Difference between revisions of "WormBase Genomes"

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(done the main ordering apart from Steinernema carpocapsae)
(put Steinernema carpocapsae with the other CLade V's, added colours)
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The '''Genes''' column in the table indicates whether gene structures have been added to WormBase.
 
The '''Genes''' column in the table indicates whether gene structures have been added to WormBase.
  
=== The genome status ===
+
=== The current genomes ===
  
 
{| class="wikitable" border="1"
 
{| class="wikitable" border="1"
Line 37: Line 37:
 
!  Clade
 
!  Clade
 
!  Species
 
!  Species
!  NCBI TaxonID
+
!  NCBI Taxon
 
!  Tier
 
!  Tier
 
!  Genome
 
!  Genome
Line 43: Line 43:
 
!  Origin
 
!  Origin
 
!  Comments
 
!  Comments
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae'']]
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae'']]
Line 52: Line 52:
 
| WashU
 
| WashU
 
| [Sept 2010] New assembly from Erich Haag being worked on. [Feb 2011] updated in WS224
 
| [Sept 2010] New assembly from Erich Haag being worked on. [Feb 2011] updated in WS224
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| Caenorhabditis species 9 strain JU1422
 
| Caenorhabditis species 9 strain JU1422
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| WashU
 
| WashU
 
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
 
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| Caenorhabditis species 5
 
| Caenorhabditis species 5
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| WashU
 
| WashU
 
|  released in WS226.
 
|  released in WS226.
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Caenorhabditis remanei|''Caenorhabditis remanei'']]
 
| [[Caenorhabditis remanei|''Caenorhabditis remanei'']]
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| WashU
 
| WashU
 
|  
 
|  
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| Caenorhabditis species 11 strain JU1373
 
| Caenorhabditis species 11 strain JU1373
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| WashU
 
| WashU
 
|  genome and deNovo gene set released in WS226. Replaced by RNAseq based gene set in WS227.  
 
|  genome and deNovo gene set released in WS226. Replaced by RNAseq based gene set in WS227.  
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Caenorhabditis brenneri|''Caenorhabditis brenneri'']]<br>(Species 4)
 
| [[Caenorhabditis brenneri|''Caenorhabditis brenneri'']]<br>(Species 4)
Line 97: Line 97:
 
| WashU
 
| WashU
 
| [Jan 2011] The current assembly contains quite a bit of heterozygosity.<br>'''Warning''' WS223-WS226 genome assembly is not in sync with the annotation files or INSDC. Please use WS227+
 
| [Jan 2011] The current assembly contains quite a bit of heterozygosity.<br>'''Warning''' WS223-WS226 genome assembly is not in sync with the annotation files or INSDC. Please use WS227+
|-bgcolor="#00D7D7"
+
|-bgcolor="#FFFF33"
 
| V
 
| V
 
| [[Caenorhabditis elegans|''Caenorhabditis elegans strain N2'']]
 
| [[Caenorhabditis elegans|''Caenorhabditis elegans strain N2'']]
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| WashU/Sanger
 
| WashU/Sanger
 
|  
 
|  
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| Caenorhabditis species 7 strain JU1286
 
| Caenorhabditis species 7 strain JU1286
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| WashU
 
| WashU
 
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
 
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica'']]
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica'']]
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| WashU
 
| WashU
 
| [Jan 2011] New/improved assembly is being worked on at WashU.<br>[Oct 2011] new assembly in WS227
 
| [Jan 2011] New/improved assembly is being worked on at WashU.<br>[Oct 2011] new assembly in WS227
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Caenorhabditis angaria|''Caenorhabditis angaria'']] (species 3 strain PS1010)
 
| [[Caenorhabditis angaria|''Caenorhabditis angaria'']] (species 3 strain PS1010)
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| CalTech
 
| CalTech
 
| Added to WormBase in release WS218.<br>[Jan 2011] This species now has an official name of '''C. angaria'''
 
| Added to WormBase in release WS218.<br>[Jan 2011] This species now has an official name of '''C. angaria'''
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Haemonchus contortus|''Haemonchus contortus'']]
 
| [[Haemonchus contortus|''Haemonchus contortus'']]
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| Sanger
 
| Sanger
 
| Added to WormBase in release WS209.
 
