Caenorhabditis elegans has scores of homoeobox-containing genes.

HOMOEOBOX-containing genes control cell identities in par-ticular spatial domains, cell lineages, or cell types during the development of Drosophila1,2 and Caenorhabditis elegans3–5, and they probably control similar processes in vertebrates6–9. More than 80 genes with homoeoboxes that have sequence similarities ranging from 25 to 100% have been isolated by genetic means or by DNA hybridization to previously isolated genes10. We synthesized 500–2,000-fold degenerate oligonucleotides corre-sponding to a set of well-conserved eight amino acid sequences from the helix-3 region of the homoeodomain11. We screened C. elegans genomic libraries with these probes and identified 49 putative homoeobox-containing loci. DNA sequencing confirmed that eight out of ten selected loci had sequences corresponding to the conserved helix-3 region11 plus additional flanking sequence similarity. One of these genes contained a sequence corresponding to a complete pou-domain12 and another was closely related to the homoeobox-containing genes caudal/cdx-113,14. The putative homoeobox loci were mapped to the physical contig map of C. elegans15,16, allowing the identification of potentially correspond-ing genes from the correlated genetic map. We estimate that the number of homoeobox-containing genes in C. elegans is at least 60, constituting ∼1% of the estimated total number of genes17.