Only a minority of the genes, identified in the Caenorhabditis elegans genome 
sequence data by computer analysis, have been characterized experimentally. We 
attempted to determine the expression patterns for a random sample of the 
annotated genes using reporter gene fusions. A low success rate was obtained for 
evolutionarily recently duplicated genes. Analysis of the data suggests that 
this is not due to conditional or low-level expression. The remaining 
explanation is that most of the annotated genes in the recently duplicated 
category are pseudogenes, a proportion corresponding to 20% of all of the 
annotated C. elegans genes. Further support for this surprisingly high figure 
was sought by comparing sequences for families of recently duplicated C. elegans 
genes. Although only a preliminary analysis, clear evidence for a gene having 
been recently inactivated by genetic drift was found for many genes in the 
recently duplicated category. At least 4% of the annotated C. elegans genes can 
be recognized as pseudogenes simply from closer inspection of the sequence data. 
Lessons learned in identifying pseudogenes in C. elegans could be of value in 
the annotation of the genomes of other species where, although there may be 
fewer pseudogenes, they may be harder to detect.