| Added to WormBase in release WS209.
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora'']]
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora'']]
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| WashU
 
| 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
 
|  [Jan 2011] Submitted to GenBank - Accession: EF043402 [Sep 2011] Gene set and Annotations are being worked on. [Nov 2011] on WormBase as of WS229
|-
+
|-bgcolor="#FFFF99"
 
| V
 
| V
 
| [[Pristionchus pacificus|''Pristionchus pacificus'']]
 
| [[Pristionchus pacificus|''Pristionchus pacificus'']]
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| WashU/MPI
 
| WashU/MPI
 
| [16 December 2010] Updated to the newest assembly and geneset in WS221  
 
| [16 December 2010] Updated to the newest assembly and geneset in WS221  
|-
+
|-bgcolor="#FFFF99"
 +
| V
 +
| Steinernema carpocapsae
 +
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
 +
|
 +
|
 +
|
 +
| Laboratorio Nacional de Genómica para la Biodiversidad / CalTech
 +
| [May 2011] Being assembled.
 +
|-bgcolor="#99FF99"
 
| IV
 
| IV
 
| [[Meloidogyne incognita|''Meloidogyne incognita'']]
 
| [[Meloidogyne incognita|''Meloidogyne incognita'']]
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| INRA
 
| INRA
 
| Added to WormBase in release WS205. Genes are not yet available.
 
| Added to WormBase in release WS205. Genes are not yet available.
|-
+
|-bgcolor="#99FF99"
 
| IV
 
| IV
 
| [[Meloidogyne hapla|''Meloidogyne hapla'']]
 
| [[Meloidogyne hapla|''Meloidogyne hapla'']]
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| NCSU hapla.org
 
| NCSU hapla.org
 
| Added to WormBase in release WS204.
 
| Added to WormBase in release WS204.
|-
+
|-bgcolor="#99FF99"
 
| IV
 
| IV
 
| [[Strongyloides ratti|''Strongyloides ratti'']]
 
| [[Strongyloides ratti|''Strongyloides ratti'']]
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| Sanger
 
| Sanger
 
| [Jan 2011] draft assembly in GenBank, released in WS226
 
| [Jan 2011] draft assembly in GenBank, released in WS226
|-
+
|-bgcolor="#99FF99"
 
| IV
 
| IV
 
| Bursaphelenchus xylophilus
 
| Bursaphelenchus xylophilus
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| Sanger
 
| Sanger
 
| [Sept 2011] published in PLOS Pathogens  [Nov 2011] added to WormBase in WS229
 
| [Sept 2011] published in PLOS Pathogens  [Nov 2011] added to WormBase in WS229
|-
+
|-bgcolor="#FF9900"
 
| III
 
| III
 
| Ascaris suum
 
| Ascaris suum
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| Davis
 
| Davis
 
| [Oct 2011] integrated the Davis genome without a reference gene set. [Nov 2011] added a reference gene set
 
| [Oct 2011] integrated the Davis genome without a reference gene set. [Nov 2011] added a reference gene set
|-
+
|-bgcolor="#FF9900"
 
| III
 
| III
 
| [[Brugia malayi|''Brugia malayi'']]
 
| [[Brugia malayi|''Brugia malayi'']]
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| TIGR -> WashU/Sanger
 
| 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.<br>[Dec 2010] merged Augustus gene predictions from Erich Schwarz into WS216
 
| [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.<br>[Dec 2010] merged Augustus gene predictions from Erich Schwarz into WS216
|-
+
|-bgcolor="#33FFFF"
 
| I
 
| I
 
| Trichinella spiralis
 
| Trichinella spiralis
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| WashU
 
| WashU
 
| [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] added to WormBase in WS225
 
| [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] added to WormBase in WS225
 
 
|-
 
| V
 
| Steinernema carpocapsae
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
 
|
 
|
 
|
 
| Laboratorio Nacional de Genómica para la Biodiversidad / CalTech
 
| [May 2011] Being assembled.
 
