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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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A Region on C. elegans Chromosome III Containing 33 Genes, and the Syntenic C. briggsae Region, Which Has 38 GenesInversions have broken the syntenic region into three conserved segments. Genes that do not have an ortholog in this syntenic region are in grey; orthologs are joined by lines. In C. elegans, genes that differ substantially in structure between the WS77 and hybrid gene sets are marked with an asterisk.
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pbio.0000045-g007: A Region on C. elegans Chromosome III Containing 33 Genes, and the Syntenic C. briggsae Region, Which Has 38 GenesInversions have broken the syntenic region into three conserved segments. Genes that do not have an ortholog in this syntenic region are in grey; orthologs are joined by lines. In C. elegans, genes that differ substantially in structure between the WS77 and hybrid gene sets are marked with an asterisk.

Mentions: The automated analysis presented above indicates that the C. briggsae sequence will suggest many changes to the C. elegans set of gene predictions. To clarify the nature of these changes, we subjected several areas of colinearity to careful hand curation. In one carefully inspected area involving three C. elegans cosmids (ZK632, R10E11, and T05G5) and 33 C. elegans predicted genes, the syntenic C. briggsae region has 38 predicted genes (Figure 7). Inversions have broken the syntenic region into three conserved segments, within which gene order and orientation are largely conserved, except for one single-gene inversion (ZK632.9). There are 30 one-to-one orthologs in the syntenic block and two one-C. elegans-to-two-C. briggsae orthologs (T05G5.6 versus CBG10003 and CBG09979, and T05G5.8 versus CBG10002 and CBG09978), where the two C. briggsae orthologs seem to have been duplicated as a block since speciation. The remaining C. elegans gene (CEG09285) belongs to a C. elegans-specific gene family; its closest C. elegans paralog is F40F12.3, a gene of unknown function that is located nearby on chromosome III.


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)

A Region on C. elegans Chromosome III Containing 33 Genes, and the Syntenic C. briggsae Region, Which Has 38 GenesInversions have broken the syntenic region into three conserved segments. Genes that do not have an ortholog in this syntenic region are in grey; orthologs are joined by lines. In C. elegans, genes that differ substantially in structure between the WS77 and hybrid gene sets are marked with an asterisk.
© Copyright Policy
Related In: Results  -  Collection

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

pbio.0000045-g007: A Region on C. elegans Chromosome III Containing 33 Genes, and the Syntenic C. briggsae Region, Which Has 38 GenesInversions have broken the syntenic region into three conserved segments. Genes that do not have an ortholog in this syntenic region are in grey; orthologs are joined by lines. In C. elegans, genes that differ substantially in structure between the WS77 and hybrid gene sets are marked with an asterisk.
Mentions: The automated analysis presented above indicates that the C. briggsae sequence will suggest many changes to the C. elegans set of gene predictions. To clarify the nature of these changes, we subjected several areas of colinearity to careful hand curation. In one carefully inspected area involving three C. elegans cosmids (ZK632, R10E11, and T05G5) and 33 C. elegans predicted genes, the syntenic C. briggsae region has 38 predicted genes (Figure 7). Inversions have broken the syntenic region into three conserved segments, within which gene order and orientation are largely conserved, except for one single-gene inversion (ZK632.9). There are 30 one-to-one orthologs in the syntenic block and two one-C. elegans-to-two-C. briggsae orthologs (T05G5.6 versus CBG10003 and CBG09979, and T05G5.8 versus CBG10002 and CBG09978), where the two C. briggsae orthologs seem to have been duplicated as a block since speciation. The remaining C. elegans gene (CEG09285) belongs to a C. elegans-specific gene family; its closest C. elegans paralog is F40F12.3, a gene of unknown function that is located nearby on chromosome III.

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