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The Wnt genes comprise a family of secreted glycoproteins involved in cell-cell signaling and pattern formation during the development of a variety of organisms. We have begun to examine Wnt gene expression in sea urchins that exhibit alternative modes of larval development but produce similar adults. Here we describe the isolation of five Wnt sequences from indirect- and direct-developing sea urchin species using a PCR-based strategy and library screening. Phylogenetic and distance analyses indicate that the five sequences represent sea urchin Wnt-1, -4, and -5 orthologs. Wnt-5 sequences were isolated from three sea urchin species and show a significantly faster rate of evolution than do their counterparts in jawed vertebrates. The genomic structure of the Wnt-5 locus was also examined, and its organization is similar to that of Wnt genes from insects and vertebrates. The temporal expression of all three sea urchin Wnt orthologs during sea urchin development was examined by RNA gel blots or RNase protection assays. Transcripts from all three sea urchin Wnts are detected at various developmental stages of both indirect- and direct-developing species. These data support the view that sea urchin Wnt genes exhibit many conserved aspects and at least three orthologs are developmentally regulated in both indirect- and direct-developing sea urchin embryos.