Difference between revisions of "WormBase Genomes"
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*[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> | *[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 | *[Dec 2010] merged Augustus gene predictions from Erich Schwarz into WS216 | ||
+ | |-bgcolor="#FF9900" | ||
+ | | 20 | ||
+ | | III | ||
+ | | [[Loa loa filariasis|''Loa loa filariasis'']] | ||
+ | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7209 7209] | ||
+ | | 86.8 Mb v1<br>87.58 Mb v2<br>91.37 Mb v3 | ||
+ | | 16,318 v1<br>14,925 v2<br>14,907 v3 | ||
+ | |[http://www.ncbi.nlm.nih.gov/genome/assembly/236638/ Genbank V1] | ||
+ | [http://www.broadinstitute.org/annotation/genome/filarial_worms/MultiDownloads.html Broad V3] | ||
+ | [http://www.ncbi.nlm.nih.gov/assembly/GCA_000183805.2/ Genbank V3] | ||
+ | | | ||
+ | *[Nov 2012] First added in WS235 | ||
|-bgcolor="#33FFFF" | |-bgcolor="#33FFFF" | ||
− | | | + | | 21 |
| I | | I | ||
| [[Trichinella spiralis|''Trichinella spiralis''<br>strain ISS 195]] | | [[Trichinella spiralis|''Trichinella spiralis''<br>strain ISS 195]] | ||
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*[Feb 2011] published in Nature.<br> | *[Feb 2011] published in Nature.<br> | ||
*[Mar 2011] First added in WS225 | *[Mar 2011] First added in WS225 | ||
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Revision as of 12:29, 13 November 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
No. | Clade | Species | NCBI Taxon | Genome | Gene-set | Assembly | Comments |
---|---|---|---|---|---|---|---|
1 | V | Caenorhabditis briggsae strain AF16 |
6238 | 108419768 bp | Curated | WashU |
|
2 | V | Caenorhabditis species 9 strain JU1422 |
870437 | 204396809 bp | External | WashU Supercontigs: 7636 N50: 196652 |
|
3 | V | Caenorhabditis species 5 strain DRD-2008/JU800 |
497829 | 131797386 bp | External | WashU Coverage: 150x Supercontigs: 15261 N50: 25,228 |
|
4 | V | Caenorhabditis remanei strain PB4641 |
31234 | 145500347 bp | Curated | WashU Coverage: 9.2x Supercontigs: 3670 N50: 461060 |
|
5 | V | Caenorhabditis species 11 strain JU1373 |
886184 | 79321433 bp | External | WashU Coverage: 19.1x Supercontigs: 665 N50: 20921866 |
|
6 | V | Caenorhabditis brenneri strain PB2801 (species 4) |
135651 | 190421492 bp | Curated | WashU Coverage: 9.5x Supercontigs: 3305 N50: 368319 |
|
7 | V | Caenorhabditis elegans strain Bristol N2 |
6239 | 100272276 bp | Curated | WashU/Sanger Coverage: 6x |
|
8 | V | Caenorhabditis species 7 strain JU1286 |
870436 | None | WashU |
| |
9 | V | Caenorhabditis japonica strain DF5080 |
281687 | 166565019 bp | Curated | WashU Coverage: 22x Supercontigs: 18817 N50: 94149 |
|
10 | V | Caenorhabditis angaria strain PS1010 (species 3) |
860376 (96668) | 79761545 bp | External | CalTech Supercontigs: 33559 N50: 9453 |
|
11 | V | Haemonchus contortus | 6289 | 297975349 bp | Predicted | Sanger Supercontigs: 59707 N50: 13338 |
|
12 | V | Heterorhabditis bacteriophora strain M31e |
37862 | 77007652 bp | External | WashU Coverage: 26.1x Supercontigs: 1263 N50: 312328 |
|
13 | V | Pristionchus pacificus strain PS312 |
54126 | 172773083 bp | External | WashU/MPI Coverage: 8.92x Supercontigs: 18083 N50: 1244534 |
|
14 | IV | Meloidogyne incognita strain Morelos |
6306 | 82095019 bp | None | INRA Supercontigs: 9538 N50: 83000 |
|
15 | IV | Meloidogyne hapla strain VW9 |
6305 | 53017507 bp | External | NCSU hapla.org Supercontigs: 3452 84000 |
|
16 | IV | Strongyloides ratti natural isolate |
34506 | 52638471 bp | Predicted | Sanger Coverage: 70x Supercontigs: 2184 N50: 359029 |
|
17 | IV | Bursaphelenchus xylophilus strain Ka4C1 |
6326 | 74561461 bp | Predicted | Sanger Coverage: 13x Supercontigs: 5527 N50: 1158000 |
|
18 | III | Ascaris suum natural isolate |
6253 | 272782664 bp | External | Davis Coverage: 70x Supercontig: 29831 N50: 407899 |
|
19 | III | Brugia malayi TRS |
6279 | 95814443 bp | External / Predicted | TIGR -> WashU/Sanger Supercontigs: 27210 N50: 37841 |
|
20 | III | Loa loa filariasis | 7209 | 86.8 Mb v1 87.58 Mb v2 91.37 Mb v3 |
16,318 v1 14,925 v2 14,907 v3 |
Genbank V1 |
|
21 | 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);