Beyond the Arabidopsis Genome: Opportunities for Comparative Genomics

Like most higher eukaryotes, flowering plants are believed to contain surprisingly similar numbers of genes. Nevertheless, angiosperm genome sizes vary over a wide range—from 50 Mb to over 120,000 Mb. Comparative mapping has shown that numerous al- terations contribute to genomic diversity among plants. Over time, chromosomes are broken, reas- sembled, partially or wholly duplicated, and even eliminated, ultimately resulting in reproductive iso- lation and speciation. However, the mechanisms that create such variation, and the evolutionary forces that fix these changes, are not well understood. Com- parative analyses of plant genomes promise to clarify the selective pressures driving these changes; such investigations will elucidate alterations at the level of whole genomes, as well as those at the level of spe- cific sequences, including genes, repetitive elements, and other non-coding regions. Although low-resolution genetic maps can identify gross chromosomal alterations, a clear understand- ing of the mechanisms behind these changes requires multispecies sequence comparisons. Such analyses reveal the composition, organization, and functional components of genomes and provide insight into regional differences in composition between related species. In addition, sequence comparisons elucidate evolutionary history; for example, the stepwise accu- mulation of nucleotide insertions/deletions (indels) only becomes clear with the analysis of multiple spe- cies. Comparative sequence analysis also aids in gene prediction and sequence annotation, and facilitates the identification and definition of regulatory ele- ments, including promoters, enhancers, and tran-