Difference between revisions of "WormBase Genomes"

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(added strain for species 5)
(Removed Tiers. Changes Genes to show the origin of the gene-set)
Line 9: Line 9:
 
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.  
 
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 ===
+
=== Gene-set ===
  
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.
+
The origin of the gene-set. One of: Curated (curated by WormBase), Predicted (predicted by WormBase), External (produced by another group), None (no gene-set available).
 
 
'''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 [http://www.ebi.ac.uk/ena/ 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 ===
 
=== Genome ===
Line 47: Line 37:
 
!  Species
 
!  Species
 
!  NCBI Taxon
 
!  NCBI Taxon
!  Tier
 
 
!  Genome
 
!  Genome
Genes
+
Gene-set
 
!  Assembly
 
!  Assembly
 
!  Comments
 
!  Comments
Line 57: Line 46:
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae''<br>strain AF16]]
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae''<br>strain AF16]]
 
| [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]
| II
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_briggsae/ 108419768 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_briggsae/ 108419768 bp]
| Yes
+
| Curated
 
| WashU  
 
| WashU  
 
| First added in WS132<br>[Sept 2010] New assembly from Erich Haag being worked on.<br>[Feb 2011] updated in WS224
 
| First added in WS132<br>[Sept 2010] New assembly from Erich Haag being worked on.<br>[Feb 2011] updated in WS224
Line 67: Line 55:
 
| ''Caenorhabditis species 9''<br>strain JU1422
 
| ''Caenorhabditis species 9''<br>strain JU1422
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
| V
 
 
| 204396809 bp
 
| 204396809 bp
|  
+
| External
 
| WashU<br>Supercontigs: 7636<br>N50: 196652
 
| WashU<br>Supercontigs: 7636<br>N50: 196652
 
| First added in WS226<br>[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.
 
| First added in WS226<br>[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.
Line 77: Line 64:
 
| ''Caenorhabditis species 5''<br>strain DRD-2008
 
| ''Caenorhabditis species 5''<br>strain DRD-2008
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=497829 497829]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=497829 497829]
| V
 
|
 
 
|  
 
|  
 +
| None
 
| WashU
 
| WashU
 
| First added in WS226
 
| First added in WS226
Line 87: Line 73:
 
| [[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]
| II
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_remanei/ 145500347 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_remanei/ 145500347 bp]
| Yes
+
| Curated
 
| WashU<br>Coverage: 9.2x<br>Supercontigs: 3670<br>N50: 461060
 
| WashU<br>Coverage: 9.2x<br>Supercontigs: 3670<br>N50: 461060
 
| First added in WS185
 
| First added in WS185
Line 97: Line 82:
 
| ''Caenorhabditis species 11''<br>strain JU1373
 
| ''Caenorhabditis species 11''<br>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]
| III
 
 
| 79321433 bp
 
| 79321433 bp
| Yes
+
| External
 
| WashU<br>Coverage: 19.1<br>Supercontigs: 665<br>N50: 20921866
 
| WashU<br>Coverage: 19.1<br>Supercontigs: 665<br>N50: 20921866
 
| First added in WS226<br>Replaced genes by RNAseq-based gene set in WS227.  
 
| First added in WS226<br>Replaced genes by RNAseq-based gene set in WS227.  
Line 107: Line 91:
 
| [[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]
| II
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_brenneri/ 190421492 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_brenneri/ 190421492 bp]
| Yes
+
| Curated
 
| WashU<br>Coverage: 9.5<br>Supercontigs: 3305<br>N50: 368319
 
| WashU<br>Coverage: 9.5<br>Supercontigs: 3305<br>N50: 368319
 
| First added in WS196<br>[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+
 
| First added in WS196<br>[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+
Line 117: Line 100:
 
| [[Caenorhabditis elegans|'''''Caenorhabditis elegans''<br>strain Bristol N2''']]
 
| [[Caenorhabditis elegans|'''''Caenorhabditis elegans''<br>strain Bristol 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]
| I
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ 100272276 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ 100272276 bp]
| Yes
+
| Curated
 
| WashU/Sanger<br>Coverage: 6x
 
| WashU/Sanger<br>Coverage: 6x
 
| First added in WS1
 
| First added in WS1
Line 127: Line 109:
 
| ''Caenorhabditis species 7''<br>strain JU1286
 
| ''Caenorhabditis species 7''<br>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]
| V
 
