Genome assemblies, genetic maps, polymorphism data and gene sets for Caenorhabditis briggsae. See also Resources for strains, stock centres and databases.
Genome assemblies
- CGC2: gap-free, telomere-to-telomere reference for AF16 (2026). No gaps, no unplaced sequence, chromosome-level contiguity, with protein-coding annotations predicted from deep RNA-seq across all developmental stages, and 108 validated indel variants lifted over to the new coordinate system. O’Connor et al. (2026) G3 16(8):jkag158
- CB4 assembly: the long-standing WormBase reference. Download from WormBase (see the ReadMe for file descriptions)
- QX1410 and VX34: chromosome-level assemblies for a strain closely related to AF16 and for a divergent Chinese isolate, plus 99 recombinant inbred lines genotyped at 2,981 SNP markers. Stevens et al. (2022) Genome Biology and Evolution
- Across the genus: assemblies and annotations for all Caenorhabditis species currently in culture, with BLAST and gene trees. Caenorhabditis Genomes Project
- Browse: WormBase JBrowse · WormBase ParaSite
Genetic linkage maps
Polymorphism-based linkage map: current version (PDF)
Source: Koboldt DC, Staisch J, Thillainathan B, Haines K, Baird SE, Chamberlin HM, Haag ES, Miller RD and Gupta BP (2010). A toolkit for rapid gene mapping in the nematode Caenorhabditis briggsae. BMC Genomics 11:236. Full text
Marker tables from that paper: Table 2 – SNPs · Table 3 – medium indels · Table 4 – small indels
Phenotypic marker-based linkage map: current version, v10.1 (PDF)
Gene order is based on three-factor mapping and/or physical position in the CB3 assembly. Linkage distances, where given, come from two-factor mapping experiments. C. elegans orthologs (prefixed Cbr) were validated by transgenic rescue, and some mutations have been sequenced. Genes and integrants that are linked but not precisely mapped are listed beside their LGI–LGX groups. Loci marked with a question mark require validation.
Polymorphisms and mapping data
- Polymorphism lists: SNPs and indels, as text files
- Raw sequence reads: HK104, VT847, HK105 and PB800
- Genetic mutations
- Linkage data
- Pairwise indel finder: design mapping markers between any two sequenced wild isolates. CaeNDR tool
Genes, contigs and annotation
- Community-curated gene models: a community effort to correct and improve C. briggsae gene structures. Novel and improved C. briggsae gene models (2023)
- TEC-RED 5′ end analysis: new exons, paralogs, and conserved and novel operons. Jhaveri et al. (2022) G3
- Assembled contigs (Hillier et al. 2007) · browse all contigs and genes
Legacy gene sets and other details
The following sets were compiled around 2010–2011 and have not been revised since. They remain useful as starting points, but should be checked against current WormBase annotations and other sources.
- Process-specific genes: vulva · dauer · sex determination · body morphology
- Non-coding RNA
- Most common InterPro domains
- Genome sizes of organisms
Key publications
- Genomics and biology of the nematode Caenorhabditis briggsae: WormBook review, Gupta, Johnsen and Chen (2007)
- Stein et al. (2003): the original genome sequence
- Hillier et al. (2007): chromosome-level assembly
- O’Connor et al. (2026): telomere-to-telomere CGC2 assembly
- Other genome sequence-related articles
Historical note
From the Sanger Institute’s announcement of the C. briggsae whole-genome shotgun assembly, 12 July 2002. Retained for historical interest; superseded by every assembly listed above.
The Washington University Genome Sequencing Center (St. Louis) has already sequenced approximately 13 Mb of the C. briggsae genome in bacterial clones. During the second half of 2001 the GSC and the Sanger Institute have each sequenced approximately 1,000,000 whole genome shotgun reads from plasmids and BAC and fosmid ends. These give a greater than 10x coverage of the genome. We have made preliminary assemblies using the PHUSION assembler of Jim Mullikin.
This C. briggsae sequence (version cb25.agp8) was assembled from 2.05 million whole genome shotgun reads, of which 88.2% are in read pairs. Using the Phusion assembler, reads were first assembled into contigs on the basis of overlap information, and then into supercontigs using read pair information to cross gaps. The supercontigs were then assembled into mapped ultracontigs on the basis of FPC fingerprint mapping, adding in some material from the previously finished clones to bridge gaps. Because of the absence of dense chromosomal maps for C. briggsae, we can not assign these ultracontigs to chromosomal locations, and so can not give draft chromosome sequences.