Systematic analysis of the Arabidopsis genome provides a basis for detailed
studies of genome structure and evolution. Members of multigene families w
ere mapped, and random sequence alignment was used to identify regions of e
xtended similarity in the Arabidopsis genome. Detailed analysis showed that
the number, order, and orientation of genes were conserved over large regi
ons of the genome, revealing extensive duplication covering the majority of
the known genomic sequence. Fine mapping analysis showed much rearrangemen
t, resulting in a patchwork of duplicated regions that indicated deletion,
insertion, tandem duplication, inversion, and reciprocal translocation. The
implications of these observations for evolution of the Arabidopsis genome
as well as their usefulness for analysis and annotation of the genomic seq
uence and in comparative genomics are discussed.