Caenorhabditis briggsae (CB4)

Caenorhabditis briggsae Assembly and Gene Annotation

NOTE: The genome sequence and annotation for C. briggsae are updated in Ensembl Metazoa infrequently. For the latest genome and annotation, please visit WormBase ParaSite (for an Ensembl-oriented view), or WormBase.

About Caenorhabditis briggsae

Caenorhabditis briggsae is a small, free-living roundworm found in decaying plant material especially compost and mushroom beds in temperate regions throughout the world. The worms feed on the bacteria and other microorganisms associated with plant decay. The biology of C. briggsae is similar to that of C. elegans, with a short generation time through four larval stages into an adult. C. briggsae is hermaphroditic like C. elegans and distinct from the other sequenced worms which have both male and female adult animals. C. briggsae is often found at the same site as both C. elegans and C. remanei. C. briggsae is frequently found associated with snails that are presumed to transport worms, especially the dormant dauer stage, from one location to another.

Assembly

Sequencing of cosmids was initiated during the C. elegans project but the majority of the sequence (approx. 90%) was derived from whole genome shotgun data from the AF16 strain.

The version of the C. briggsae genome sequence in Ensembl Metazoa (CB4) was produced by the University of Maryland in September 2010. Around 170 AF16/HK104 advanced-intercross recombinant inbred lines were successfully genotyped at about 1000 single nucleotide polymorphism (SNP) markers. The resulting data were used to estimate high-density genetic maps. Sequences were assembled by combining the physical positions (based on the original CB25 assembly: Stein et al, 2003) and genetic positions of the SNPs to inform the process of ordering and orienting the CB25 supercontigs into new chromosome assemblies. Detailed methods are presented in Ross et al, 2011.

Annotation

Genome annotation continues to undertaken by the WormBase group based in part on the high quality C. elegans annotations and guided by the nGASP assessment project (Coghlan et al, 2008). The annotation here corresponds with WormBase WS269.

References

  1. Caenorhabditis briggsae recombinant inbred line genotypes reveal inter-strain incompatibility and the evolution of recombination.
    Ross JA, Koboldt DC, Staisch JE, Chamberlin HM, Gupta BP, Miller RD, Baird SE, Haag ES. 2011. PLoS Genetics. 7:e1002174.
  2. nGASP--the nematode genome annotation assessment project.
    Coghlan A, Fiedler TJ, McKay SJ, Flicek P, Harris TW, Blasiar D, nGASP Consortium, Stein LD. 2008. BMC Bioinformatics. 9:549.
  3. The genome sequence of Caenorhabditis briggsae: a platform for comparative genomics.
    Stein LD, Bao Z, Blasiar D, Blumenthal T, Brent MR, Chen N, Chinwalla A, Clarke L, Clee C, Coghlan A et al. 2003. PLoS Biology. 1:E45.

Statistics

Summary

AssemblyCB4, INSDC Assembly GCA_000004555.3,
Database version104.269
Golden Path Length108,384,165
Genebuild byWormBase
Genebuild methodImport
Data sourceWormBase

Gene counts

Coding genes20,996
Non coding genes1,281
Small non coding genes1,259
Long non coding genes22
Pseudogenes1,000
Gene transcripts27,267

About this species