Roundworm Genome Sequencing

The National Human Genome Research Institute (NHGRI) has supported a number of sequencing projects aimed at producing draft assemblies of roundworm (Caenorhabditis) genomes. The nematode species for which genome sequencing projects exist are:

• Caenorhabditis elegans
• Caenorhabditis briggsae
• Caenorhabditis remanei
• Caenorhabditis japonica
• Caenorhabditis n. sp. CB5161

C. elegans

The Caenorhabditis elegans genome (WGS) sequencing project was essentially completed and published in Science in 1998. The final gaps were filled in by October 2002. The genome of C. elegans was the first of any multicellular organism to be sequenced in its entirety. The genome is approximately 97Mb in size, and encodes over 19,000 proteins. The project was divided between the Washington University Genome Sequencing Center (WUGSC) and the Sanger Institute, and was supported by the National Human Genome Research Institute (NHGRI) and The Wellcome Trust.

Project Links:

• Washington University Genome Sequencing Center [genome.wustl.edu]
• Sanger Institute [sanger.ac.uk]

Supporting Institutions:

• The Wellcome Trust [wellcome.ac.uk]

C. briggsae

The genome of a related nematode, Caenorhabditis briggsae, was sequenced by a whole genome shotgun (WGS) sequencing approach. As with C. elegans, that project is supported by the NHGRI and The Welcome Trust and is being carried out in collaboration between the Washington University Genome Sequencing Center and the Sanger Institute. A preliminary assembly of the genome, based on plasmid, fosmid, and BAC-end reads that constitute 10-fold coverage of the genome, was made available in the summer of 2002.

Project Links:

• Washington University Genome Sequencing Center [genome.wustl.edu]
• Sanger Institute [sanger.ac.uk]

Supporting Institutions:

• The Wellcome Trust [wellcome.ac.uk]

Contributing Organizations:

• Sanger Institute [sanger.ac.uk]

C. remanei, C. japonica, C. sp. CB5161

In January 2004, NHGRI announced their support of a sequencing project meant to enhance the utility of the existing C. elegans genome assembly. The sequencing of the genomes of three additional roundworm species -- C. remanei, C. japonica, and C. sp. CB5161 -- and subsequent analyses to compare the resulting data to the existing roundworm genomes should allow for more thorough annotation of the C. elegans genome. The project aims to produce nine-fold genome coverage of each of these three species using a whole genome shotgun (WGS) sequencing approach. This sequencing project is being led by the Washington University (St. Louis) Genome Sequencing Center.

Genome Sequencing Whitepaper Proposal

• C. remanei, C. japonica, C. sp. CB5161
  (Submitted Oct. 2003)

Additional Resources

Sequence and Assembly

• Individual Sequence Reads
  • NCBI Trace Archive
    • C. elegans [ncbi.nlm.nih.gov]
    • C. briggsae [ncbi.nlm.nih.gov]
       
• Sequence Assembly
  • C. elegans
    • Washington University Genome Sequencing Center [genome.wustl.edu]
    • Sanger Institute [sanger.ac.uk]
    • Ensembl genome browser [useast.ensembl.org]
    • NCBI [ncbi.nlm.nih.gov]
    • UCSC [genome.cse.ucsc.edu]
       
  • C. briggsae
    • Washington University Genome Sequencing Center [genome.wustl.edu]
    • Sanger Institute [ftp - sanger.ac.uk]
    • UCSC [genome.cse.ucsc.edu]

Model Organism Database - WormBase

• C. elegans [wormbase.org]
• C. briggsae [wormbase.org]

ESTs

• dbEST - Database of ESTs at NCBI [ncbi.nlm.nih.gov]

cDNAs

• Invitrogen [invitrogen.com]

SNPs

• Database of Single Nucleotide - dbSNP [ncbi.nlm.nih.gov]- Polymorphisms at NCBI
• Washington University Genome Sequencing Center [genome.wustl.edu]- C. elegans

BAC Libraries

• Children's Hospital Oakland Research Institute (CHORI) [bacpac.chori.org]- C. briggsae BAC libraries

Other Helpful Websites

• Nematode.net [www.nematode.net]