Caenorhabditis brenneri Assembly and Gene Annotation

NOTE: The genome sequence and annotation for C. brenneri are updated in Ensembl Metazoa infrequently. The data here corresponds with WormBase WS250. For the latest genome and annotation, please visit WormBase ParaSite (for an Ensembl-oriented view), or WormBase.

About Caenorhabditis brenneri

Caenorhabditis brenneri is a small, free-living round worm found in decaying plant material throughout the tropics. The worms feed on the bacteria and other micro-organisms associated with plant decay. The biology of C. brenneri is similar to that of C. elegans with a short generation time through four larval stages into an adult. C.brenneri has both male and female adults, unlike the hermaphroditic species such as C. elegans and C. briggsae.

C. brenneri was previously known as Caenorhabditis n. sp. 4 or PB2801 prior to the type description and renaming in 2007 (Sudhaus & Kiontke). The sequenced strain PB2801 was derived from a wild isolate LKC28, isolated by Hernan Ruiz from the roots of Liriope (Convallariaceae) in 2003, grown in an Costa Rican nursery. The wild isolate was inbred for 20 generations in the lab of Scott Baird by transferral of a single gravid female per generation.

Assembly

The C. brenneri genome was sequenced by the Genome Institute at Washington University as part of a larger NHGRI funded Roundworm Genome Sequencing project to expand the Caenorhabditis clade. The genome is approximately 115 Mb in size, some 15% larger than that of the model Rhabditid C. elegans. The assembly was performed using PCAP.

Annotation

Genome annotation was initially 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). Since then, many gene structures have been manually revised by WormBase curators. The annotation shown here corresponds with WormBase WS250.

Other data viewable on the genome browser

  • Alignments of C. brenneri mRNAs and ESTs to the genome.

References

  1. Comparison of the cryptic nematode species Caenorhabditis brenneri sp. n. and C. remanei (Nematoda: Rhabditidae) with the stem species pattern of the Caenorhabditis Elegans group.
    Sudhaus W, Kiontke K. 2007. Zootaxa. 1456:45-62.
  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.

More information

General information about this species can be found in Wikipedia.

Statistics

Summary

AssemblyC_brenneri-6.0.1b, INSDC Assembly GCA_000143925.2, Jul 2011
Database version90.250
Base Pairs190,369,721
Golden Path Length190,369,721
Genebuild byWormBase
Genebuild methodImport
Data sourceWormBase

Gene counts

Coding genes30,660
Non coding genes2,151
Small non coding genes2,151
Pseudogenes413
Gene transcripts33,311

About this species