysis of the Arabidopsis ETR1 receiver domain, antisense studies of the tomato ethylene receptor genes LeETR4 and NR , and the cloning and functional characterization of several Arabidopsis EREBP-related transcription activators and repressors, and of an ...
163 Citations Source Cite
Published on Oct 1, 2000in Molecular Cell 14.25
Anthony G. Uren19
Estimated H-index: 19
(Genentech),
Karen O'Rourke36
Estimated H-index: 36
(Genentech)
+ 4 AuthorsVishva M. Dixit133
Estimated H-index: 133
(Genentech)
Abstract Caspases are cysteine proteases essential to apoptosis. We have identified two families of caspase-like proteins, Paracaspases (found in metazoans and Dictyostelium ) and metacaspases (found in plants, fungi, and protozoa). Metazoan paracaspase prodomains contain a death domain and immunoglobulin domains. Several plant metacaspase prodomains contain zinc finger motifs resembling those in the plant hypersensitive response/cell death protein lsd-1. The human paracaspase prodomain binds Bc...
851 Citations Source Cite
Published on Oct 1, 2000in Cell 31.40
Donald R. McCarty46
Estimated H-index: 46
(University of Florida),
Joanne Chory113
Estimated H-index: 113
(Salk Institute for Biological Studies)
In this brief survey, we have highlighted just a few examples where we can begin to trace the origins of novelty in the evolution of plant signaling pathways. The source materials derive from some expected sources, such as the progenitor of the chloroplast genome and genes inherited from the common ancestor of all eukaryotes, but also include a surprising number of novel genes of unknown origin. While the mechanisms that allow evolution of new functions for old genes are presumably similar in eu...
107 Citations Source Cite
Published on Oct 1, 2000in Plant Physiology 5.95
Todd Richmond42
Estimated H-index: 42
(Carnegie Institution for Science),
Chris Somerville107
Estimated H-index: 107
(Carnegie Institution for Science)
The availability of a nearly complete genome sequence for Arabidopsis has created many novel opportunities to identify, by computational methods, the genes that encode enzymes, which have been difficult to characterize by conventional means. We have used this approach to identify a large family of
411 Citations Source Cite
Published on Oct 1, 2000in Current Opinion in Plant Biology 7.35
Jose Luis Riechmann7
Estimated H-index: 7
(Mendel Biotechnology, Inc.),
Oliver J. Ratcliffe13
Estimated H-index: 13
(Mendel Biotechnology, Inc.)
Data from the Arabidopsis genome project suggest that more than 5% of the genes of this plant encode transcription factors. The necessity for the use of genomic analytical approaches becomes clear when it is considered that less than 10% of these factors have been genetically characterized. A variety of tools for functional genomic analyses in plants have been developed over the past few years. The availability of the full complement of Arabidopsis transcription factors, together with the result...
309 Citations Source Cite
Published on Sep 1, 2000in Cell 31.40
Claudio A. P. Joazeiro25
Estimated H-index: 25
(Salk Institute for Biological Studies),
Allan M. Weissman57
Estimated H-index: 57
Ubiquitination is a highly regulated and common cellular process with E3s as central players. RING finger proteins represent the largest class of E3s to date. Whether RING fingers are primarily modules that mediate ubiquitination and other protein modifications or if they have other discrete functions should soon become apparent. Mammalian genomes encode hundreds of RING finger proteins. Extrapolating from in vitro studies, we predict that many of these have the capacity to interact with E2s and...
1,005 Citations Source Cite
Published on Aug 4, 2000in Science 41.06
Carl A. Strayer7
Estimated H-index: 7
,
Tokitaka Oyama22
Estimated H-index: 22
+ 6 AuthorsSteve A. Kay98
Estimated H-index: 98
The toc1 mutation causes shortened circadian rhythms in light-grown Arabidopsis plants. Here, we report the same toc1 effect in the absence of light input to the clock. We also show that TOC1 controls photoperiodic flowering response through clock function. The TOC1 gene was isolated and found to encode a nuclear protein containing an atypical response regulator receiver domain and two motifs that suggest a role in transcriptional regulation: a basic motif conserved within the CONSTANS family of...
628 Citations Source Cite
Cited By6776
Newest
Published on Feb 21, 2019in Genome Biology 13.21
Xin Qiao5
Estimated H-index: 5
(Nanjing Agricultural University),
Qionghou Li (Nanjing Agricultural University)+ 5 AuthorsAndrew H. Paterson100
Estimated H-index: 100
(University of Georgia)
Background The sharp increase of plant genome and transcriptome data provide valuable resources to investigate evolutionary consequences of gene duplication in a range of taxa, and unravel common principles underlying duplicate gene retention.
