WormBase Genomes

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Revision as of 14:30, 15 December 2011 by Gwilliams (talk | contribs) (added strain for species 5)
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WormBase Genomes

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 Major Clades of Blaxter et al 1998 ("Bclades"), as systematised by De Ley and Blaxter 2002-2004.


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 - No curation by WormBase. We will set up the genome on WormBase with any gene structures that the authors of this genome have predicted.

Tier IV - No curation by WormBase. Only transcriptome information provided by the authors and no coherent genome.

Tier V - No curation by WormBase. Only genome information provided by the authors and no coherent transcriptome.


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 Supercontig N50. And anything else that we know about it.

The current genomes

Clade Species NCBI Taxon Tier Genome Genes Assembly Comments
V Caenorhabditis briggsae
strain AF16
6238 II 108419768 bp Yes WashU First added in WS132
[Sept 2010] New assembly from Erich Haag being worked on.
[Feb 2011] updated in WS224
V Caenorhabditis species 9
strain JU1422
870437 V 204396809 bp WashU
Supercontigs: 7636
N50: 196652
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.
V Caenorhabditis species 5
strain DRD-2008
497829 V WashU First added in WS226
V Caenorhabditis remanei 31234 II 145500347 bp Yes WashU
Coverage: 9.2x
Supercontigs: 3670
N50: 461060
First added in WS185
V Caenorhabditis species 11
strain JU1373
886184 III 79321433 bp Yes WashU
Coverage: 19.1
Supercontigs: 665
N50: 20921866
First added in WS226
Replaced genes by RNAseq-based gene set in WS227.
V Caenorhabditis brenneri
(species 4)
135651 II 190421492 bp Yes WashU
Coverage: 9.5
Supercontigs: 3305
N50: 368319
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 I 100272276 bp Yes WashU/Sanger
Coverage: 6x
First added in WS1
V Caenorhabditis species 7
strain JU1286
870436 V WashU First added in WS226.
WARNING the genome sequence contains contaminations
V Caenorhabditis japonica
strain DF5080
281687 II 166565019 bp Yes WashU
Coverage: 22x
Supercontigs: 18817
N50: 94149
First added in WS195
[Jan 2011] New/improved assembly is being worked on at WashU.
[Oct 2011] new assembly in WS227
V Caenorhabditis angaria
strain PS1010

(species 3)
96668 III 79761545 bp Yes CalTech
Supercontigs: 33559
N50: 9453
First added in WS218
[Jan 2011] This species now has an official name of C. angaria
V Haemonchus contortus 6289 III 297975349 bp Yes Sanger
Supercontigs: 59707
N50: 13338
First added in WS209.
V Heterorhabditis bacteriophora
strain M31e
37862 V 76974349 bp WashU
Coverage: 26.1
Supercontigs: 1240
N50: 312328
First added in WS229
[Jan 2011] Submitted to GenBank - Accession: EF043402
[Sep 2011] Gene set and Annotations are being worked on.
V Pristionchus pacificus
strain PS312
54126 II 172773083 bp Yes WashU/MPI
Coverage: 8.92
Supercontigs: 18083
N50: 1244534
First added in WS194
[16 December 2010] Updated to the newest assembly and geneset in WS221
V Steinernema carpocapsae 34508 III 230 Mb LANGEBIO / CalTech [May 2011] Being assembled.
IV Meloidogyne incognita 6306 III 82095019 bp INRA
Supercontigs: 9538
N50: 83000
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 III 53017507 bp Yes NCSU hapla.org
Supercontigs: 3452
First added in WS204
IV Strongyloides ratti
natural isolate
34506 III 52638471 bp Sanger
Coverage: 70x
Supercontigs: 2184
N50: 359029
[Jan 2011] draft assembly in GenBank
First added in WS226
IV Bursaphelenchus xylophilus
strain Ka4C1
6326 III 74561461 bp Yes Sanger
Coverage: 13x
Supercontigs: 5527
N50: 1158000
[Sept 2011] published in PLOS Pathogens
[Nov 2011] First added in WS229
III Ascaris suum
natural isolate
6253 III 272782664 bp Yes Davis
Coverage: 70x
Supercontig: 29831
N50: 407899
First added in WS229
[Oct 2011] integrated the Davis genome without a reference gene set.
[Nov 2011] added a reference gene set
III Brugia malayi
natural isolate
6279 III 95814443 bp Yes TIGR -> WashU/Sanger
Supercontigs: 27210
N50: 37841
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 6334 III 56779425 bp Yes WashU
Supercontigs: 6863
N50: 3383625
[Sept 2010] Being assembled.
[Feb 2011] published in Nature.
[Mar 2011] First added in WS225

Genomes coming soon

Clade Species NCBI Taxon Tier Genome Genes Assembly Comments
V Caenorhabditis drosophilae 96641 III WashU [Sept 2010] being assembled
V Caenorhabditis elegans
strain DR1035
6239 III 100 Mb Mark Blaxter status unclear
Onchocerca volvulus 6282 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


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

((((((((((((C.briggsae,C.sp9),C.sp5),C.remanei),(C.sp11,C.brenneri)),C.elegans),(C.sp7,C.japonica)),C.angaria),(H.contortus,H.bacteriophora)),P.pacificus),((M.incognita,M.hapla), (S.ratti,B.xylophilus))),(A.suum,B.malayi)),T.spiralis);


See also