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.
Highlights
Comparative sequence analysis is a global approach toward recognizing much of the functional sequence in a genome
We found that breakpoints between regions of colinearity are strongly biased towards junctions that are within the same arm of the same chromosome (Table 10; p, 10À4, v2 test)
We have performed an initial characterization of the genome, including an analysis of the gene content and a comparison of the C. briggsae genome with its cousin C. elegans
Summary
Comparative sequence analysis is a global approach toward recognizing much of the functional sequence in a genome. Comparisons of genomes of appropriate evolutionary distance can aid in defining protein-coding genes, in recognizing noncoding genes, and in finding regulatory sequences and other functional elements of a genome. The soil-dwelling nematode Caenorhabditis elegans has been intensively studied over the past several decades to establish the molecular genetic basis of its development and behavior. The completion of its genome sequence (C. elegans Sequencing Consortium 1998) provides a complete description of the genetic information, but decoding the program embedded in the sequence remains a challenge.
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