Sequence and analysis of chromosome 4 of the plant Arabidopsis thaliana

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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.

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Figure 2: Functional analysis of genes.
Figure 3: Distribution of multigene families and gene clusters on Arabidopsis chromosomes.
Figure 4: Fluorescent in situ hybridization analysis of sequences in the heterochromatic region.
Figure 5: Distribution of sequence repeats.
Figure 1: Distribution of predicted genes, repeats and transcript levels on sequenced regions of chromosome 4.

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Data deposits

The sequence and preliminary analysis of clones and PCR products were made available immediately after completion through the MATDB database12. The results of computational analyses, including the functional and structural characterization of the protein sequences involved, are available at the PEDANT-pro genome analysis server ( Underlying recombinant clones can be obtained from the NASC ( The accession numbers for chromosome 4 are: short arm, AJ270058; long arm, AJ270060.


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We wish to thank A. Schäffer for invaluable assistance with the IMPALA software and S. Brenner for providing an up-to-date version of the SCOP database. We are grateful to S. Choi for a copy of his large-insert BAC library. Scientists at the John Innes Centre are acknowledged for their help in interpreting gene function. This work was funded in part by Contracts from the European Commission, by the National Science Foundation (NSF) Cooperative Agreement (funded by the NSF, US Department of Agriculture and the US Department of Energy), and by a grant from the USDA NRI Plant Genome Program. Additional support from the Biotechnology and Biological Sciences Research Council, Bundesministerium f. Bildung, Forschung und Technologie, Groupe de Recherche et d'etude des Genomes, Plan Nacional de Investigacion Cientifica y Technica, Westvaco Corporation and D. L. Luke III is gratefully acknowledged.

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Correspondence to M. Bevan.

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