The genome sequence of the flowering plant Arabidopsis thaliana has been analyzed, revealing 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. 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. The genome sequence of Arabidopsis provides a means for understanding the genetic basis of differences between plants and other eukaryotes, and provides the foundation for detailed functional characterization of plant genes. Arabidopsis has many advantages for genome analysis, including a short generation time, small size, large number of offspring, and a relatively small nuclear genome. These advantages promoted the growth of a scientific community that has investigated the biological processes of Arabidopsis and has characterized many genes. To support these activities, an international collaboration (the Arabidopsis Genome Initiative, AGI) began sequencing the genome in 1996. The analysis of the completed Arabidopsis genome sequence, including annotation of predicted genes and assignment of functional categories, is reported. The genome sequence of a plant provides a means for understanding the genetic basis of differences between plants and other eukaryotes, and provides the foundation for detailed functional characterization of plant genes. The genome sequence of Arabidopsis has been compared to other plant species and accessions, revealing differences in gene structure, function, and organization. The genome of Arabidopsis contains a large number of tandemly repeated gene arrays, which may indicate more relaxed constraints on genome size in plants, or a more prominent role of unequal crossing over to generate new gene copies. The genome of Arabidopsis contains a large number of transposable elements, which are classified into different classes based on their mobility and structure. The genome of Arabidopsis contains a large number of rDNA, telomeres, and centromeres, which are important for the structure and function of the genome. The genome of Arabidopsis contains a large number of genes involved in membrane transport, including transporters for organic nutrients, inorganic ions, and toxic compounds. The genome of Arabidopsis contains a large number of genes involved in the regulation of gene expression, including transcription factors and other regulatory proteins. The genome of Arabidopsis contains a large number of genes involved in the response to environmental stimuli, including defense against pathogens and other stress factors. The genome of Arabidopsis contains a large number of genes involved in theThe genome sequence of the flowering plant Arabidopsis thaliana has been analyzed, revealing 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. 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. The genome sequence of Arabidopsis provides a means for understanding the genetic basis of differences between plants and other eukaryotes, and provides the foundation for detailed functional characterization of plant genes. Arabidopsis has many advantages for genome analysis, including a short generation time, small size, large number of offspring, and a relatively small nuclear genome. These advantages promoted the growth of a scientific community that has investigated the biological processes of Arabidopsis and has characterized many genes. To support these activities, an international collaboration (the Arabidopsis Genome Initiative, AGI) began sequencing the genome in 1996. The analysis of the completed Arabidopsis genome sequence, including annotation of predicted genes and assignment of functional categories, is reported. The genome sequence of a plant provides a means for understanding the genetic basis of differences between plants and other eukaryotes, and provides the foundation for detailed functional characterization of plant genes. The genome sequence of Arabidopsis has been compared to other plant species and accessions, revealing differences in gene structure, function, and organization. The genome of Arabidopsis contains a large number of tandemly repeated gene arrays, which may indicate more relaxed constraints on genome size in plants, or a more prominent role of unequal crossing over to generate new gene copies. The genome of Arabidopsis contains a large number of transposable elements, which are classified into different classes based on their mobility and structure. The genome of Arabidopsis contains a large number of rDNA, telomeres, and centromeres, which are important for the structure and function of the genome. The genome of Arabidopsis contains a large number of genes involved in membrane transport, including transporters for organic nutrients, inorganic ions, and toxic compounds. The genome of Arabidopsis contains a large number of genes involved in the regulation of gene expression, including transcription factors and other regulatory proteins. The genome of Arabidopsis contains a large number of genes involved in the response to environmental stimuli, including defense against pathogens and other stress factors. The genome of Arabidopsis contains a large number of genes involved in the