Difference between revisions of "WormBase Genomes"

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== WormBase Genomes ==
 
== WormBase Genomes ==
  
This is a record of the current and proposed set of genomes in WormBase.
+
An up to date list of genomes in WormBase can be found at: http://www.wormbase.org/species/all
 
 
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 [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 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 ===
 
 
 
{| class="wikitable" border="1"
 
|-
 
!  Clade
 
!  Species
 
!  NCBI Taxon
 
!  Genome
 
!  Gene-set
 
!  Assembly
 
!  Comments
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae''<br>strain AF16]]
 
| [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]
 
| Curated
 
| WashU
 
| First added in WS132<br>[Sept 2010] New assembly from Erich Haag being worked on.<br>[Feb 2011] updated in WS224
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis species 9|''Caenorhabditis species 9''<br>strain JU1422]]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
 
| 204396809 bp
 
| External
 
| 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] '''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.
 
 
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis species 5|''Caenorhabditis species 5''<br>strain DRD-2008/JU800]]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=497829 497829]
 
| 131797386 bp
 
| External
 
| WashU<br>Coverage: 150x<br>Supercontigs: 15261<br>N50: 25,228
 
| First added in WS226
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis remanei|''Caenorhabditis remanei''<br>strain PB4641]]
 
| [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]
 
| Curated
 
| WashU<br>Coverage: 9.2x<br>Supercontigs: 3670<br>N50: 461060
 
| First added in WS185
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis species 11|''Caenorhabditis species 11''<br>strain JU1373]]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=886184 886184]
 
| 79321433 bp
 
| External
 
| 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.
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis brenneri|''Caenorhabditis brenneri''<br>strain PB2801]]<br>(species 4)
 
| [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]
 
| Curated
 
| 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+
 
 
 
|-bgcolor="#FFFF33"
 
| V
 
| [[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.wormbase.org/db/gb2/gbrowse/c_elegans/ 100272276 bp]
 
| Curated
 
| WashU/Sanger<br>Coverage: 6x
 
| First added in WS1
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis species 7|''Caenorhabditis species 7''<br>strain JU1286]]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870436 870436]
 
|
 
| None
 
| WashU
 
| First added in WS226.<br>'''WARNING''' the genome sequence contains contaminations.
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica''<br>strain DF5080]]
 
| [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]
 
| Curated
 
| 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
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[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.wormbase.org/db/gb2/gbrowse/c_angaria/ 79761545 bp]
 
| External
 
| CalTech<br>Supercontigs: 33559<br>N50: 9453
 
| First added in WS218<br>[Jan 2011] This species now has an official name of '''C. angaria'''
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Haemonchus contortus|''Haemonchus contortus'']]
 
| [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]
 
| Predicted
 
| Sanger<br>Supercontigs: 59707<br>N50: 13338
 
| First added in WS209.
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora''<br>strain M31e]]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=37862 37862]
 
| 76974349 bp
 
| None
 
| 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.
 
 
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Pristionchus pacificus|''Pristionchus pacificus''<br>strain PS312]]
 
| [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]
 
| External
 
| 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
 
 
 
|-bgcolor="#99FF99"
 
| IV
 
| [[Meloidogyne incognita|''Meloidogyne incognita''<br>strain Morelos]]
 
| [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]
 
| None
 
| [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.
 
 
 
|-bgcolor="#99FF99"
 
| IV
 
| [[Meloidogyne hapla|''Meloidogyne hapla''<br>strain VW9]]
 
| [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]
 
| External
 
| NCSU hapla.org<br>Supercontigs: 3452<br>84000
 
| First added in WS204
 
 
 
|-bgcolor="#99FF99"
 
| IV
 
| [[Strongyloides ratti|''Strongyloides ratti''<br>natural isolate]]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34506 34506]
 
| 52638471 bp
 
| Predicted
 
| Sanger<br>Coverage: 70x<br>Supercontigs: 2184<br>N50: 359029
 
| [Jan 2011] draft assembly in GenBank<br>First added in WS226
 
 
 
|-bgcolor="#99FF99"
 
| IV
 
| [[Bursaphelenchus xylophilus|''Bursaphelenchus xylophilus''<br>strain Ka4C1]]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6326 6326]
 
| 74561461 bp
 
| Predicted
 
| Sanger<br>Coverage: 13x<br>Supercontigs: 5527<br>N50: 1158000
 
| [Sept 2011] published in PLOS Pathogens<br>[Nov 2011] First added in WS229
 
 
 
|-bgcolor="#FF9900"
 
| III
 
| [[Ascaris suum|''Ascaris suum''<br>natural isolate]]
 
| [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]
 
| External
 
| 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
 
 
 
|-bgcolor="#FF9900"
 
| III
 
| [[Brugia malayi|''Brugia malayi''<br>TRS]]
 
| [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]
 
| External / Predicted
 
| 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
 
 
 
|-bgcolor="#33FFFF"
 
| I
 
| [[Trichinella spiralis|''Trichinella spiralis''<br>strain ISS 195]]
 
| [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]
 
| External
 
| WashU<br>Supercontigs: 6863<br>N50: 3383625
 
| [Sept 2010] Being assembled.<br>[Feb 2011] published in Nature.<br>[Mar 2011] First added in WS225
 
|}
 
 
 
