LINKAGE MAPS
Polymorphis-based linkage map – CURRENT
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).
Tables from the paper (Koboldt et al. 2010) – Table 2 (SNPs), Table 3 (medium Indels), Table 4 (small indels)
List of polymorphisms (SNPs and indels) – text files
Old webpage listing polymorphisms
Phenotypic marker-based linkage map – CURRENT (v10.1)
In this update new loci/genes have been added. The order of genes is based 3-factor mapping and/or physical locations in the CB3 assembly. Linkage distance, where mentioned, is based on 2-factor mapping experiments. The C. elegans orthologs (indicated by a ‘Cbr’ prefix) were validated by transgenic rescue experiments. Some of the mutations have been sequenced. Genes and integrants that are linked but not precisely mapped are listed next to LGI to LGX groups. Question marked (?) loci require validation.
Older versions of maps can be found here.
GENOME SEQUENCE
Download CB4 assembly – WormBase FTP (see ReadMe file)
GENES AND CONTIGS
Assembled contigs (Hillier et al. 2007)
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Search Wormbase
PROCESS-SPECIFIC GENES
(gene sets are not updated!)
Vulva
Dauer
Sex-determination
Body morphology
MESCELLANEOUS
(information not up to date)
Non-coding RNA
Most common InterPro domains
Genome sizes of organisms
SELECTED PUBLICATIONS
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.
Chromosome assembly of C. briggsae genome (Hillier et al. 2007)