WormBase Genomes

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.

Clade

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

Tiers

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.

Genome

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.

Gene

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

Assembly

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 84000	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

Phylogeny

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

• Caenorhabditis elegans
  • Wikipedia entry on C. elegans
  • About C. elegans
  • Key publications
  • Genetic Nomenclature
  • Other nematodes
  • Nematode resequencing and diversity
  • The C. elegans Parts List (List of Cells)
• Possible_assembly_errors - in all Caenorhabditis species