The Arabidopsis Genome Initiative reports the analysis of the genomic sequence of *Arabidopsis thaliana*, a flowering plant model system. The sequenced regions cover 115.4 megabases of the 125-megabase genome, extending into centromeric regions. The genome evolution involved a whole-genome duplication followed by gene loss and local duplications, resulting in a dynamic genome with lateral gene transfer from a cyanobacterial-like ancestor. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of *Drosophila* and *Caenorhabditis elegans*. The analysis includes annotation of predicted genes, chromosome dynamics, distribution of transposable elements, and comparison with other Arabidopsis accessions and plant species. The study highlights new protein families, plant-specific functions, and uncharacterized metabolic pathways, providing insights into plant-specific gene functions and facilitating crop improvement. The genome sequence also reveals insights into plant evolution, gene duplication, and the integration of nuclear and organelle genomes. Comparative analysis with other plant genera and the identification of transposable elements and rDNA, telomeres, and centromeres further enhance our understanding of plant genome organization and evolution.The Arabidopsis Genome Initiative reports the analysis of the genomic sequence of *Arabidopsis thaliana*, a flowering plant model system. The sequenced regions cover 115.4 megabases of the 125-megabase genome, extending into centromeric regions. The genome evolution involved a whole-genome duplication followed by gene loss and local duplications, resulting in a dynamic genome with lateral gene transfer from a cyanobacterial-like ancestor. The genome contains 25,498 genes encoding proteins from 11,000 families, similar to the functional diversity of *Drosophila* and *Caenorhabditis elegans*. The analysis includes annotation of predicted genes, chromosome dynamics, distribution of transposable elements, and comparison with other Arabidopsis accessions and plant species. The study highlights new protein families, plant-specific functions, and uncharacterized metabolic pathways, providing insights into plant-specific gene functions and facilitating crop improvement. The genome sequence also reveals insights into plant evolution, gene duplication, and the integration of nuclear and organelle genomes. Comparative analysis with other plant genera and the identification of transposable elements and rDNA, telomeres, and centromeres further enhance our understanding of plant genome organization and evolution.