Caenorhabditis japonica
Roundworm
Habitat
Caenorhabditis japonica is a small, free-living, round worm, but unlike C. elegans it is not found in nutrient- and microorganism-rich habitats feeding on bacteria and other microorganisms. C. japonica appears to be closely-associated with shield, or stink, bugs (commonly found on cabbage), where it has been found feeding in the bug's nest feeding on dead eggs and adult bugs. It has only been isolated on the Japanese islands of Saga and Shikoku. Like all other Caenorhabditis species it is not parasitic, as are many other nematodes.
Biology
The biology of C. japonica is similar to that of C. elegans, C. briggsae and C. remanei, in that it has a short generation time and goes through four larval stages before becoming an adult. It can also adapt an alternative life-form called a the dauer larva, but unlike C. elegans and the others that form dauers in response to overcrowding or the absence of an adequate food supply, there is evidence that C. japonica may enter the dauer stage regardless of food availability or overcrowding.
C. japonica, like C. remanei, differs from that of C. elegans and C. briggsae in one major way. Adults are either female or male, whereas C. elegans and C. briggsae adults are hermaphrodites; when they first become adults they have all the characteristics of a male but later become female.
C. japonica's genome is estimated to be approximately 83 Mb, roughly the size of the genome of the other Caenorhabditis species being sequenced.
Sequencing Plan
The sequencing plan for C. japonica calls for high-quality draft sequence. This will be accomplished with 6x whole genome shotgun coverage from short insert plasmid and larger insert fosmid libraries, and an additional 6x coverage in 454 reads.
Contacts
| Name | Affiliation |
|---|---|
| John Spieth | The Genome Institute, Washington University School of Medicine |
| Paul Sternberg | California Institute of Technology |
Sequences & Maps
Assemblies
| Name | Date | Description | Blast DBs |
| Caenorhabditis_japonica-3.0.2 | Mar 11, 2008 | 6.3X | contigs supercontigs |
| Caenorhabditis_japonica-4.0.1 | Dec 15, 2008 | 9X | supercontigs removed_data |
| Caenorhabditis_japonica-7.0.1 | Jul 12, 2010 | 22x | contigs supercontigs |
Sequences
| Name | Date | Description | Blast DBs |
| Caenorhabditis_japonica | Mar 30, 2008 | Fosmid ends | fosmid_ends |
Related Links
Sequence Data
Others
Publications
Parkinson J, Mitreva M, Hall N, Blaxter M, McCarter JP.
400000 nematode ESTs on the Net.
Trends Parasitol. 2003 Jul;19(7):283-6. PubMed | View Abstract
Scholl EH, Thorne JL, McCarter JP, Bird DM.
Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach.
Genome Biol. 2003;4(6):R39. Epub 2003 May 19. PubMed | View Abstract
McCarter, J., P. Abad, J. T. Jones, and D. Bird.
Rapid Gene Discovery in Plant Parasitic Nematodes Via Expressed Sequence Tags
Nematology, 2(7):719-731. Link | View Abstract
Harris TW, Chen N, Cunningham F, Tello-Ruiz M, Antoshechkin I, Bastiani C, Bieri T, Blasiar…
WormBase: a multi-species resource for nematode biology and genomics.
Nucleic Acids Res. 2004 Jan 1;32 Database issue:D411-7. PubMed | View Abstract
Harris TW, Lee R, Schwarz E, Bradnam K, Lawson D, Chen W, Blasier D, Kenny…
WormBase: a cross-species database for comparative genomics.
Nucleic Acids Res. 2003 Jan 1;31(1):133-7. PubMed | View Abstract
Wylie T, Martin JC, Dante M, Mitreva MD, Clifton SW, Chinwalla A, Waterston RH, Wilson…
Nematode.net: a tool for navigating sequences from parasitic and free-living nematodes.
Nucleic Acids Res. 2004 Jan 1;32 Database issue:D423-6. PubMed | View Abstract
