The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics

Lincoln D. Stein, Zhirong Bao, Darin Blasiar, Thomas Blumenthal, Michael R. Brent, Nansheng Chen, Asif Chinwalla, Laura Clarke, Chris Clee, Avril Coghlan, Alan Coulson, Peter D'Eustachio, David H A Fitch, Lucinda A. Fulton, Robert E. Fulton, Sam Griffiths-Jones, Todd W. Harris, LaDeana W. Hillier, Ravi Kamath, Patricia E. KuwabaraElaine R. Mardis, Marco A. Marra, Tracie L. Miner, Patrick Minx, James C. Mullikin, Robert W. Plumb, Jane Rogers, Jacqueline E. Schein, Marc Sohrmann, John Spieth, Jason E. Stajich, Chaochun Wei, David Willey, Richard K. Wilson, Richard Durbin, Robert H. Waterston

Research output: Contribution to journalArticle

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.

Original languageEnglish (US)
JournalPLoS Biology
Volume1
Issue number2
DOIs
StatePublished - 2003

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Caenorhabditis
Caenorhabditis briggsae
Caenorhabditis elegans
Genomics
Genes
Genome
genomics
genome
genes
Genome Size
Untranslated RNA
Caenorhabditis elegans Proteins
soil nematodes
Gene Order
repetitive sequences
proteins
Nucleic Acid Repetitive Sequences
operon
Operon
Protein C

ASJC Scopus subject areas

  • Agricultural and Biological Sciences(all)

Cite this

Stein, L. D., Bao, Z., Blasiar, D., Blumenthal, T., Brent, M. R., Chen, N., ... Waterston, R. H. (2003). The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics. PLoS Biology, 1(2). https://doi.org/10.1371/journal.pbio.0000045

The genome sequence of Caenorhabditis briggsae : A platform for comparative genomics. / Stein, Lincoln D.; Bao, Zhirong; Blasiar, Darin; Blumenthal, Thomas; Brent, Michael R.; Chen, Nansheng; Chinwalla, Asif; Clarke, Laura; Clee, Chris; Coghlan, Avril; Coulson, Alan; D'Eustachio, Peter; Fitch, David H A; Fulton, Lucinda A.; Fulton, Robert E.; Griffiths-Jones, Sam; Harris, Todd W.; Hillier, LaDeana W.; Kamath, Ravi; Kuwabara, Patricia E.; Mardis, Elaine R.; Marra, Marco A.; Miner, Tracie L.; Minx, Patrick; Mullikin, James C.; Plumb, Robert W.; Rogers, Jane; Schein, Jacqueline E.; Sohrmann, Marc; Spieth, John; Stajich, Jason E.; Wei, Chaochun; Willey, David; Wilson, Richard K.; Durbin, Richard; Waterston, Robert H.

In: PLoS Biology, Vol. 1, No. 2, 2003.

Research output: Contribution to journalArticle

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, DHA, 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 2003, 'The genome sequence of Caenorhabditis briggsae: A platform for comparative genomics', PLoS Biology, vol. 1, no. 2. https://doi.org/10.1371/journal.pbio.0000045
Stein, Lincoln D. ; Bao, Zhirong ; Blasiar, Darin ; Blumenthal, Thomas ; Brent, Michael R. ; Chen, Nansheng ; Chinwalla, Asif ; Clarke, Laura ; Clee, Chris ; Coghlan, Avril ; Coulson, Alan ; D'Eustachio, Peter ; Fitch, David H A ; Fulton, Lucinda A. ; Fulton, Robert E. ; Griffiths-Jones, Sam ; Harris, Todd W. ; Hillier, LaDeana W. ; Kamath, Ravi ; Kuwabara, Patricia E. ; Mardis, Elaine R. ; Marra, Marco A. ; Miner, Tracie L. ; Minx, Patrick ; Mullikin, James C. ; Plumb, Robert W. ; Rogers, Jane ; Schein, Jacqueline E. ; Sohrmann, Marc ; Spieth, John ; Stajich, Jason E. ; Wei, Chaochun ; Willey, David ; Wilson, Richard K. ; Durbin, Richard ; Waterston, Robert H. / The genome sequence of Caenorhabditis briggsae : A platform for comparative genomics. In: PLoS Biology. 2003 ; Vol. 1, No. 2.
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AU - Stein, Lincoln D.

AU - Bao, Zhirong

AU - Blasiar, Darin

AU - Blumenthal, Thomas

AU - Brent, Michael R.

AU - Chen, Nansheng

AU - Chinwalla, Asif

AU - Clarke, Laura

AU - Clee, Chris

AU - Coghlan, Avril

AU - Coulson, Alan

AU - D'Eustachio, Peter

AU - Fitch, David H A

AU - Fulton, Lucinda A.

AU - Fulton, Robert E.

AU - Griffiths-Jones, Sam

AU - Harris, Todd W.

AU - Hillier, LaDeana W.

AU - Kamath, Ravi

AU - Kuwabara, Patricia E.

AU - Mardis, Elaine R.

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AU - Miner, Tracie L.

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AU - Mullikin, James C.

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AU - Rogers, Jane

AU - Schein, Jacqueline E.

AU - Sohrmann, Marc

AU - Spieth, John

AU - Stajich, Jason E.

AU - Wei, Chaochun

AU - Willey, David

AU - Wilson, Richard K.

AU - Durbin, Richard

AU - Waterston, Robert H.

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