|
 
 
|  
 
|  
 +
| None
 
| WashU
 
| WashU
 
| First added in WS226.<br>'''WARNING''' the genome sequence contains contaminations
 
| First added in WS226.<br>'''WARNING''' the genome sequence contains contaminations
Line 137: Line 118:
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica''<br>strain DF5080]]
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica''<br>strain DF5080]]
 
| [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]
| II
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_japonica/ 166565019 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_japonica/ 166565019 bp]
| Yes
+
| Curated
 
| WashU<br>Coverage: 22x<br>Supercontigs: 18817<br>N50: 94149
 
| WashU<br>Coverage: 22x<br>Supercontigs: 18817<br>N50: 94149
 
| First added in WS195<br>[Jan 2011] New/improved assembly is being worked on at WashU.<br>[Oct 2011] new assembly in WS227
 
| First added in WS195<br>[Jan 2011] New/improved assembly is being worked on at WashU.<br>[Oct 2011] new assembly in WS227
Line 147: Line 127:
 
| [[Caenorhabditis angaria|''Caenorhabditis angaria''<br>strain PS1010]]<br>(species 3)
 
| [[Caenorhabditis angaria|''Caenorhabditis angaria''<br>strain PS1010]]<br>(species 3)
 
| [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]
| III
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_angaria/ 79761545 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_angaria/ 79761545 bp]
| Yes
+
| External
 
| CalTech<br>Supercontigs: 33559<br>N50: 9453
 
| CalTech<br>Supercontigs: 33559<br>N50: 9453
 
| First added in WS218<br>[Jan 2011] This species now has an official name of '''C. angaria'''
 
| First added in WS218<br>[Jan 2011] This species now has an official name of '''C. angaria'''
Line 157: Line 136:
 
| [[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]
| III
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/h_contortus/ 297975349 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/h_contortus/ 297975349 bp]
| Yes
+
| Predicted
 
| Sanger<br>Supercontigs: 59707<br>N50: 13338
 
| Sanger<br>Supercontigs: 59707<br>N50: 13338
 
| First added in WS209.
 
| First added in WS209.
Line 167: Line 145:
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora''<br>strain M31e]]
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora''<br>strain M31e]]
 
| [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]
| V
 
 
| 76974349 bp
 
| 76974349 bp
|  
+
| None
 
| WashU<br>Coverage: 26.1<br>Supercontigs: 1240<br>N50: 312328
 
| WashU<br>Coverage: 26.1<br>Supercontigs: 1240<br>N50: 312328
 
| First added in WS229<br>[Jan 2011] Submitted to GenBank - Accession: EF043402<br>[Sep 2011] Gene set and Annotations are being worked on.
 
| First added in WS229<br>[Jan 2011] Submitted to GenBank - Accession: EF043402<br>[Sep 2011] Gene set and Annotations are being worked on.
Line 177: Line 154:
 
| [[Pristionchus pacificus|''Pristionchus pacificus''<br>strain PS312]]
 
| [[Pristionchus pacificus|''Pristionchus pacificus''<br>strain PS312]]
 
| [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]
| II
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/p_pacificus/ 172773083 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/p_pacificus/ 172773083 bp]
| Yes
+
| External
 
| WashU/MPI<br>Coverage: 8.92<br>Supercontigs: 18083<br>N50: 1244534
 
| WashU/MPI<br>Coverage: 8.92<br>Supercontigs: 18083<br>N50: 1244534
 
| First added in WS194<br>[16 December 2010] Updated to the newest assembly and geneset in WS221  
 
| First added in WS194<br>[16 December 2010] Updated to the newest assembly and geneset in WS221  
Line 187: Line 163:
 
| ''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]
| III
 
 
| 230 Mb
 
| 230 Mb
|  
+
| None
 
| [http://www.langebio.cinvestav.mx/ LANGEBIO] / CalTech
 
| [http://www.langebio.cinvestav.mx/ LANGEBIO] / CalTech
 
| [May 2011] Being assembled.
 
