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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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Distribution of KA/KS Ratio among Ortholog Pairs
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pbio.0000045-g002: Distribution of KA/KS Ratio among Ortholog Pairs

Mentions: The KA/KS ratio, a measure of selective pressure, is expected to be 1.0 for genes that are under no selective pressure (for example, pseudogenes), less than 1.0 for genes under purifying selection, and greater than 1.0 for genes under positive selection. As expected, we found that nearly all the genes in ortholog pairs are under purifying selection (Figure 2). However, the extent of this purifying selection is more marked in genes with essential functions. For example, ortholog pairs which exhibit an embryonic lethal phenotype in systematic RNA inhibition (RNAi) screens of the C. elegans ortholog partner (Maeda et al. 2001; Piano and Gunsalus 2002; Kamath et al. 2003) show a markedly lower KA/KS ratio than do pairs for which a wild-type phenotype was observed (KA/KS, 0.0445 ± 0.0340 versus 0.0627 ± 0.0494; p < 1 × 10−16 by the Welch two-sample t-test). We also confirmed the findings of Castillo-Davis and Hartl (2002), who showed that genes involved early in development tend to be less prone to duplications and have a lower KS value than late-development genes (data not shown).


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)

Distribution of KA/KS Ratio among Ortholog Pairs
© Copyright Policy
Related In: Results  -  Collection

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

pbio.0000045-g002: Distribution of KA/KS Ratio among Ortholog Pairs
Mentions: The KA/KS ratio, a measure of selective pressure, is expected to be 1.0 for genes that are under no selective pressure (for example, pseudogenes), less than 1.0 for genes under purifying selection, and greater than 1.0 for genes under positive selection. As expected, we found that nearly all the genes in ortholog pairs are under purifying selection (Figure 2). However, the extent of this purifying selection is more marked in genes with essential functions. For example, ortholog pairs which exhibit an embryonic lethal phenotype in systematic RNA inhibition (RNAi) screens of the C. elegans ortholog partner (Maeda et al. 2001; Piano and Gunsalus 2002; Kamath et al. 2003) show a markedly lower KA/KS ratio than do pairs for which a wild-type phenotype was observed (KA/KS, 0.0445 ± 0.0340 versus 0.0627 ± 0.0494; p < 1 × 10−16 by the Welch two-sample t-test). We also confirmed the findings of Castillo-Davis and Hartl (2002), who showed that genes involved early in development tend to be less prone to duplications and have a lower KS value than late-development genes (data not shown).

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