The forkhead gene family of Caenorhabditis elegans.

The forkhead genes encode a family of transcriptional regulators with important roles in the control of animal development. The genomic sequence has revealed Caenorhabditis elegans has 15 forkhead genes of which six had been experimentally characterised previously. The remaining nine have now been investigated by RNAi and reporter gene expression pattern analysis. Two (B0286.5 and F26B1.7) have key developmental roles, four (F26D12.1, K03C7.2, F40H3.4 and C25A1.2) are expressed in, and may function in, the nervous system and three (C29F7.4, C29F7.5 and F26A1.2), which are closely related to each other, do not appear to be essential. Conservation with forkhead genes in the closely related nematode Caenorhabditis briggsae does not appear to correspond completely with demonstrated functionality in C. elegans. Comparisons of expression patterns and RNAi/mutant phenotypes for all 15 C. elegans forkhead genes reveal the potential complexity of functional interactions for this gene family.

Evidence suggesting that a fifth of annotated Caenorhabditis elegans genes may be pseudogenes.

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.