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Published on May 1, 2019in Horticulture research 3.37
Rachel Shahan3
Estimated H-index: 3
(University of Maryland, College Park),
Dongdong Li (University of Maryland, College Park), Zhongchi Liu25
Estimated H-index: 25
(University of Maryland, College Park)
Fragaria vesca (F. vesca), the wild strawberry, is a diploid model for the commercial, octoploid strawberry as well as other members of the economically relevant Rosaceae family. Unlike the fruits of tomato and Arabidopsis, the fleshy fruit of strawberry is unique in that it is derived from the floral receptacle and has an external seed configuration. Thus, identification and subsequent characterization of receptacle-expressed genes may shed light on novel developmental processes or provide insi...
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Published on May 6, 2019in Scientific Reports 4.12
Jinglei Wang , Tianhua Hu2
Estimated H-index: 2
+ 3 AuthorsChonglai Bao2
Estimated H-index: 2
The leucine-rich repeat receptor-like protein kinase (LRR-RLK) plays an important role in plant development and disease defence. Although genome-wide studies of LRR-RLKs have been performed in several species, a comprehensive analysis, including evolutionary, structural and expressional analyses and their relationships to function, has not been carried out in the radish (Raphanus sativus L.). In this study, we identified 292 LRR-RLK genes in the R. sativus genome and classified them into 23 subg...
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Published on Feb 13, 2019in Scientific Reports 4.12
Fatemeh Ghaderiardakani1
Estimated H-index: 1
(University of Birmingham),
Ellen Collas (University of Birmingham)+ 3 AuthorsJuliet C. Coates17
Estimated H-index: 17
(University of Birmingham)
The growing population requires sustainable, environmentally-friendly crops. The plant growth-enhancing properties of algal extracts have suggested their use as biofertilisers. The mechanism(s) by which algal extracts affect plant growth are unknown. We examined the effects of extracts from the common green seaweed Ulva intestinalis on germination and root development in the model land plant Arabidopsis thaliana. Ulva extract concentrations above 0.1% inhibited Arabidopsis germination and root g...
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Published on Jan 25, 2019in Nature Communications 12.35
Junpeng Shi4
Estimated H-index: 4
(China Agricultural University),
Xuxu Ma1
Estimated H-index: 1
(China Agricultural University)
+ 13 AuthorsWei Zhan
Broomcorn millet (Panicum miliaceum L.) has strong tolerance to abiotic stresses, and is probably one of the oldest crops, with its earliest cultivation that dated back to ca. ~10,000 years. We report here its genome assembly through a combination of PacBio sequencing, BioNano, and Hi-C (in vivo) mapping. The 18 super scaffolds cover ~95.6% of the estimated genome (~887.8 Mb). There are 63,671 protein-coding genes annotated in this tetraploid genome. About ~86.2% of the syntenic genes in foxtail...
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Published on Mar 14, 2019in Nature Communications 12.35
Min Xie9
Estimated H-index: 9
(The Chinese University of Hong Kong),
Claire Yik-Lok Chung1
Estimated H-index: 1
(The Chinese University of Hong Kong)
+ 27 AuthorsSuk-Wah Tong3
Estimated H-index: 3
(The Chinese University of Hong Kong)
Efficient crop improvement depends on the application of accurate genetic information contained in diverse germplasm resources. Here we report a reference-grade genome of wild soybean accession W05, with a final assembled genome size of 1013.2 Mb and a contig N50 of 3.3 Mb. The analytical power of the W05 genome is demonstrated by several examples. First, we identify an inversion at the locus determining seed coat color during domestication. Second, a translocation event between chromosomes 11 a...
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Published on Jul 4, 2019in Critical Reviews in Biotechnology 5.24
Tong Li2
Estimated H-index: 2
(Nanjing Agricultural University),
Ya-Hui Wang1
Estimated H-index: 1
(Nanjing Agricultural University)
+ 3 AuthorsAi-Sheng Xiong30
Estimated H-index: 30
(Nanjing Agricultural University)
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Published on Jul 1, 2019in Phytochemistry 3.19
Dan Liu1
Estimated H-index: 1
(Southwest University),
Shuai Meng1
Estimated H-index: 1
(Southwest University)
+ 2 AuthorsGuangwei Yang1
Estimated H-index: 1
(Southwest University)
Abstract Herein, five polyphenol oxidases (PPOs) obtained from Morus notabilis (Mn) were characterized. Chlorogenic acid was the most readily oxidized substrate by these MnPPOs, and the products derived from the oxidation of chlorogenic acid by MnPPOs were tested for antimicrobial activity. The results showed that products of the five MnPPOs exhibited good inhibitory effects against Escherichia coli , Pseudomonas aeruginosa , Staphylococcus aureus , Sclerotinia sclerotiorum , and Botrytis cinere...
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