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The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH - PLoS Biol. (2003)

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.. lstein@cshl.org

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.

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Joint Refinement of C. elegans and C. briggsae Gene Models: acy-4When annotating the C. briggsae and C. elegans acy-4 orthologs, we chose the Genefinder ce-acy-4 prediction and the Genefinder cb-acy-4 prediction because, out of the 12 possible combinations of a C. briggsae and a C. elegans prediction, this pair shows the most similarity to each other. Coding sequence (CDS) conservation between cb-acy-4 and ce-acy-4 provides evidence for as many as 12 additional N-terminal exons in the Genefinder ce-acy-4 prediction, as compared to T01C2.1, the WS77 ce-acy-4 prediction. Subsequently, four of the additional N-terminal exons that were predicted by FGENESH and Genefinder were confirmed by new EST data (marked with asterisks).
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pbio.0000045-g001: Joint Refinement of C. elegans and C. briggsae Gene Models: acy-4When annotating the C. briggsae and C. elegans acy-4 orthologs, we chose the Genefinder ce-acy-4 prediction and the Genefinder cb-acy-4 prediction because, out of the 12 possible combinations of a C. briggsae and a C. elegans prediction, this pair shows the most similarity to each other. Coding sequence (CDS) conservation between cb-acy-4 and ce-acy-4 provides evidence for as many as 12 additional N-terminal exons in the Genefinder ce-acy-4 prediction, as compared to T01C2.1, the WS77 ce-acy-4 prediction. Subsequently, four of the additional N-terminal exons that were predicted by FGENESH and Genefinder were confirmed by new EST data (marked with asterisks).

Mentions: To select among overlapping predictions produced by different programs, we reasoned that the most likely gene model is the one that maximizes the similarity between the gene sets in two related species (Figure 1). For each C. briggsae region that had multiple overlapping but inconsistent predictions, our selection procedure chose the prediction that had the most extensive similarity to the matching C. elegans prediction. The extent of similarity was measured by the fraction of the C. briggsae prediction that aligned to the matching C. elegans prediction at the protein level. Likewise, from all the predictions for a C. elegans gene, we chose the prediction having the most extensive similarity to its C. briggsae match. This selection step produced two gene sets, one each for C. briggsae and C. elegans. The gene sets were then filtered to remove transposons and putative pseudogenes.


The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.

Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A, Coulson A, D'Eustachio P, Fitch DH, Fulton LA, Fulton RE, Griffiths-Jones S, Harris TW, Hillier LW, Kamath R, Kuwabara PE, Mardis ER, Marra MA, Miner TL, Minx P, Mullikin JC, Plumb RW, Rogers J, Schein JE, Sohrmann M, Spieth J, Stajich JE, Wei C, Willey D, Wilson RK, Durbin R, Waterston RH - PLoS Biol. (2003)

Joint Refinement of C. elegans and C. briggsae Gene Models: acy-4When annotating the C. briggsae and C. elegans acy-4 orthologs, we chose the Genefinder ce-acy-4 prediction and the Genefinder cb-acy-4 prediction because, out of the 12 possible combinations of a C. briggsae and a C. elegans prediction, this pair shows the most similarity to each other. Coding sequence (CDS) conservation between cb-acy-4 and ce-acy-4 provides evidence for as many as 12 additional N-terminal exons in the Genefinder ce-acy-4 prediction, as compared to T01C2.1, the WS77 ce-acy-4 prediction. Subsequently, four of the additional N-terminal exons that were predicted by FGENESH and Genefinder were confirmed by new EST data (marked with asterisks).
© Copyright Policy
Related In: Results  -  Collection

Show All Figures
getmorefigures.php?uid=PMC261899&req=5

pbio.0000045-g001: Joint Refinement of C. elegans and C. briggsae Gene Models: acy-4When annotating the C. briggsae and C. elegans acy-4 orthologs, we chose the Genefinder ce-acy-4 prediction and the Genefinder cb-acy-4 prediction because, out of the 12 possible combinations of a C. briggsae and a C. elegans prediction, this pair shows the most similarity to each other. Coding sequence (CDS) conservation between cb-acy-4 and ce-acy-4 provides evidence for as many as 12 additional N-terminal exons in the Genefinder ce-acy-4 prediction, as compared to T01C2.1, the WS77 ce-acy-4 prediction. Subsequently, four of the additional N-terminal exons that were predicted by FGENESH and Genefinder were confirmed by new EST data (marked with asterisks).
Mentions: To select among overlapping predictions produced by different programs, we reasoned that the most likely gene model is the one that maximizes the similarity between the gene sets in two related species (Figure 1). For each C. briggsae region that had multiple overlapping but inconsistent predictions, our selection procedure chose the prediction that had the most extensive similarity to the matching C. elegans prediction. The extent of similarity was measured by the fraction of the C. briggsae prediction that aligned to the matching C. elegans prediction at the protein level. Likewise, from all the predictions for a C. elegans gene, we chose the prediction having the most extensive similarity to its C. briggsae match. This selection step produced two gene sets, one each for C. briggsae and C. elegans. The gene sets were then filtered to remove transposons and putative pseudogenes.

Bottom Line: 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.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.

View Article: PubMed Central - PubMed

Affiliation: Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.. lstein@cshl.org

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.

Show MeSH
Related in: MedlinePlus