| [May 2011] Being assembled.
Line 197: Line 172:
 
| [[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]
| III
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/m_incognita/ 82095019 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/m_incognita/ 82095019 bp]
|  
+
| None
 
| [http://www.inra.fr/meloidogyne_incognita/genomic_resources INRA]<br>Supercontigs: 9538<br>N50: 83000
 
| [http://www.inra.fr/meloidogyne_incognita/genomic_resources INRA]<br>Supercontigs: 9538<br>N50: 83000
 
| First added in WS205<br>Genes are not yet available. The official M.incognita genes are only available at [http://www.inra.fr/meloidogyne_incognita/genomic_resources INRA] and their structure hasn't been made public.
 
| First added in WS205<br>Genes are not yet available. The official M.incognita genes are only available at [http://www.inra.fr/meloidogyne_incognita/genomic_resources INRA] and their structure hasn't been made public.
Line 207: Line 181:
 
| [[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]
| III
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/m_hapla/ 53017507 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/m_hapla/ 53017507 bp]
| Yes
+
| External
 
| NCSU hapla.org<br>Supercontigs: 3452<br>84000
 
| NCSU hapla.org<br>Supercontigs: 3452<br>84000
 
| First added in WS204
 
| First added in WS204
Line 217: Line 190:
 
| [[Strongyloides ratti|''Strongyloides ratti''<br>natural isolate]]
 
| [[Strongyloides ratti|''Strongyloides ratti''<br>natural isolate]]
 
| [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]
| III
 
 
| 52638471 bp
 
| 52638471 bp
|  
+
| Predicted
 
| Sanger<br>Coverage: 70x<br>Supercontigs: 2184<br>N50: 359029
 
| Sanger<br>Coverage: 70x<br>Supercontigs: 2184<br>N50: 359029
 
| [Jan 2011] draft assembly in GenBank<br>First added in WS226
 
| [Jan 2011] draft assembly in GenBank<br>First added in WS226
Line 227: Line 199:
 
| ''Bursaphelenchus xylophilus''<br>strain Ka4C1
 
| ''Bursaphelenchus xylophilus''<br>strain Ka4C1
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6326 6326]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6326 6326]
| III
 
 
| 74561461 bp
 
| 74561461 bp
| Yes
+
| Predicted
 
| Sanger<br>Coverage: 13x<br>Supercontigs: 5527<br>N50: 1158000
 
| Sanger<br>Coverage: 13x<br>Supercontigs: 5527<br>N50: 1158000
 
| [Sept 2011] published in PLOS Pathogens<br>[Nov 2011] First added in WS229
 
| [Sept 2011] published in PLOS Pathogens<br>[Nov 2011] First added in WS229
Line 237: Line 208:
 
| ''Ascaris suum''<br>natural isolate
 
| ''Ascaris suum''<br>natural isolate
 
| [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]
| III
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/a_suum/ 272782664 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/a_suum/ 272782664 bp]
| Yes
+
| External
 
| Davis<br>Coverage: 70x<br>Supercontig: 29831<br>N50: 407899
 
| Davis<br>Coverage: 70x<br>Supercontig: 29831<br>N50: 407899
 
| First added in WS229<br>[Oct 2011] integrated the Davis genome without a reference gene set.<br>[Nov 2011] added a reference gene set
 
| First added in WS229<br>[Oct 2011] integrated the Davis genome without a reference gene set.<br>[Nov 2011] added a reference gene set
Line 247: Line 217:
 
| [[Brugia malayi|''Brugia malayi''<br>natural isolate]]
 
| [[Brugia malayi|''Brugia malayi''<br>natural isolate]]
 
| [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]
| III
 
 
| [http://www.wormbase.org/db/gb2/gbrowse/b_malayi/ 95814443 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/b_malayi/ 95814443 bp]
| Yes
+
| External / Predicted
 
| TIGR -> WashU/Sanger<br>Supercontigs: 27210<br>N50: 37841
 
| TIGR -> WashU/Sanger<br>Supercontigs: 27210<br>N50: 37841
 
| First added in WS185<br>[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
 
| First added in WS185<br>[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
Line 257: Line 226:
 
| ''Trichinella spiralis''
 
| ''Trichinella spiralis''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6334 6334]
 
| [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/ 56779425 bp]
 
| [http://www.wormbase.org/db/gb2/gbrowse/t_spiralis/ 56779425 bp]
| Yes
+
| External
 
| WashU<br>Supercontigs: 6863<br>N50: 3383625
 
| WashU<br>Supercontigs: 6863<br>N50: 3383625
 
| [Sept 2010] Being assembled.<br>[Feb 2011] published in Nature.<br>[Mar 2011] First added in WS225
 
| [Sept 2010] Being assembled.<br>[Feb 2011] published in Nature.<br>[Mar 2011] First added in WS225
Line 271: Line 239:
 
