Genetics & Genomics

Genetic Mutations

Linkage data

Linkage maps

Visible marker-based mapCURRENT (v10.0)
In this update several new loci/genes have been added. The order of genes is based 3-factor mapping and/or physical locations in CB3 assembly. In some cases linkage distance between two genes have also been determined. This was done by 2-factor mapping by constructing double mutants. The C. elegans orthologs are identified by a ‘Cbr’ prefix. These genes are validated by transgenic rescue of mutant alleles. In some cases, mutations have also been sequenced. Some genes and integrants (listed on the right of LGI to LGX) are partially mapped. Their precise locations need to be determined. Question marked (?) loci require validation.

Polymorphis-based mapCURRENT
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 (http://www.biomedcentral.com/1471-2164/11/236).

Non-coding RNA

Polymorphisms
Most common InterPro domains
Genome sizes of organisms

Download annotated C. briggsae genome

(Newest assembly is CB4)
WormBase FTP  (see ReadMe file for details)

Genes and Contigs

Assembled contigs (Hillier et al. 2007)
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Search Wormbase

Process-specific
Vulva
– Dauer
– Sex-determination
– Body morphology

Selected publications

Review (Wormbook)

Genome sequence (Stein et al. 2003)
Partial text of the C. briggsae whole-genome shotgun assembly announcement on July 12, 2002 (Sanger Institute website).

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.

Other genome sequence-related articles

Chromosome assembly of C. briggsae genome (Hillier et al. 2007)