Members of the YABBY gene family, recently discovered in Arabidopsis thaliana, are crucial for the establishment of abaxial identity in diverse organs including leaves, floral appendages and ovules. YABBY genes encode putative transcription factors with a zinc finger domain near the N-terminus, a central variable region, and a YABBY domain near the C-terminus. To explore the patterns and rates of diversification among members of the YABBY gene family across angiosperms, we isolated several homologs from two Asterids, Lycopersicon esculentum and Antirrhinnum majus, and a monocot, Zea mays. Amino acid sequences of both the zinc finger and YABBY regions from all isolated genes were easily aligned. The central variable regions among these genes exhibited some similarities but could not be unambiguously aligned. Phylogenetic analysis of these genes, using the PAM-250 amino acid transition matrix, identified five distinct molecular lineages, with high bootstrap support, that correspond to functional categories identified in A. thaliana. Within these lineages, the zinc finger regions, having an average sequence dissimilarity of 18.6%, are evolving more rapidly than the YABBY regions, which have an average sequence dissimilarity of 6.7%. Orthologs of INNER NO OUTER, a gene required for outer integument development in A. thaliana, have been identified in both the Asterid and monocot lineages. Orthologs of CRABS CLAW, a gene involved in abaxial differentiation of the carpel, have also been identified in these lineages. In situ hybridization of orthologs of INNER NO OUTER and CRABS CLAW in L. esculentum indicates that they are expressed in the same tissues as their counterparts in A. thaliana, but also exhibit expanded expression patterns relative to A. thaliana. The pattern of INNER NO OUTER expression in ovules of L. esculentum may provide insights into the origin of unitegmy in the Asterids, in particular, and the relationship between molecular and morphological evolution, more generally.

Key words: Carpel Diversification, CRABS CLAW, Evolution of Development, INNER NO OUTER, Ovule Diversification, YABBY gene family