 
|}
 
|}
  
  
  
 
+
=== Genomes coming soon ===
  
 
{| class="wikitable" border="1"
 
{| class="wikitable" border="1"
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!  Clade
 
!  Clade
 
!  Species
 
!  Species
!  NCBI TaxonID
+
!  NCBI Taxon
 
!  Tier
 
!  Tier
 
!  Genome
 
!  Genome
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!  Origin
 
!  Origin
 
!  Comments
 
!  Comments
|-
+
|-bgcolor="#CC9999"
 
| V
 
| V
 
| Caenorhabditis drosophilae
 
| Caenorhabditis drosophilae
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| WashU
 
| WashU
 
| [Sept 2010] being assembled
 
| [Sept 2010] being assembled
|-
+
|-bgcolor="#CC9999"
 
| V
 
| V
 
| Caenorhabditis elegans strain DR1035
 
| Caenorhabditis elegans strain DR1035
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| Mark Blaxter
 
| Mark Blaxter
 
| status unclear
 
| status unclear
|-
+
|-bgcolor="#CC9999"
 +
|
 
| Onchocerca volvulus
 
| Onchocerca volvulus
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
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| Sanger
 
| Sanger
 
|
 
|
|-
+
|-bgcolor="#CC9999"
 +
|
 
| Globodera pallida
 
| Globodera pallida
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36090 36090]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36090 36090]
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| Sanger
 
| Sanger
 
|
 
|
|-
+
|-bgcolor="#CC9999"
 +
|
 
| Nippostrongylus brasiliensis
 
| Nippostrongylus brasiliensis
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27835 27835]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27835 27835]
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| Sanger
 
| Sanger
 
|
 
|
|-
+
|-bgcolor="#CC9999"
 +
|
 
| Strongyloides ransomi
 
| Strongyloides ransomi
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=553534 553534]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=553534 553534]
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| Sanger
 
| Sanger
 
|  
 
|  
|-
+
|-bgcolor="#CC9999"
 +
|
 
| Teladorsagia circumcincta
 
| Teladorsagia circumcincta
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
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| Sanger
 
| Sanger
 
|
 
|
|-
+
|-bgcolor="#CC9999"
 +
|
 
| Trichuris muris
 
| Trichuris muris
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=70415 70415]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=70415 70415]

Revision as of 10:58, 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.

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 - 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.

Genome

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

Gene

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 Yes 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 WashU released in WS226. WARNING the genome sequence contains contaminations
V Caenorhabditis species 5 ? V WashU released in WS226.
V Caenorhabditis remanei 31234 II Yes Yes WashU
V Caenorhabditis species 11 strain JU1373 886184 III Yes 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 Yes 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 N2 6239 I Yes 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 Yes 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 Yes 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 Yes Yes Sanger Added to WormBase in release WS209.
V Heterorhabditis bacteriophora 37862 V Yes 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 Yes Yes WashU/MPI [16 December 2010] Updated to the newest assembly and geneset in WS221
V Steinernema carpocapsae 34508 Laboratorio Nacional de Genómica para la Biodiversidad / CalTech [May 2011] Being assembled.
IV Meloidogyne incognita 6306 III Yes INRA Added to WormBase in release WS205. Genes are not yet available.
IV Meloidogyne hapla 6305 III Yes Yes NCSU hapla.org Added to WormBase in release WS204.
IV Strongyloides ratti 34506 III Yes Sanger [Jan 2011] draft assembly in GenBank, released in WS226
IV Bursaphelenchus xylophilus 6326 III Yes Yes Sanger [Sept 2011] published in PLOS Pathogens [Nov 2011] added to WormBase in WS229
III Ascaris suum 6253 III Yes 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 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
I Trichinella spiralis 6334 III Yes 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 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);

Treeprint5.png

See also