Plants and prokaryotes share thousands of genes. Those with known functions mostly encode enzymes of primary metabolism or other key biochemical components, and the same is almost surely true of those whose function is still obscure. The availability of hundreds of sequenced genomes and of rich postgenomic resources now makes possible the use of comparative genomics ('phylogenomics') of plants and prokaryotes to infer, and then verify, functions for such unknown genes. In this type of analysis, plant and prokaryote data each inform the search for function, and do so synergistically. This breaks with the past pattern of gene discovery, in which the information flow was most often unidirectional from prokaryotes to plants.