=== Genomes coming soon ===
 
 
 
{| class="wikitable" border="1"
 
|-
 
!  Clade
 
!  Species
 
!  NCBI Taxon
 
!  Genome
 
!  Gene-set
 
!  Assembly
 
!  Comments
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Steinernema carpocapsae|''Steinernema carpocapsae'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
 
| 230 Mb
 
| None
 
| [http://www.langebio.cinvestav.mx/ LANGEBIO] / CalTech
 
| [May 2011] Being assembled.
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Caenorhabditis drosophilae|''Caenorhabditis drosophilae'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96641 96641]
 
|
 
| None
 
| WashU
 
| [Sept 2010] being assembled
 
 
 
|-bgcolor="#CC9999"
 
| III
 
| [[Onchocerca volvulus|''Onchocerca volvulus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
 
|
 
| None
 
| Sanger
 
|
 
 
 
|-bgcolor="#CC9999"
 
| IV
 
| [[Globodera pallida|''Globodera pallida'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36090 36090]
 
|
 
| None
 
| Sanger
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Nippostrongylus brasiliensis|''Nippostrongylus brasiliensis'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27835 27835]
 
|
 
| None
 
| Sanger
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Strongyloides ransomi|''Strongyloides ransomi'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=553534 553534]
 
|
 
| None
 
| Sanger
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Teladorsagia circumcincta|''Teladorsagia circumcincta'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
 
|
 
| None
 
| Sanger
 
|
 
 
 
|-bgcolor="#CC9999"
 
| II
 
| [[Trichuris muris|''Trichuris muris'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=70415 70415]
 
|
 
| None
 
| Sanger
 
|
 
 
 
|-bgcolor="#CC9999"
 
| III
 
| [[Loa loa|''Loa loa'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=7209 7209]
 
|
 
| None
 
| [http://www.broadinstitute.org/annotation/genome/filarial_worms/GenomesIndex.html Broad]
 
| May 2010 - draft released
 
 
 
|-bgcolor="#CC9999"
 
| III
 
| [[Onchocerca volvulus|''Onchocerca volvulus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
 
|
 
| None
 
| [http://www.broadinstitute.org/annotation/genome/filarial_worms/GenomesIndex.html Broad]
 
| May 2010 - draft released
 
 
 
|-bgcolor="#CC9999"
 
| III
 
| [[Wuchereria bancrofti|''Wuchereria bancrofti'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6293 6293]
 
|
 
| None
 
| [http://www.broadinstitute.org/annotation/genome/filarial_worms/GenomesIndex.html Broad]
 
| May 2010 - draft released
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Ancylostoma caninum|''Ancylostoma caninum'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=29170 29170]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/ancylostoma_caninum Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Ancylostoma ceylanicum|''Ancylostoma ceylanicum'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=53326 53326]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/ancylostoma_ceylanicum Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Ancylostoma duodenale|''Ancylostoma duodenale'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=51022 51022]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/ancylostoma_duodenale Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Cooperia oncophora|''Cooperia oncophora'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27828 27828]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/cooperia_oncophora Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Dictyocaulus viviparus|''Dictyocaulus viviparus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=29172 29172]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/dictyocaulus_viviparus Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Necator americanus|''Necator americanus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=51031 51031]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/necator_americanus Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Nematodirus battus|''Nematodirus battus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=28839 28839]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/nematodirus_battus Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Oesophagostomum dentatum|''Oesophagostomum dentatum'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=61180 61180]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/oesophagostomum_dentatum Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
| V
 
| [[Ostertagia ostertagi|''Ostertagia ostertagi'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6317 6317]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/ostertagia_ostertagi Washu]
 
|
 
 
 
|-bgcolor="#CC9999"
 
|
 
| [[Teladorsagia circumcincta|''Teladorsagia circumcincta'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
 
|
 
| None
 
| [http://genome.wustl.edu/genomes/view/teladorsagia_circumcincta Washu]
 
|
 
|}
 
 
 
== Phylogeny ==
 
 
 
Given my understanding of the current phylogenetic literature (and based on personal communications with [http://www.wormbase.org/db/misc/person?name=WBPerson2076;class=Person Karin Kiontke],[http://www.wormbase.org/db/misc/person?name=WBPerson178;class=Person David Fitch] and [http://www.wormbase.org/db/misc/person?name=WBPerson69;class=Person Mark Blaxter]), the correct guide tree would be:
 
<pre>
 
((((((((((((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);
 
</pre>
 
[[File:Treeprint5.png]]
 
  
 
== See also ==
 
== See also ==

Latest revision as of 15:07, 14 January 2016