Our knowledge of the Caenorhabditis elegans genome has increased substantially since the publication of the 1988 C. elegans book (Emmons 1988); even the genome size has changed from an estimated 80 × 10⁶ base pairs to 100 × 10⁶ base pairs. Systematic study of the genome in the intervening years has seen the construction of a nearly complete physical map and the release of more than half the assembled sequence. Yet it is an awkward time to be writing about the genome, since our view of the genome is changing rapidly (˜2 Mb of newly assembled sequence is being released per month), and as yet most of the sequence has been obtained from the gene-rich regions of the genome, with very little from the gene-poor autosomal arms. As a result, analysis of the overall sequence remains frustratingly anecdotal. Nevertheless, much has been learned, and this chapter will attempt to summarize our current understanding of the C. elegans genome.

The genome is the physical basis for genetics and includes both nuclear and cytoplasmic DNAs. For C. elegans, the mitochondrial genome (13,794 bp) has been fully sequenced (Okimoto et al. 1992). The nuclear genome contains approximately 100 × 10⁶ base pairs, organized into six chromosomes ranging in size from 14 × 10⁶ to 22 × 10⁶ base pairs (Coulson et al. 1991), which is approximately 20 times the size of Escherichia coli (the underestimate of the E. coli genome size, used as a standard, led to the underestimate of the C. elegans genome size by reassociation kinetics) and about 1/30 the size of the human genome. Most of the sequence is unique, with only 17% assigned to the repetitive class by reassociation kinetics (Sulston and Brenner 1974). The genome is on average 36% GC (Sulston and Brenner 1974). Although coding sequences are clearly higher in GC content and noncoding sequences are higher in AT content, surprisingly little variation in content exists over larger regions as determined first by isopycnic banding of genomic DNA and confirmed more recently by sequencing (Brenner and Sulston 1974; Wilson et al. 1994 and unpubl.). The exception to this is the ribosomal gene cluster containing about 70–100 copies of the genes for 18S and 28S rRNAs: it is 51% GC (Ellis et al. 1986). No methylated bases have been detected, despite the use of methods capable of detecting 1 methylcytosine in 10,000 cytosine residues (Simpson et al. 1986).