The Taxonomy of Developmental Control in Caenorhabditis elegans

Author:

Ruvkun Gary1,Hobert Oliver1

Affiliation:

1. The authors are in the Department of Molecular Biology, Massachusetts General Hospital, Department of Genetics, Harvard Medical School, Boston, MA 02114, USA.

Abstract

The Caenorhabditis elegans genome sequence was surveyed for transcription factor and signaling gene families that have been shown to regulate development in a variety of species. About 10 to 25 percent of the genes in most of the gene families already have been genetically analyzed in C. elegans , about half of the genes detect probable orthologs in other species, and about 10 to 25 percent of the genes are, at present, unique to C. elegans . Caenorhabditis elegans is also missing genes that are found in vertebrates and other invertebrates. Thus the genome sequence reveals universals in developmental control that are the legacy of metazoan complexity before the Cambrian explosion, as well as genes that have been more recently invented or lost in particular phylogenetic lineages.

Publisher

American Association for the Advancement of Science (AAAS)

Subject

Multidisciplinary

Reference78 articles.

1. W. B. Wood Ed. The Nematode C. elegans (Cold Spring Harbor Laboratory Cold Spring Harbor NY 1988)

2. D. L. Riddle et al. Eds. C. elegans II (Cold Spring Harbor Laboratory Cold Spring Harbor NY 1997).

3. We classify gene superfamilies mainly based on phylogenetic analyses that are presented on the Web page www.sciencemag.org/feature/data/985556.shl. Routinely searches were first performed using BLASTP on the Wormpep dataset posted on the C. elegans genome blast server www.sanger.ac.uk/projects/c_elegans/blast_server.shtml (which at the time of this analysis was Wormpep15 plus a number of unannotated sequences now included in Wormpep16) and afterward confirmed using TBLASTN on the genomic sequence dataset on the C. elegans blast server. The probable ortholog of a C. elegans gene is the most closely related vertebrate or other invertebrate protein that by BLAST and/or dendrogram analysis (using the neighbor-joining method on a distance matrix created with the Kimura protein distance algorithm) is significantly more closely related than the next most closely related member of the gene superfamily. General information about the datasets and annotations can be found at: .

4. Vulval development in Caenorhabditis elegans

5. The ins and outs of programmed cell death duringC. elegansdevelopment

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