Author
B. Obermaier
Bio: B. Obermaier is an academic researcher from MediGene. The author has contributed to research in topics: Gene & Genome. The author has an hindex of 7, co-authored 7 publications receiving 2222 citations.
Topics: Gene, Genome, Sequence analysis, Chromosome 19, Chromosome 4
Papers
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John Innes Centre1, Harvard University2, Ghent University3, University of Paris4, Trinity College, Dublin5, University of East Anglia6, Spanish National Research Council7, Agricultural University of Athens8, MediGene9, Centre national de la recherche scientifique10, Katholieke Universiteit Leuven11, Max Planck Society12
TL;DR: Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases, and 54% of the predicted genes had significant similarity to known genes, and other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, and the frequent occurrence of clustered gene families.
Abstract: The plant Arabidopsis thaliana (Arabidopsis) has become an important model species for the study of many aspects of plant biology. The relatively small size of the nuclear genome and the availability of extensive physical maps of the five chromosomes provide a feasible basis for initiating sequencing of the five chromosomes. The YAC (yeast artificial chromosome)-based physical map of chromosome 4 was used to construct a sequence-ready map of cosmid and BAC (bacterial artificial chromosome) clones covering a 1.9-megabase (Mb) contiguous region, and the sequence of this region is reported here. Analysis of the sequence revealed an average gene density of one gene every 4.8 kilobases (kb), and 54% of the predicted genes had significant similarity to known genes. Other interesting features were found, such as the sequence of a disease-resistance gene locus, the distribution of retroelements, the frequent occurrence of clustered gene families, and the sequence of several classes of genes not previously encountered in plants.
832 citations
TL;DR: Analysis of 17.38 megabases of unique sequence, representing about 17% of the Arabidopsis genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements.
Abstract: The higher plant Arabidopsis thaliana (Arabidopsis) is an important model for identifying plant genes and determining their function. To assist biological investigations and to define chromosome structure, a coordinated effort to sequence the Arabidopsis genome was initiated in late 1996. Here we report one of the first milestones of this project, the sequence of chromosome 4. Analysis of 17.38 megabases of unique sequence, representing about 17% of the genome, reveals 3,744 protein coding genes, 81 transfer RNAs and numerous repeat elements. Heterochromatic regions surrounding the putative centromere, which has not yet been completely sequenced, are characterized by an increased frequency of a variety of repeats, new repeats, reduced recombination, lowered gene density and lowered gene expression. Roughly 60% of the predicted protein-coding genes have been functionally characterized on the basis of their homology to known genes. Many genes encode predicted proteins that are homologous to human and Caenorhabditis elegans proteins.
411 citations
Centre national de la recherche scientifique1, Foundation for Research & Technology – Hellas2, Université libre de Bruxelles3, University of Salamanca4, Autonomous University of Madrid5, University of Paris6, Instituto Gulbenkian de Ciência7, Goethe University Frankfurt8, Ludwig Maximilian University of Munich9, University of Manchester10, Pasteur Institute11, Université catholique de Louvain12, Royal Children's Hospital13, French Institute of Health and Medical Research14, John Radcliffe Hospital15, VU University Amsterdam16, University of Konstanz17, Carlsberg Laboratory18, University of Wrocław19
TL;DR: The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined, and the 666,448-base-pair sequence has revealed general chromosome patterns.
Abstract: The complete DNA sequence of the yeast Saccharomyces cerevisiae chromosome XI has been determined. In addition to a compact arrangement of potential protein coding sequences, the 666,448-base-pair sequence has revealed general chromosome patterns; in particular, alternating regional variations in average base composition correlate with variations in local gene density along the chromosome. Significant discrepancies with the previously published genetic map demonstrate the need for using independent physical mapping criteria.
383 citations
Washington University in St. Louis1, Max Planck Society2, Université libre de Bruxelles3, German Cancer Research Center4, Goethe University Frankfurt5, Université catholique de Louvain6, University of Liège7, John Radcliffe Hospital8, MediGene9, Vrije Universiteit Brussel10, Katholieke Universiteit Leuven11
TL;DR: No correlation was found between G+C content and gene density along the chromosome, and their variations are random, so accurate verification procedures demonstrate that there are less than two errors per 10,000 base pairs in the published sequence.
Abstract: Here we report the sequence of 569,202 base pairs of Saccharomyces cerevisiae chromosome V. Analysis of the sequence revealed a centromere, two telomeres and 271 open reading frames (ORFs) plus 13 tRNAs and four small nuclear RNAs. There are two Ty1 transposable elements, each of which contains an ORF (included in the count of 271). Of the ORFs, 78 (29%) are new, 81 (30%) have potential homologues in the public databases, and 112 (41%) are previously characterized yeast genes.
