WormBase Genomes

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WormBase Genomes

This is a record of the current and proposed set of genomes in WormBase.

I think that this page is a correct statement of our intentions.

We may, of course, alter our plans for which species to include as circumstances dictate and so the list of organisms which should be included should be treated as somewhat tentative.


The different genomes in WormBase are classified in various tiers which depend on the amount of curation effort we are able to put into maintaining them.

Tier I - All efforts are made to curate the gene structures and any other genetic or metabolic information. Only C. elegans is in this group.

Tier II - Efforts are made, where practical, to manually curate the gene structure and possibly some other genomic information. WormBase 'owns' the assembly in the ENA and GenBank so that new gene annotations can be submitted to the ENA/GenBank by WormBase.

Tier III - We will set up the genome on WormBase with any gene structures that the authors of this genome have predicted. No further curation efforts are made by the WormBase consortium.

Tier IV - Proposed tier for organisms with only transcriptome information and no coherent genome. There are no examples of this in WormBase at present.

Tier V - Proposed tier for organisms with only genome information and no coherent transcriptome. There are no examples of this in WormBase at present.


The Genome column in the table indicates whether the genome has been added to WormBase.


The Genes column in the table indicates whether gene structures have been added to WormBase.

The genome status

Species NCBI TaxonID Tier Genome Genes Origin Comments
Caenorhabditis briggsae 6238 II Yes Yes WashU [Sept 2010] New assembly from Erich Haag being worked on.
Caenorhabditis remanei 31234 II Yes Yes WashU
Caenorhabditis brenneri
(Species 4)
135651 II Yes Yes WashU [Jan 2011] The current assembly contains quite a bit of heterozygosity
Caenorhabditis elegans strain N2 6239 I Yes Yes WashU/Sanger
Caenorhabditis elegans strain DR1035 6239 III Mark Blaxter status unclear
Caenorhabditis japonica 281687 II Yes Yes WashU [Jan 2011] New/improved assembly is being worked on at WashU
Caenorhabditis drosophilae 96641 III WashU [Sept 2010] being assembled
Caenorhabditis angaria (species 3 strain PS1010) 96668 III Yes Yes CalTech Added to WormBase in release WS218.
[Jan 2011] This species now has an official name of C. angaria
Caenorhabditis species 7 strain JU1286 870436 V WashU released in WS226
Caenorhabditis species 9 strain JU1422 870437 V WashU released in WS226
Caenorhabditis species 11 strain JU1373 886184 V WashU released in WS226
Heterorhabditis bacteriophora 37862 V WashU Jan 2011 - Submitted to GenBank - Accession: EF043402 Sep 2011 - Gene set and Annotations are being worked on.
Pristionchus pacificus 54126 II Yes Yes WashU/MPI [16 December 2010] Updated to the newest assembly and geneset in WS221
Haemonchus contortus 6289 III Yes Yes Sanger Added to WormBase in release WS209.
Strongyloides ratti 34506 III Sanger [Jan 2011] draft assembly in GenBank, released in WS226
Meloidogyne hapla 6305 III Yes Yes NCSU hapla.org Added to WormBase in release WS204.
Meloidogyne incognita 6306 III Yes INRA Added to WormBase in release WS205. Genes are not yet available.
Brugia malayi 6279 III Yes Yes TIGR -> WashU/Sanger [Sept 2010] Currently using the old TIGR assembly. Waiting for WashU (did assembly) and Sanger (did gene models) to publish, then we will use the new assembly.
[Dec 2010] merged Augustus gene predictions from Erich Schwarz into WS216
Onchocerca volvulus 6282 III Sanger
Ascaris suum 6253 III Sanger
Globodera pallida 36090 III Sanger
Nippostrongylus brasiliensis 27835 III Sanger
Strongyloides ransomi 553534 III Sanger
Teladorsagia circumcincta 45464 III Sanger
Trichuris muris 70415 III Sanger
Trichinella spiralis 6334 III WashU [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] will be in WS225
Steinernema carpocapsae 34508 Laboratorio Nacional de Genómica para la Biodiversidad / CalTech [May 2011] Being assembled.


Given my understanding of the current phylogenetic literature (and based on personal communications with Karin Kiontke), the correct guide tree would be:

((((((((C.elegans,(((C.briggsae, C.sp9), C.remanei),(C.sp11, C.brenneri))),(C.sp7, C.japonica)), C.angaria), (H.contortus,H.bacteriophora)), P.pacificus),((M.incognita, M.hapla), S.ratti)), B.malayi), T.spiralis);


See also