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The Genome Sequence of Caenorhabditis briggsae: A Platform for Comparative Genomics.
Stein LD1 , Bao Z2,9 , Blasiar D3 , Blumenthal T4 , Brent M5 , Chen N1 , Chinwalla A3 , Clarke L6 , Clee C6 , Coghlan A7 , Coulson A8,13 , D'Eustachio P1,8 , Fitch DHA14 , Fulton L3 , Fulton R3 , Griffiths-Jones S3 , Harris TW1 , Hillier L3,9 , Kamath R6 , Kuwabara P6 , Mardis E3 , Marra M3,10 , Miner T3 , Minx P3 , Mullikin JC6,11 , Plumb R6 , Rogers J6 , Schein J3,10 , Sohrmann M6 , Spieth J3 , Stajich JE12 , Wei C5 , Willey D6 , Wilson R3 , Durbin R6 , Waterston R3,9
2003. Public Library Of Science. 1(2): 166-192.
1 Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
2 Department of Genetics, Washington University School of Medicine, St. Louis, MO
3 Genome Sequencing Center, Washington University School of Medicine, St. Louis, MO
4 Biochemistry and Molecular Genetics, University of Colorado, Denver, CO
5 Department of Computer Science and Engineering, Washington University at St. Louis, St. Louis, MO
6 Wellcome Trust Sanger Institute, Hinxton, UK
7 Department of Genetics, Trinity College, Dublin, Ireland
8 New York University School of Medicine, New York, NY
9 Department of Genome Sciences, University of Washington, Seattle, WA
10 Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, Canada
11 National Institutes of Health, Bethesda, MD
12 Department of Molecular Genetics and Microbiology, Duke University, Durham, NC
13 MRC Laboratory of Molecular Biology, Cambridge, UK
14 Department of Biology, New York University, New York, NY
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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.