Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
TL;DR: 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.
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.
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TL;DR: The finding that the upstream sequences of Mn and peroxisomal Cu/Zn SODs have three common elements suggests a common regulatory pathway, which is borne out in the research literature.
Abstract: Reactive O2 species (ROS) are produced in both unstressed and stressed cells. Plants have welldeveloped defence systems against ROS, involving both limiting the formation of ROS as well as instituting its removal. Under unstressed conditions, the formation and removal of O2 are in balance. However, the defence system, when presented with increased ROS formation under stress conditions, can be overwhelmed. Within a cell, the superoxide dismutases (SODs) constitute the first line of defence against ROS. Specialization of function among the SODs may be due to a combination of the influence of subcellular location of the enzyme and upstream sequences in the genomic sequence. The commonality of elements in the upstream sequences of Fe, Mn and CuuZn SODs suggests a relatively recent origin for those regulatory regions. The differences in the upstream regions of the three FeSOD genes suggest differing regulatory control which is borne out in the research literature. The finding that the upstream sequences of Mn and peroxisomal CuuZn SODs have three common elements suggests a common regulatory pathway. The tools are available to dissect further the molecular basis for antioxidant defence responses in plant cells. SODs are clearly among the most important of those defences, when coupled with the necessary downstream events for full detoxification of ROS.
2,378 citations
TL;DR: This work predicts regulatory targets for 14 Arabidopsis microRNAs (miRNAs) by identifying mRNAs with near complementarity and identifies members of transcription factor gene families involved in developmental patterning or cell differentiation.
2,221 citations
Cites background from "Analysis of the genome sequence of ..."
...For the control study, the identical vations argue strongly for a role in targeting mRNAs in GenomeScan/PatScan procedure was applied to the 44 Arabidopsis mRNAs with sites complementary (allowing up to three mismatches)addition to any possible role in targeting DNA....
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...Oryza genes are labeled either by their tentative consensus (TC) numbers from the TIGR rice gene index (version 9.0) or by the genomic contig of the mRNA predicted by GenomeScan. miRNA targets that act as developmental regulators computational approach could also identify miRNA targets in C. elegans and D. melanogaster....
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...Plant Cell 9, 841–857. the miRNA complementarity site in the mRNA without Arabidopsis Genome Initiative (2000)....
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...In gous Oryza proteins were predicted from the unannotated Oryza those cases where the miRNAs might not be mediating contigs (Yu et al., 2002) by GenomeScan, a program that identifies mRNA cleavage, they might attenuate translation (Olsen genes within genomic sequence using homology to input protein sequences combined with an ab initio gene-finding algorithm (Yehand Ambros, 1999), act as guide RNAs for mRNA modifiet al., 2001)....
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...13, 497–498.from the genomic GenBank files, January 2002 release (Arabidopsis Genome Initiative, 2000)....
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TL;DR: Mutation of an Arabidopsis Dicer homolog, CARPEL FACTORY, prevents the accumulation of miRNAs, showing that similar mechanisms direct miRNA processing in plants and animals.
Abstract: The present invention generally relates to the production and expression of microRNA (miRNA) in plants. In some cases, production and expression of miRNA can be used to at least partially inhibit or alter gene expression in plants. For instance, in some embodiments, a nucleotide sequence, which may encode a sequence substantially complementary to a gene to be inhibited or otherwise altered, may be prepared and inserted into a plant cell. Expression of the nucleotide sequence may cause the formation of precursor miRNA, which may, in turn, be cleaved (for example, with Dicer or other nucleases, including, for example, nucleases associated with RNA interference), to produce an miRNA sequence substantially complementary to the gene. The miRNA sequence may then interact with the gene (e.g., complementary binding) to inhibit the gene. In some cases, the nucleotide sequence may be an isolated nucleotide sequence. Other embodiments of the invention are directed to the precursor miRNA and/or the final miRNA sequence, as well as methods of making, promoting, and use thereof.
