Difference between revisions of "WormBase Genomes"
m (→The current genomes: comment formatting and warning highlights) |
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| Curated | | 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 | ||
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
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| External | | 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.<br>[Feb 2012] ''' | + | | |
− | + | * 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.<br> | |
+ | * [Feb 2012] <font color=red>'''WARNING'''</font> The C. species 9 assembly in WormBase WS226-WS230 has some confirmed contamination by C. species 7. Since species 9 has mostly species 9 genes and some species 7 genes, there is actually added value to having it, as long as people know of the potential problem with "apparent paralogs" that are actually sp. 7 genes. | ||
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| External | | External | ||
| WashU<br>Coverage: 150x<br>Supercontigs: 15261<br>N50: 25,228 | | WashU<br>Coverage: 150x<br>Supercontigs: 15261<br>N50: 25,228 | ||
− | | First added in WS226 | + | | |
− | + | *First added in WS226 | |
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| Curated | | 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 | |
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| External | | External | ||
| WashU<br>Coverage: 19.1x<br>Supercontigs: 665<br>N50: 20921866 | | WashU<br>Coverage: 19.1x<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. | ||
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| Curated | | Curated | ||
| WashU<br>Coverage: 9.5x<br>Supercontigs: 3305<br>N50: 368319 | | WashU<br>Coverage: 9.5x<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> | ||
+ | *<font color=red>'''Warning'''</font> WS223-WS226 genome assembly is not in sync with the annotation files or INSDC. Please use WS227+ | ||
|-bgcolor="#FFFF33" | |-bgcolor="#FFFF33" | ||
| V | | V | ||
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| Curated | | Curated | ||
| WashU/Sanger<br>Coverage: 6x | | WashU/Sanger<br>Coverage: 6x | ||
− | | First added in WS1 | + | | |
− | + | *First added in WS1 | |
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| None | | None | ||
| WashU | | WashU | ||
− | | First added in WS226.<br>'''WARNING''' the genome sequence contains contaminations. | + | | |
− | + | *First added in WS226.<br> | |
+ | *<font color=red>'''WARNING'''</font> the genome sequence contains contaminations. | ||
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| Curated | | 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 | ||
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| External | | 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''' | ||
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| Predicted | | Predicted | ||
| Sanger<br>Supercontigs: 59707<br>N50: 13338 | | Sanger<br>Supercontigs: 59707<br>N50: 13338 | ||
− | | First added in WS209. | + | | |
− | + | *First added in WS209. | |
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| None | | None | ||
| WashU<br>Coverage: 26.1x<br>Supercontigs: 1240<br>N50: 312328 | | WashU<br>Coverage: 26.1x<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. | ||
|-bgcolor="#FFFF99" | |-bgcolor="#FFFF99" | ||
| V | | V | ||
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| External | | External | ||
| WashU/MPI<br>Coverage: 8.92x<br>Supercontigs: 18083<br>N50: 1244534 | | WashU/MPI<br>Coverage: 8.92x<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 | ||
|-bgcolor="#99FF99" | |-bgcolor="#99FF99" | ||
| IV | | IV | ||
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| None | | 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. | ||
|-bgcolor="#99FF99" | |-bgcolor="#99FF99" | ||
| IV | | IV | ||
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| External | | 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 | |
|-bgcolor="#99FF99" | |-bgcolor="#99FF99" | ||
| IV | | IV | ||
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| Predicted | | 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 | ||
|-bgcolor="#99FF99" | |-bgcolor="#99FF99" | ||
| IV | | IV | ||
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| Predicted | | 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 | ||
|-bgcolor="#FF9900" | |-bgcolor="#FF9900" | ||
| III | | III | ||
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| External | | 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 | ||
|-bgcolor="#FF9900" | |-bgcolor="#FF9900" | ||
| III | | III | ||
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| External / Predicted | | 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 | ||
|-bgcolor="#33FFFF" | |-bgcolor="#33FFFF" | ||
| I | | I | ||
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| External | | 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 | ||
|} | |} | ||
Revision as of 10:23, 28 February 2012
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.
The following are some of the columns in the Genome Table.
