Difference between revisions of "WormBase Genomes"

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(started adding more data to the table - added clade, moving species into a more taxonomic order)
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This is a record of the current and proposed set of genomes in WormBase.
 
This is a record of the current and proposed set of genomes in WormBase.
  
−
I think that this page is a correct statement of our intentions.
+
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.
  
−
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 [http://www.nature.com/nature/journal/v392/n6671/full/392071a0.html Blaxter et al 1998] ("Bclades"), as systematised by De Ley and Blaxter 2002-2004.
  
 
=== Tiers ===
 
=== Tiers ===
Line 34: Line 35:
 
{| class="wikitable" border="1"
 
{| class="wikitable" border="1"
 
|-
 
|-
 +
!  Clade
 
!  Species
 
!  Species
 
!  NCBI TaxonID
 
!  NCBI TaxonID
Line 42: Line 44:
 
!  Comments
 
!  Comments
 
|-
 
|-
 +
| V
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae'']]
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6238 6238]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6238 6238]
Line 50: Line 53:
 
| [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
 
|-
 
|-
 +
| V
 +
| Caenorhabditis species 9 strain JU1422
 +
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
 +
| V
 +
|
 +
|
 +
| WashU
 +
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
 +
|-
 +
| V
 
| [[Caenorhabditis remanei|''Caenorhabditis remanei'']]
 
| [[Caenorhabditis remanei|''Caenorhabditis remanei'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=31234 31234]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=31234 31234]
Line 58: Line 71:
 
|  
 
|  
 
|-
 
|-
 +
| V
 
| [[Caenorhabditis brenneri|''Caenorhabditis brenneri'']]<br>(Species 4)
 
| [[Caenorhabditis brenneri|''Caenorhabditis brenneri'']]<br>(Species 4)
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135651 135651]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135651 135651]
Line 66: Line 80:
 
| [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="#00D7D7"
 +
| V
 
| [[Caenorhabditis elegans|''Caenorhabditis elegans strain N2'']]
 
| [[Caenorhabditis elegans|''Caenorhabditis elegans strain N2'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
Line 74: Line 89:
 
|  
 
|  
 
|-
 
|-
 +
| V
 
| Caenorhabditis elegans strain DR1035
 
| Caenorhabditis elegans strain DR1035
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
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| status unclear
 
| status unclear
 
|-
 
|-
 +
| V
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica'']]
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=281687 281687]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=281687 281687]
Line 90: Line 107:
 
| [Jan 2011] New/improved assembly is being worked on at WashU [Oct 2011] new assembly in WS227
 
| [Jan 2011] New/improved assembly is being worked on at WashU [Oct 2011] new assembly in WS227
 
|-
 
|-
 +
| V
 
| Caenorhabditis drosophilae
 
| Caenorhabditis drosophilae
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96641 96641]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96641 96641]
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| [Sept 2010] being assembled
 
| [Sept 2010] being assembled
 
|-
 
|-
 +
| V
 
| [[Caenorhabditis angaria|''Caenorhabditis angaria'']] (species 3 strain PS1010)
 
| [[Caenorhabditis angaria|''Caenorhabditis angaria'']] (species 3 strain PS1010)
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96668 96668]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96668 96668]
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| 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'''
 
|-
 
|-
 +
| V
 
| Caenorhabditis species 7 strain JU1286
 
| Caenorhabditis species 7 strain JU1286
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870436 870436]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870436 870436]
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|  released in WS226. '''WARNING''' the genome sequence contains contaminations
 
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
 
|-
 
|-
−
| Caenorhabditis species 9 strain JU1422
 
−
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
 
 
| V
 
| V
−
|
 
−
|
 
−
| WashU
 
−
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
 
−
|-
 
 
| Caenorhabditis species 11 strain JU1373
 
| Caenorhabditis species 11 strain JU1373
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=886184 886184]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=886184 886184]
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|  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.  
 
|-
 
|-
 +
| V
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora'']]
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=37862 37862]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=37862 37862]
Line 138: Line 152:
 
|  [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
 
|-
 
|-
 +
| V
 
| [[Pristionchus pacificus|''Pristionchus pacificus'']]
 
| [[Pristionchus pacificus|''Pristionchus pacificus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=54126 54126]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=54126 54126]
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| [16 December 2010] Updated to the newest assembly and geneset in WS221  
 
| [16 December 2010] Updated to the newest assembly and geneset in WS221  
 
|-
 
|-
 +
| V
 
| [[Haemonchus contortus|''Haemonchus contortus'']]
 
| [[Haemonchus contortus|''Haemonchus contortus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6289 6289]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6289 6289]
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| Added to WormBase in release WS209.
 
| Added to WormBase in release WS209.
 
