Genome Mapping and Genomics of Caenorhabditis elegans

Abstract

The nematode Caenorhabditis elegans is one of the most extensively studied and utilized model organisms, owing to experimental advantages such as its ease of culture and rapid growth, facile genetics, cellular simplicity, and complete transparency throughout life. Its compact 100 Mb genome sequence was the first to be completely determined for any multicellular organism, in 1998. Early linkage mapping by recombinational methods and cytology defined a nuclear genome of five autosomes and one X (sex) chromosome, of roughly equal size. The two natural sexes are both autosomally diploid; hermaphrodites have two X chromosomes (XX) while males have one (XO). All chromosomes are holocentric, but each contains a central region where recombination is reduced and conserved house-keeping genes are more frequent. Centromeres and extended heterochromatic regions are absent. Telomeres are conventional. Annotation of the genome has defined over 20,000 protein-coding genes, with relatively few pseudogenes. About 15 % of these genes are transcribed as multicistronic operons, which are divided up into mRNAs by trans-splicing. The genome also contains many noncoding RNA genes, including a well-defined set of miRNAs. Families of transposons and repeated sequences are present but less abundant than in vertebrates. Postgenomic approaches include extensive resequencing, transcriptomics, microarray analyses and proteomics, together with determination of spatial and temporal gene expression patterns using GFP reporter transgenes, and functional testing by systematic gene deletion and global RNAi knockdown screens. Protein–protein interactions have been explored by large-scale yeast two-hybrid testing. Genome sequences for several other species within the genus Caenorhabditis have been determined; these provide a major resource for comparative genomics, and reveal a high degree of synteny between the different species.