RESEARCH ARTICLE Phylum-Level Conservation of Regulatory Information in Nematodes despite Extensive Non-coding Sequence Divergence

Gene regulatory information guides development and shapes the course of evolution. To test conservation of gene regulation within the phylum Nematoda, we compared the func-tions of putative cis-regulatory sequences of four sets of orthologs (unc-47, unc-25,mec-3 and elt-2) from distantly-related nematode species. These species, Caenorhabditis ele-gans, its congeneric C. briggsae, and three parasitic speciesMeloidogyne hapla, Brugia malayi, and Trichinella spiralis, represent four of the five major clades in the phylum Nema-toda. Despite the great phylogenetic distances sampled and the extensive sequence diver-gence of nematode genomes, all but one of the regulatory elements we tested are able to drive at least a subset of the expected gene expression patterns. We show that functionally conserved cis-regulatory elements have no more extended sequence similarity to their C. elegans orthologs than would be expected by chance, but they do harbor motifs that are important for proper expression of the C. elegans genes. These motifs are too short to be distinguished from the background level of sequence similarity, and while identical in se-quence they are not conserved in orientation or position. Functional tests reveal that som