|-
 
|-
 +
| IV
 
| [[Strongyloides ratti|''Strongyloides ratti'']]
 
| [[Strongyloides ratti|''Strongyloides ratti'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34506 34506]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34506 34506]
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| [Jan 2011] draft assembly in GenBank, released in WS226
 
| [Jan 2011] draft assembly in GenBank, released in WS226
 
|-
 
|-
 +
| IV
 
| [[Meloidogyne hapla|''Meloidogyne hapla'']]
 
| [[Meloidogyne hapla|''Meloidogyne hapla'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6305 6305]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6305 6305]
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| Added to WormBase in release WS204.
 
| Added to WormBase in release WS204.
 
|-
 
|-
 +
| IV
 
| [[Meloidogyne incognita|''Meloidogyne incognita'']]
 
| [[Meloidogyne incognita|''Meloidogyne incognita'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6306 6306]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6306 6306]
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| Added to WormBase in release WS205. Genes are not yet available.
 
| Added to WormBase in release WS205. Genes are not yet available.
 
|-
 
|-
 +
| III
 
| [[Brugia malayi|''Brugia malayi'']]
 
| [[Brugia malayi|''Brugia malayi'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6279 6279]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6279 6279]
Line 186: Line 206:
 
| [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
 
|-
 
|-
−
| Onchocerca volvulus
 
−
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
 
 
| III
 
| III
−
|
 
−
|
 
−
| Sanger
 
−
|
 
−
|-
 
 
| Ascaris suum
 
| Ascaris suum
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6253 6253]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6253 6253]
Line 201: Line 214:
 
| 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
 +
|-
 +
| I
 +
| Trichinella spiralis
 +
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6334 6334]
 +
| III
 +
| [http://www.wormbase.org/db/gb2/gbrowse/t_spiralis/ Yes]
 +
| Yes
 +
| WashU
 +
| [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] added to WormBase in WS225
 +
|-
 +
| IV
 +
| Bursaphelenchus xylophilus
 +
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6326 6326]
 +
| III
 +
| Yes
 +
| Yes
 +
| Sanger
 +
| [Sept 2011] published in PLOS Pathogens  [Nov 2011] added to WormBase in WS229
 +
|-
 +
| 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.
 +
|}
 +
 +
 +
 +
 +
 +
{| class="wikitable" border="1"
 +
|-
 +
!  Clade
 +
!  Species
 +
!  NCBI TaxonID
 +
!  Tier
 +
!  Genome
 +
!  Genes
 +
!  Origin
 +
!  Comments
 +
|-
 +
| Onchocerca volvulus
 +
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
 +
| III
 +
|
 +
|
 +
| Sanger
 +
|
 
|-
 
|-
 
| Globodera pallida
 
| Globodera pallida
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| Sanger
 
| Sanger
 
|
 
|
−
|-
 
−
| Trichinella spiralis
 
−
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6334 6334]
 
−
| III
 
−
| [http://www.wormbase.org/db/gb2/gbrowse/t_spiralis/ Yes]
 
−
| Yes
 
−
| WashU
 
−
| [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] added to WormBase in WS225
 
−
|-
 
−
| ''Bursaphelenchus xylophilus''
 
−
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6326 6326]
 
−
| III
 
−
| Yes
 
−
| Yes
 
−
| Sanger
 
−
| [Sept 2011] published in PLOS Pathogens  [Nov 2011] added to WormBase in WS229
 
−
|-
 
−
| 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.
 
 
|}
 
|}
 +
 +
 +
 +
 +
 +
  
 
== Phylogeny ==
 
== Phylogeny ==

Revision as of 10:14, 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 genome status

Clade Species NCBI TaxonID 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 remanei 31234 II Yes Yes WashU
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 elegans strain DR1035 6239 III Mark Blaxter status unclear
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 drosophilae 96641 III WashU [Sept 2010] being assembled
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 Caenorhabditis species 7 strain JU1286 870436 V WashU released in WS226. WARNING the genome sequence contains contaminations
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 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 Haemonchus contortus 6289 III Yes Yes Sanger Added to WormBase in release WS209.
IV Strongyloides ratti 34506 III Yes Sanger [Jan 2011] draft assembly in GenBank, released in WS226
IV Meloidogyne hapla 6305 III Yes Yes NCSU hapla.org Added to WormBase in release WS204.
IV Meloidogyne incognita 6306 III Yes INRA Added to WormBase in release WS205. Genes are not yet available.
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
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
I Trichinella spiralis 6334 III Yes Yes WashU [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] added to WormBase in WS225
IV Bursaphelenchus xylophilus 6326 III Yes Yes Sanger [Sept 2011] published in PLOS Pathogens [Nov 2011] added to WormBase in WS229
V Steinernema carpocapsae 34508 Laboratorio Nacional de Genómica para la Biodiversidad / CalTech [May 2011] Being assembled.



Clade Species NCBI TaxonID Tier Genome Genes Origin Comments
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

Retrieved from "https://wiki.wormbase.org/index.php?title=WormBase_Genomes&oldid=13038"