!  Species
 
!  Species
 
!  NCBI Taxon
 
!  NCBI Taxon
!  Tier
 
 
!  Genome
 
!  Genome
Genes
+
Gene-set
 
!  Assembly
 
!  Assembly
 
!  Comments
 
!  Comments
Line 281: Line 248:
 
| ''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]
| III
 
|
 
 
|  
 
|  
 +
| None
 
| WashU
 
| WashU
 
| [Sept 2010] being assembled
 
| [Sept 2010] being assembled
Line 291: Line 257:
 
| ''Caenorhabditis elegans''<br>strain DR1035
 
| ''Caenorhabditis elegans''<br>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]
| III
 
 
| 100 Mb
 
| 100 Mb
|  
+
| None
 
| Mark Blaxter
 
| Mark Blaxter
 
| status unclear
 
| status unclear
Line 301: Line 266:
 
| ''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]
| III
 
|
 
 
|  
 
|  
 +
| None
 
| Sanger
 
| Sanger
 
|
 
|
Line 311: Line 275:
 
| ''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]
| III
 
|
 
 
|  
 
|  
 +
| None
 
| Sanger
 
| Sanger
 
|
 
|
Line 321: Line 284:
 
| ''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]
| III
 
|
 
 
|  
 
|  
 +
| None
 
| Sanger
 
| Sanger
 
|
 
|
Line 331: Line 293:
 
| ''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]
| III
 
|
 
 
|  
 
|  
 +
| None
 
| Sanger
 
| Sanger
 
|  
 
|  
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| ''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]
| III
 
|
 
 
|  
 
|  
 +
| None
 
| Sanger
 
| Sanger
 
|
 
|
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| ''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]
| III
 
|
 
 
|  
 
|  
 +
| None
 
| Sanger
 
| Sanger
 
|
 
|

Revision as of 15:01, 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.

Gene-set

The origin of the gene-set. One of: Curated (curated by WormBase), Predicted (predicted by WormBase), External (produced by another group), None (no gene-set available).

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 Genome Gene-set Assembly Comments
V Caenorhabditis briggsae
strain AF16
6238 108419768 bp Curated 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 204396809 bp External 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 None WashU First added in WS226
V Caenorhabditis remanei 31234 145500347 bp Curated WashU
Coverage: 9.2x
Supercontigs: 3670
N50: 461060
First added in WS185
V Caenorhabditis species 11
strain JU1373
886184 79321433 bp External 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 190421492 bp Curated 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 100272276 bp Curated WashU/Sanger
Coverage: 6x
First added in WS1
V Caenorhabditis species 7
strain JU1286
870436 None WashU First added in WS226.
WARNING the genome sequence contains contaminations
V Caenorhabditis japonica
strain DF5080
281687 166565019 bp Curated 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 79761545 bp External 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 297975349 bp Predicted Sanger
Supercontigs: 59707
N50: 13338
First added in WS209.
V Heterorhabditis bacteriophora
strain M31e
37862 76974349 bp None 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 172773083 bp External 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 230 Mb None LANGEBIO / CalTech [May 2011] Being assembled.
IV Meloidogyne incognita 6306 82095019 bp None 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 53017507 bp External NCSU hapla.org
Supercontigs: 3452
84000
First added in WS204
IV Strongyloides ratti
natural isolate
34506 52638471 bp Predicted Sanger
Coverage: 70x
Supercontigs: 2184
N50: 359029
[Jan 2011] draft assembly in GenBank
First added in WS226
IV Bursaphelenchus xylophilus
strain Ka4C1
6326 74561461 bp Predicted 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 272782664 bp External 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 95814443 bp External / Predicted 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 56779425 bp External 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 Genome Gene-set Assembly Comments
V Caenorhabditis drosophilae 96641 None WashU [Sept 2010] being assembled
V Caenorhabditis elegans
strain DR1035
6239 100 Mb None Mark Blaxter status unclear
Onchocerca volvulus 6282 None Sanger
Globodera pallida 36090 None Sanger
Nippostrongylus brasiliensis 27835 None Sanger
Strongyloides ransomi 553534 None Sanger
Teladorsagia circumcincta 45464 None Sanger
Trichuris muris 70415 None 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