372 citations
Max Planck Society1, University of Padua2, University of Valencia3, University of Perpignan4, Université catholique de Louvain5, University of Amsterdam6, University of Grenoble7, Spanish National Research Council8, University of Naples Federico II9, J. Craig Venter Institute10, University of Chicago11, Celera Corporation12
TL;DR: In this paper, the authors present the sequence of chromosome 3, organized into four sequence segments (contigs), and the two largest (13.5 and 9.2 Mb) correspond to the top (long) and bottom (short) arms of the chromosome 3 and two small contigs are located in the genetically defined centromere.
Abstract: Arabidopsis thaliana is an important model system for plant biologists. In 1996 an international collaboration (the Arabidopsis Genome Initiative) was formed to sequence the whole genome of Arabidopsis and in 1999 the sequence of the first two chromosomes was reported. The sequence of the last three chromosomes and an analysis of the whole genome are reported in this issue. Here we present the sequence of chromosome 3, organized into four sequence segments (contigs). The two largest (13.5 and 9.2 Mb) correspond to the top (long) and the bottom (short) arms of chromosome 3, and the two small contigs are located in the genetically defined centromere. This chromosome encodes 5,220 of the roughly 25,500 predicted protein-coding genes in the genome. About 20% of the predicted proteins have significant homology to proteins in eukaryotic genomes for which the complete sequence is available, pointing to important conserved cellular functions among eukaryotes.
174 citations
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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.
8,742 citations
TL;DR: A neural network-based tool, TargetP, for large-scale subcellular location prediction of newly identified proteins has been developed and it is estimated that 10% of all plant proteins are mitochondrial and 14% chloroplastic, and that the abundance of secretory proteins, in both Arabidopsis and Homo, is around 10%.
4,268 citations
TL;DR: A dominant resistance module, for selection of S. cerevisiae transformants, which entirely consists of heterologous DNA is constructed and tested, and some kanMX modules are flanked by 470 bp direct repeats, promoting in vivo excision with frequencies of 10–3–10–4.
Abstract: We have constructed and tested a dominant resistance module, for selection of S. cerevisiae transformants, which entirely consists of heterologous DNA. This kanMX module contains the known kanr open reading-frame of the E. coli transposon Tn903 fused to transcriptional and translational control sequences of the TEF gene of the filamentous fungus Ashbya gossypii. This hybrid module permits efficient selection of transformants resistant against geneticin (G418). We also constructed a lacZMT reporter module in which the open reading-frame of the E. coli lacZ gene (lacking the first 9 codons) is fused at its 3' end to the S. cerevisiae ADH1 terminator. KanMX and the lacZMT module, or both modules together, were cloned in the center of a new multiple cloning sequence comprising 18 unique restriction sites flanked by Not I sites. Using the double module for constructions of in-frame substitutions of genes, only one transformation experiment is necessary to test the activity of the promotor and to search for phenotypes due to inactivation of this gene. To allow for repeated use of the G418 selection some kanMX modules are flanked by 470 bp direct repeats, promoting in vivo excision with frequencies of 10(-3)-10(-4). The 1.4 kb kanMX module was also shown to be very useful for PCR based gene disruptions. In an experiment in which a gene disruption was done with DNA molecules carrying PCR-added terminal sequences of only 35 bases homology to each target site, all twelve tested geneticin-resistant colonies carried the correctly integrated kanMX module.
2,727 citations
TL;DR: The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms and reveals the evolutionary generation of diversity in the regulation of transcription.
Abstract: The completion of the Arabidopsis thaliana genome sequence allows a comparative analysis of transcriptional regulators across the three eukaryotic kingdoms. Arabidopsis dedicates over 5% of its genome to code for more than 1500 transcription factors, about 45% of which are from families specific to plants. Arabidopsis transcription factors that belong to families common to all eukaryotes do not share significant similarity with those of the other kingdoms beyond the conserved DNA binding domains, many of which have been arranged in combinations specific to each lineage. The genome-wide comparison reveals the evolutionary generation of diversity in the regulation of transcription.
2,582 citations
TL;DR: The WRKY proteins are a superfamily of transcription factors with up to 100 representatives in Arabidopsis that appear to be involved in the regulation of various physio-logical programs that are unique to plants, including pathogen defense, senescence and trichome development.
2,447 citations