Caenorhabditis japonica (C_japonica-7.0.1)

Caenorhabditis japonica Assembly and Gene Annotation

NOTE: The genome sequence and annotation for C. japonica are updated in Ensembl Metazoa infrequently. The data here corresponds with WormBase WS260. For the latest genome and annotation, please visit WormBase ParaSite (for an Ensembl-oriented view), or WormBase.

About Caenorhabditis japonica

Caenorhabditis japonica is a small, free-living roundworm which appears to be closely-associated with shield, or stink, bugs. Frequently, these insects can be found on cabbage plants and the worms have been reported feeding in the bug's nest on dead eggs and adult bugs. C. japonica has only been isolated on the Japanese islands of Saga and Shikoku. The biology of C. japonica is similar to that of C. elegans with the exception that C. japonica has both male and female adults.

C. japonica was first described by Kiontke, Hironaka and Sudhaus in 2002 (Kiontke & Sudhaus, 2006). The sequenced strain DF5081 was derived from a wild isolate DF5080, isolated from a dead shield bug (Parastrachia japonensis) in Takeo, Japan by Toyoshi Yoshiga. The wild isolate was inbred for 20 generations in the lab of David Fitch by transferral of a single plugged gravid female per generation.

Genome Sequencing and Annotation

The C. japonica genome has been sequenced by the the Genome Institue at Washington University as part of a larger NHGRI funded Roundworm Genome Sequencing project to expand the Caenorhabditis clade. The genome is approximately 107 Mb in size, similar to that of the model Rhabditid C. elegans.

Annotation

Genome annotation was 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 improved by WormBase curators. The annotation here corresponds with WormBase WS260.

References

  1. Ecology of Caenorhabditis species.
    Kiontke K, Sudhaus W. 2006. WormBook. :1-14.
  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.

Statistics

Summary

AssemblyC_japonica-7.0.1, INSDC Assembly GCA_000147155.1,
Database version93.260
Base Pairs166,256,191
Golden Path Length166,256,191
Genebuild byWormBase
Genebuild methodImport
Data sourceWormBase

Gene counts

Coding genes29,931
Non coding genes1,875
Small non coding genes1,875
Pseudogenes599
Gene transcripts38,557

About this species