Caenorhabditis brenneri Assembly and Gene Annotation
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.
- C. brenneri data at WormBase
- C. brenneri data at WormBase ParaSite
- Roundworm Genome Sequencing white paper
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.
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 WS260.
- 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.
- 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.
|Assembly||C_brenneri-6.0.1b, INSDC Assembly GCA_000143925.2,|
|Golden Path Length||190,369,721|
|Non coding genes||2,171|
|Small non coding genes||2,171|