Difference between revisions of "WormBase Genomes"

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| ''Steinernema carpocapsae''
| ''Steinernema carpocapsae''
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
| 230 Mb
| 230 Mb
| [http://www.langebio.cinvestav.mx/ LANGEBIO] / CalTech
| [http://www.langebio.cinvestav.mx/ LANGEBIO] / CalTech

Revision as of 11:46, 15 December 2011

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 - 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 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.

The current genomes

Clade Species NCBI Taxon Tier Genome Genes Origin Comments
V Caenorhabditis briggsae 6238 II 108419768 bp Yes WashU [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 released in WS226. WARNING the genome sequence contains contaminations
V Caenorhabditis species 5 ? V WashU released in WS226.
V Caenorhabditis remanei 31234 II 145500347 bp Yes WashU
V Caenorhabditis species 11
strain JU1373
886184 III 79321433 bp Yes WashU genome and deNovo gene set released in WS226.
Replaced by RNAseq based gene set in WS227.
V Caenorhabditis brenneri
species 4
135651 II 190421492 bp Yes WashU [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
V Caenorhabditis species 7
strain JU1286
870436 V WashU released in WS226.
WARNING the genome sequence contains contaminations
V Caenorhabditis japonica 281687 II 166565019 bp Yes WashU [Jan 2011] New/improved assembly is being worked on at WashU.
[Oct 2011] new assembly in WS227
V Caenorhabditis angaria
species 3 strain PS1010
96668 III 79761545 bp Yes CalTech Added to WormBase in release WS218.
[Jan 2011] This species now has an official name of C. angaria
V Haemonchus contortus 6289 III 297975349 bp Yes Sanger Added to WormBase in release WS209.
V Heterorhabditis bacteriophora 37862 V 76974349 bp WashU [Jan 2011] Submitted to GenBank - Accession: EF043402
[Sep 2011] Gene set and Annotations are being worked on.
[Nov 2011] on WormBase as of WS229
V Pristionchus pacificus 54126 II 172773083 bp Yes WashU/MPI [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 Added to WormBase in release WS205.
Genes are not yet available.
IV Meloidogyne hapla 6305 III 53017507 bp Yes NCSU hapla.org Added to WormBase in release WS204.
IV Strongyloides ratti 34506 III 52638471 bp Sanger [Jan 2011] draft assembly in GenBank, released in WS226
IV Bursaphelenchus xylophilus 6326 III 74561461 bp Yes Sanger [Sept 2011] published in PLOS Pathogens
[Nov 2011] added to WormBase in WS229
III Ascaris suum 6253 III 272782664 bp Yes Davis [Oct 2011] integrated the Davis genome without a reference gene set.
[Nov 2011] added a reference gene set
III Brugia malayi 6279 III 95814443 bp 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
I Trichinella spiralis 6334 III 56779425 bp Yes WashU [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] added to WormBase in WS225

Genomes coming soon

Clade Species NCBI Taxon Tier Genome Genes Origin 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