WormBase Genomes

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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 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.
[Feb 2012] Warning 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.


V Caenorhabditis species 5
strain DRD-2008/JU800
497829 131797386 bp External WashU
Coverage: 150x
Supercontigs: 15261
N50: 25,228
First added in WS226
V Caenorhabditis remanei
strain PB4641
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: 19.1x
Supercontigs: 665
N50: 20921866
First added in WS226
Replaced genes by RNAseq-based gene set in WS227.
V Caenorhabditis brenneri
strain PB2801

(species 4)
135651 190421492 bp Curated WashU
Coverage: 9.5x
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: 26.1x
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: 8.92x
Supercontigs: 18083
N50: 1244534
First added in WS194
[16 December 2010] Updated to the newest assembly and geneset in WS221
IV Meloidogyne incognita
strain Morelos
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
strain VW9
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 (Gasser)
natural isolate
6253 272782664 bp External Davis
Coverage: 70x
Supercontig: 29831
N50: 407899
First added in WS229
[Oct 2011] integrated the Gasser genome without a reference gene set.
[Nov 2011] added a reference gene set
III Ascaris suum (Davis)
natural isolate
6253 [265577339 bp] External Davis
Coverage: x
Supercontig: 31538
N50:
First added in WS236
[Jan 2013] Integrated the Davis genome assembly (Privatre submission) containing a gene set and germline somatic eliminated regions.
III Brugia malayi
TRS
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
strain ISS 195
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 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
III Loa loa 7209 None Broad May 2010 - draft released
III Onchocerca volvulus 6282 None Broad May 2010 - draft released
III Wuchereria bancrofti 6293 None Broad May 2010 - draft released
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);

Treeprint5.png

See also