Annotation of the briggsae genomic sequence predicts over 25,000 genes, more than in the canonical elegans set, and preliminary reannotation of C. elegans based on similarity to briggsae suggests that tallies of the elegans gene space may need to be revised upward. Roughly half the protein coding genes identified in briggsae have orthologs in elegans, and most of the remainder are homologous to one or more elegans genes. Co-clustering of briggsae and elegans proteins with TRIBE-ML leads to 2847 protein families, most of which are shared between the two species. However some have undergone expansion or contraction since divergence from the common ancestor. ÊÊÊ Analysis of nucleotide and protein-level similarity between the C. briggsae and elegans genomes reveals extensive colinearity with a marked trend toward longer regions of colinearity in the chromosomal centers than in the arms. This pattern correlates with the distribution of orthologs and essential genes, and inversely with the distribution of repetitive elements and non-homologous genes. The rate of neutral mutation also appears to be higher in the arms than in the centers.

This draft will greatly improve the annotation of the elegans genome by providing a new line of evidence for checking and modifying gene models. In addition, the sequence promises to open up new avenues for exploring genome structure and regulation. The sequence and annotations are freely available at www.wormbase.org.