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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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Related in: MedlinePlus

A WABA Alignment over a Known C. elegans Gene (snt-1)WABA coding segments are shown as dark blue, strong alignments as medium blue, and weak alignments as grey. Regions that do not align are shown as dotted lines. The alignments of three sequenced C. elegans mRNA sequences are also shown for comparison.
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pbio.0000045-g004: A WABA Alignment over a Known C. elegans Gene (snt-1)WABA coding segments are shown as dark blue, strong alignments as medium blue, and weak alignments as grey. Regions that do not align are shown as dotted lines. The alignments of three sequenced C. elegans mRNA sequences are also shown for comparison.

Mentions: As indicated by Kent and Zahler (2000), although there is a preference of WABA coding blocks for coding regions and strong blocks for intergenic regions, there is not a clear delineation. Figure 4 shows a C. elegans gene (snt-1) and its WABA alignment to part of C. briggsae supercontig cb25.fpc2454. WABA blocks covered the snt-1 CDS and predicted 3′ UTR. Coding WABA blocks (dark blue in Figure 4) correlate well with exons of both of the alternatively spliced transcripts of snt-1. However, there are also small coding blocks between exons 1 and 2 and between exons 2 and 3. These could be missed exons in the C. elegans gene model or conserved functional elements, but there are no experimental data to support either supposition.


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 WABA Alignment over a Known C. elegans Gene (snt-1)WABA coding segments are shown as dark blue, strong alignments as medium blue, and weak alignments as grey. Regions that do not align are shown as dotted lines. The alignments of three sequenced C. elegans mRNA sequences are also shown for comparison.
© Copyright Policy
Related In: Results  -  Collection

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

pbio.0000045-g004: A WABA Alignment over a Known C. elegans Gene (snt-1)WABA coding segments are shown as dark blue, strong alignments as medium blue, and weak alignments as grey. Regions that do not align are shown as dotted lines. The alignments of three sequenced C. elegans mRNA sequences are also shown for comparison.
Mentions: As indicated by Kent and Zahler (2000), although there is a preference of WABA coding blocks for coding regions and strong blocks for intergenic regions, there is not a clear delineation. Figure 4 shows a C. elegans gene (snt-1) and its WABA alignment to part of C. briggsae supercontig cb25.fpc2454. WABA blocks covered the snt-1 CDS and predicted 3′ UTR. Coding WABA blocks (dark blue in Figure 4) correlate well with exons of both of the alternatively spliced transcripts of snt-1. However, there are also small coding blocks between exons 1 and 2 and between exons 2 and 3. These could be missed exons in the C. elegans gene model or conserved functional elements, but there are no experimental data to support either supposition.

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