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 (made by a gene-prediction pipeline), 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 number of Supercontigs. 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 |
|
V | Caenorhabditis species 9 strain JU1422 |
870437 | 204396809 bp | External | WashU Supercontigs: 7636 N50: 196652 |
|
V | Caenorhabditis species 5 strain DRD-2008/JU800 |
497829 | 131797386 bp | External | WashU Coverage: 150x Supercontigs: 15261 N50: 25,228 |
|
V | Caenorhabditis remanei strain PB4641 |
31234 | 145500347 bp | Curated | WashU Coverage: 9.2x Supercontigs: 3670 N50: 461060 |
|
V | Caenorhabditis species 11 strain JU1373 |
886184 | 79321433 bp | External | WashU Coverage: 19.1x Supercontigs: 665 N50: 20921866 |
|
V | Caenorhabditis brenneri strain PB2801 (species 4) |
135651 | 190421492 bp | Curated | WashU Coverage: 9.5x Supercontigs: 3305 N50: 368319 |
|
V | Caenorhabditis elegans strain Bristol N2 |
6239 | 100272276 bp | Curated | WashU/Sanger Coverage: 6x |
|
V | Caenorhabditis species 7 strain JU1286 |
870436 | None | WashU |
| |
V | Caenorhabditis japonica strain DF5080 |
281687 | 166565019 bp | Curated | WashU Coverage: 22x Supercontigs: 18817 N50: 94149 |
|
V | Caenorhabditis angaria strain PS1010 (species 3) |
96668 | 79761545 bp | External | CalTech Supercontigs: 33559 N50: 9453 |
|
V | Haemonchus contortus | 6289 | 297975349 bp | Predicted | Sanger Supercontigs: 59707 N50: 13338 |
|
V | Heterorhabditis bacteriophora strain M31e |
37862 | 76974349 bp | None | WashU Coverage: 26.1x Supercontigs: 1240 N50: 312328 |
|
V | Pristionchus pacificus strain PS312 |
54126 | 172773083 bp | External | WashU/MPI Coverage: 8.92x Supercontigs: 18083 N50: 1244534 |
|
IV | Meloidogyne incognita strain Morelos |
6306 | 82095019 bp | None | INRA Supercontigs: 9538 N50: 83000 |
|
IV | Meloidogyne hapla strain VW9 |
6305 | 53017507 bp | External | NCSU hapla.org Supercontigs: 3452 84000 |
|
IV | Strongyloides ratti natural isolate |
34506 | 52638471 bp | Predicted | Sanger Coverage: 70x Supercontigs: 2184 N50: 359029 |
|
IV | Bursaphelenchus xylophilus strain Ka4C1 |
6326 | 74561461 bp | Predicted | Sanger Coverage: 13x Supercontigs: 5527 N50: 1158000 |
|
III | Ascaris suum natural isolate |
6253 | 272782664 bp | External | Davis Coverage: 70x Supercontig: 29831 N50: 407899 |
|
III | Brugia malayi TRS |
6279 | 95814443 bp | External / Predicted | TIGR -> WashU/Sanger Supercontigs: 27210 N50: 37841 |
|
I | Trichinella spiralis strain ISS 195 |
6334 | 56779425 bp | External | WashU Supercontigs: 6863 N50: 3383625 |
|
Genomes coming soon
Clade | Species | NCBI Taxon | Genome | Gene-set | Assembly | Comments |
---|---|---|---|---|---|---|
V | Steinernema carpocapsae | 34508 | 230 Mb | None | LANGEBIO / CalTech | [May 2011] Being assembled. |
V | Caenorhabditis drosophilae | 96641 | None | WashU | [Sept 2010] being assembled | |
III | Onchocerca volvulus | 6282 | None | Sanger | ||
IV | Globodera pallida | 36090 | None | Sanger | ||
V | Nippostrongylus brasiliensis | 27835 | None | Sanger | ||
V | Strongyloides ransomi | 553534 | None | Sanger | ||
V | Teladorsagia circumcincta | 45464 | None | Sanger | ||
II | Trichuris muris | 70415 | None | Sanger | ||
V | Ancylostoma caninum | 29170 | None | Washu | ||
V | Ancylostoma ceylanicum | 53326 | None | Washu | ||
V | Ancylostoma duodenale | 51022 | None | Washu | ||
V | Cooperia oncophora | 27828 | None | Washu | ||
V | Dictyocaulus viviparus | 29172 | None | Washu | ||
V | Necator americanus | 51031 | None | Washu | ||
V | Nematodirus battus | 28839 | None | Washu | ||
V | Oesophagostomum dentatum | 61180 | None | Washu | ||
V | Ostertagia ostertagi | 6317 | None | Washu | ||
V | Teladorsagia circumcincta | 45464 | None | Washu |
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);