Stein, L. D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M. R., Chen, N., Chinwalla, A., Clarke, L., Clee, C., Coghlan, A., Coulson, A., D'Eustachio, P., Fitch, D. H., Fulton, L. A., Fulton, R. E., Griffiths-Jones, S., Harris, T. W., Hillier, L. W., Kamath, R., Kuwabara, P. E., Mardis, E. R., Marra, M. A., Miner, T. L., Minx, P., Mullikin, J. C., Plumb, R. W., Rogers, J., Schein, J. E., Sohrmann, M., Spieth, J., Stajich, J. E., Wei, C., Willey, D., Wilson, R. K., Durbin, R., Waterston, R. H. (November 2003) The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics. PLoS Biology, 1 (2). E45. ISSN 1544-9173
Preview |
PDF (Paper)
Stein PLoS Biology 2003.pdf - Published Version Download (821kB) | Preview |
Abstract
The soil nematodes Caenorhabditis briggsae and Caenorhabditis elegans diverged from a common ancestor roughly 100 million years ago and yet are almost indistinguishable by eye. They have the same chromosome number and genome sizes, and they occupy the same ecological niche. To explore the basis for this striking conservation of structure and function, we have sequenced the C. briggsae genome to a high-quality draft stage and compared it to the finished C. elegans sequence. We predict approximately 19,500 protein-coding genes in the C. briggsae genome, roughly the same as in C. elegans. Of these, 12,200 have clear C. elegans orthologs, a further 6,500 have one or more clearly detectable C. elegans homologs, and approximately 800 C. briggsae genes have no detectable matches in C. elegans. Almost all of the noncoding RNAs (ncRNAs) known are shared between the two species. The two genomes exhibit extensive colinearity, and the rate of divergence appears to be higher in the chromosomal arms than in the centers. Operons, a distinctive feature of C. elegans, are highly conserved in C. briggsae, with the arrangement of genes being preserved in 96% of cases. The difference in size between the C. briggsae (estimated at approximately 104 Mbp) and C. elegans (100.3 Mbp) genomes is almost entirely due to repetitive sequence, which accounts for 22.4% of the C. briggsae genome in contrast to 16.5% of the C. elegans genome. Few, if any, repeat families are shared, suggesting that most were acquired after the two species diverged or are undergoing rapid evolution. Coclustering the C. elegans and C. briggsae proteins reveals 2,169 protein families of two or more members. Most of these are shared between the two species, but some appear to be expanding or contracting, and there seem to be as many as several hundred novel C. briggsae gene families. The C. briggsae draft sequence will greatly improve the annotation of the C. elegans genome. Based on similarity to C. briggsae, we found strong evidence for 1,300 new C. elegans genes. In addition, comparisons of the two genomes will help to understand the evolutionary forces that mold nematode genomes.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Animals Caenorhabditis/*genetics Caenorhabditis elegans/*genetics Chromosome Mapping Chromosomes, Artificial, Bacterial Cluster Analysis Codon Conserved Sequence Evolution Evolution, Molecular Exons Gene Library *Genome Genomics/*methods Interspersed Repetitive Sequences Introns MicroRNAs/genetics Models, Genetic Models, Statistical Molecular Sequence Data Multigene Family Open Reading Frames Physical Chromosome Mapping Plasmids/metabolism Protein Structure, Tertiary Proteins/chemistry RNA/chemistry RNA, Ribosomal/genetics RNA, Spliced Leader RNA, Transfer/genetics Sequence Analysis, DNA Species Specificity |
| Subjects: | organism description > animal > C elegans bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification bioinformatics > genomics and proteomics > genetics & nucleic acid processing bioinformatics > genomics and proteomics organism description > animal bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosome bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > chromosomes, structure and function > chromosome bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes |
| CSHL Authors: | |
| Communities: | CSHL labs > Stein lab |
| Depositing User: | Matt Covey |
| Date: | November 2003 |
| Date Deposited: | 28 Mar 2013 14:19 |
| Last Modified: | 28 Mar 2013 14:19 |
| PMCID: | PMC261899 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/28006 |
Actions (login required)
 |
Administrator's edit/view item |