This is a record of the current and proposed set of genomes in WormBase.
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 following are some of the columns in the Genome Table.
The Major Clades of Blaxter et al 1998 ("Bclades"), as systematised by De Ley and Blaxter 2002-2004.
The origin of the gene-set. One of: Curated (curated by WormBase), Predicted (made by a gene-prediction pipeline), External (produced by another group), None (no gene-set available).
The Genome column in the table gives the assembly size and a link to the genome in WormBase, or the approximate size if it has not been assembled.
The Genes column in the table indicates whether gene structures have been added to WormBase.
Which lab did the assembly. The sequence coverage. The number of Supercontigs. The Supercontig N50. And anything else that we know about it.
The current genomes
|V|| Caenorhabditis briggsae
|6238||108419768 bp||Curated||WashU|| First added in WS132|
[Sept 2010] New assembly from Erich Haag being worked on.
[Feb 2011] updated in WS224
|V|| Caenorhabditis species 9
|870437||204396809 bp||External|| WashU
| First added in WS226|
[Dec 2011]Update on contamination: There is no evidence that C. sp. 9 underwent cross-contamination, and the "C sp. 7" contaminants in the sp. 9 genome and transcriptome may actually be sp. 9 contaminants which got put into sp. 7.
[Feb 2012] Warning The C. species 9 assembly in WormBase WS226-WS230 has some confirmed contamination by C. species 7. Since species 9 has mostly species 9 genes and some species 7 genes, there is actually added value to having it, as long as people know of the potential problem with "apparent paralogs" that are actually sp. 7 genes.
|V|| Caenorhabditis species 5
|497829||131797386 bp||External|| WashU
|First added in WS226|
|V|| Caenorhabditis remanei
|31234||145500347 bp||Curated|| WashU
|First added in WS185|
|V|| Caenorhabditis species 11
|886184||79321433 bp||External|| WashU
| First added in WS226|
Replaced genes by RNAseq-based gene set in WS227.
|V|| Caenorhabditis brenneri
|135651||190421492 bp||Curated|| WashU
| First added in WS196|
[Jan 2011] The current assembly contains quite a bit of heterozygosity.
Warning WS223-WS226 genome assembly is not in sync with the annotation files or INSDC. Please use WS227+
|V|| Caenorhabditis elegans
strain Bristol N2
|6239||100272276 bp||Curated|| WashU/Sanger
|First added in WS1|
|V|| Caenorhabditis species 7
|870436||None||WashU|| First added in WS226.|
WARNING the genome sequence contains contaminations.
|V|| Caenorhabditis japonica
|281687||166565019 bp||Curated|| WashU
| First added in WS195|
[Jan 2011] New/improved assembly is being worked on at WashU.
[Oct 2011] new assembly in WS227
|V|| Caenorhabditis angaria
|96668||79761545 bp||External|| CalTech
| First added in WS218|
[Jan 2011] This species now has an official name of C. angaria
|V||Haemonchus contortus||6289||297975349 bp||Predicted|| Sanger
|First added in WS209.|
|V|| Heterorhabditis bacteriophora
|37862||76974349 bp||None|| WashU
| First added in WS229|
[Jan 2011] Submitted to GenBank - Accession: EF043402
[Sep 2011] Gene set and Annotations are being worked on.
|V|| Pristionchus pacificus
|54126||172773083 bp||External|| WashU/MPI
| First added in WS194|
[16 December 2010] Updated to the newest assembly and geneset in WS221
|IV|| Meloidogyne incognita
|6306||82095019 bp||None|| INRA
| First added in WS205|
Genes are not yet available. The official M.incognita genes are only available at INRA and their structure hasn't been made public.
|IV|| Meloidogyne hapla
|6305||53017507 bp||External|| NCSU hapla.org
|First added in WS204|
|IV|| Strongyloides ratti
|34506||52638471 bp||Predicted|| Sanger
| [Jan 2011] draft assembly in GenBank|
First added in WS226
|IV|| Bursaphelenchus xylophilus
|6326||74561461 bp||Predicted|| Sanger
| [Sept 2011] published in PLOS Pathogens|
[Nov 2011] First added in WS229
|III|| Ascaris suum (Gasser)
|6253||272782664 bp||External|| Davis
| First added in WS229|
[Oct 2011] integrated the Gasser genome without a reference gene set.
[Nov 2011] added a reference gene set
|III|| Ascaris suum (Davis)
|6253||[265577339 bp]||External|| Davis
| First added in WS236|
[Jan 2013] Integrated the Davis genome assembly (Privatre submission) containing a gene set and germline somatic eliminated regions.
|III|| Brugia malayi
|6279||95814443 bp||External / Predicted|| TIGR -> WashU/Sanger
| First added in WS185|
[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
|I|| Trichinella spiralis
strain ISS 195
|6334||56779425 bp||External|| WashU
| [Sept 2010] Being assembled.|
[Feb 2011] published in Nature.
[Mar 2011] First added in WS225
Genomes coming soon