Difference between revisions of "WormBase Genomes"
(added strain for species 5) |
(Removed Tiers. Changes Genes to show the origin of the gene-set) |
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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. | ||
− | === | + | === Gene-set === |
− | The | + | 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). |
− | |||
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− | |||
− | |||
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=== Genome === | === Genome === | ||
Line 47: | Line 37: | ||
! Species | ! Species | ||
! NCBI Taxon | ! NCBI Taxon | ||
− | |||
! Genome | ! Genome | ||
− | ! | + | ! 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/c_briggsae/ 108419768 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/c_briggsae/ 108419768 bp] | ||
− | | | + | | 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] | ||
− | |||
| 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] | ||
− | |||
− | |||
| | | | ||
+ | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/c_remanei/ 145500347 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/c_remanei/ 145500347 bp] | ||
− | | | + | | 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] | ||
− | |||
| 79321433 bp | | 79321433 bp | ||
− | | | + | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/c_brenneri/ 190421492 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/c_brenneri/ 190421492 bp] | ||
− | | | + | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ 100272276 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ 100272276 bp] | ||
− | | | + | | 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] | ||
− | |||
− | |||
| | | | ||
+ | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/c_japonica/ 166565019 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/c_japonica/ 166565019 bp] | ||
− | | | + | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/c_angaria/ 79761545 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/c_angaria/ 79761545 bp] | ||
− | | | + | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/h_contortus/ 297975349 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/h_contortus/ 297975349 bp] | ||
− | | | + | | 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] | ||
− | |||
| 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/p_pacificus/ 172773083 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/p_pacificus/ 172773083 bp] | ||
− | | | + | | 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] | ||
− | |||
| 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] | ||
− | |||
| [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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/m_hapla/ 53017507 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/m_hapla/ 53017507 bp] | ||
− | | | + | | 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] | ||
− | |||
| 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] | ||
− | |||
| 74561461 bp | | 74561461 bp | ||
− | | | + | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/a_suum/ 272782664 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/a_suum/ 272782664 bp] | ||
− | | | + | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/b_malayi/ 95814443 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/b_malayi/ 95814443 bp] | ||
− | | | + | | 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] | ||
− | |||
| [http://www.wormbase.org/db/gb2/gbrowse/t_spiralis/ 56779425 bp] | | [http://www.wormbase.org/db/gb2/gbrowse/t_spiralis/ 56779425 bp] | ||
− | | | + | | 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 | ||
− | |||
! Genome | ! Genome | ||
− | ! | + | ! 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] | ||
− | |||
− | |||
| | | | ||
+ | | 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] | ||
− | |||
| 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] | ||
− | |||
− | |||
| | | | ||
+ | | 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] | ||
− | |||
− | |||
| | | | ||
+ | | 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] | ||
− | |||
− | |||
| | | | ||
+ | | 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] | ||
− | |||
− | |||
| | | | ||
+ | | None | ||
| Sanger | | Sanger | ||
| | | | ||
Line 341: | Line 302: | ||
| ''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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Revision as of 15:01, 15 December 2011
Contents
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);