2,179 citations
TL;DR: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
Abstract: An annotated reference sequence representing the hexaploid bread wheat genome in 21 pseudomolecules has been analyzed to identify the distribution and genomic context of coding and noncoding elements across the A, B, and D subgenomes. With an estimated coverage of 94% of the genome and containing 107,891 high-confidence gene models, this assembly enabled the discovery of tissue- and developmental stage-related coexpression networks by providing a transcriptome atlas representing major stages of wheat development. Dynamics of complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. This community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding.
2,118 citations
Book•
01 Jan 2002
TL;DR: This chapter discusses the organization and structure of Photosynthetic Systems, as well as the history and development of Photosynthesis, and the origins and evolution of photosynthesis.
Abstract: 1. Light and Energy. 2. Organization and Structure of Photosynthetic Systems. 3. History and Development of Photosynthesis. 4. Photosynthetic Pigments-Structure and Spectroscopy. 5. Antenna Complexes and Energy Transfer Processes. 6. Reaction Center Complexes. 7. Electron Transfer Pathways and Components. 8. Chemiosmotic Coupling and ATP Synthesis. 9. Carbon Metabolism. 10. Genetics, Assembly and Regulation of Photosynthetic. Systems. 11. Origin and Evolution of Photosynthesis. Appendix 1. Light, Energy and Kinetics
2,070 citations
References
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TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
88,255 citations
TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
Abstract: We describe a program, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases. Two previously described tRNA detection programs are used as fast, first-pass prefilters to identify candidate tRNAs, which are then analyzed by a highly selective tRNA covariance model. This work represents a practical application of RNA covariance models, which are general, probabilistic secondary structure profiles based on stochastic context-free grammars. tRNAscan-SE searches at approximately 30 000 bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA homologues such as selenocysteine tRNAs, tRNA-derived repetitive elements and tRNA pseudogenes.
9,629 citations
TL;DR: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.
Abstract: The 4,639,221-base pair sequence of Escherichia coli K-12 is presented. Of 4288 protein-coding genes annotated, 38 percent have no attributed function. Comparison with five other sequenced microbes reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident. The largest family of paralogous proteins contains 80 ABC transporters. The genome as a whole is strikingly organized with respect to the local direction of replication; guanines, oligonucleotides possibly related to replication and recombination, and most genes are so oriented. The genome also contains insertion sequence (IS) elements, phage remnants, and many other patches of unusual composition indicating genome plasticity through horizontal transfer.
7,723 citations
TL;DR: This database provides a detailed and comprehensive description of the structural and evolutionary relationships of the proteins of known structure and provides for each entry links to co-ordinates, images of the structure, interactive viewers, sequence data and literature references.
6,603 citations
Mark Raymond Adams1, Susan E. Celniker2, Robert A. Holt1, Cheryl A. Evans1 +191 more•Institutions (23)
TL;DR: The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.
Abstract: The fly Drosophila melanogaster is one of the most intensively studied organisms in biology and serves as a model system for the investigation of many developmental and cellular processes common to higher eukaryotes, including humans. We have determined the nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map. Efforts are under way to close the remaining gaps; however, the sequence is of sufficient accuracy and contiguity to be declared substantially complete and to support an initial analysis of genome structure and preliminary gene annotation and interpretation. The genome encodes approximately 13,600 genes, somewhat fewer than the smaller Caenorhabditis elegans genome, but with comparable functional diversity.
6,180 citations
"Analysis of the genome sequence of ..." refers background or methods in this paper
...Gene ®nding involved three steps: (1) analysis of BAC sequences using a computational gene ®nder; (2) alignment of the sequence to the protein and EST databases; (3) assignment of functions to each of the genes....
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...The Arabidopsis genome has a wealth of class I (2,109) and II (2,203) elements, including several new groups (1,209 elements; Supplementary Information Table 4)....
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