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.
 
 
 
=== 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.
 
 
 
=== Tiers ===
 
 
 
The different genomes in WormBase are classified in various tiers which depend on the amount of curation effort we are able to put into maintaining them.
 
 
 
'''Tier I''' - All efforts are made to curate the gene structures and any other genetic or metabolic information. Only '''C. elegans''' is in this group.
 
 
 
'''Tier II''' - Efforts are made, where practical, to manually curate the gene structure and possibly some other genomic information. WormBase 'owns' the assembly in the [http://www.ebi.ac.uk/ena/ ENA] and GenBank so that new gene annotations can be submitted to the ENA/GenBank by WormBase.
 
 
 
'''Tier III''' - We will set up the genome on WormBase with any gene structures that the authors of this genome have predicted. No further curation efforts are made by the WormBase consortium.
 
 
 
'''Tier IV''' - Proposed tier for organisms with only transcriptome information and no coherent genome. There are no examples of this in WormBase at present.
 
 
 
'''Tier V''' - Proposed tier for organisms with only genome information and no coherent transcriptome. There are no examples of this in WormBase at present.
 
 
 
=== 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.
 
 
 
=== The current genomes ===
 
 
 
{| class="wikitable" border="1"
 
|-
 
!  Clade
 
!  Species
 
!  NCBI Taxon
 
!  Tier
 
!  Genome
 
!  Genes
 
!  Origin
 
!  Comments
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis briggsae|''Caenorhabditis briggsae'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6238 6238]
 
| II
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_briggsae/ 108419768 bp]
 
| Yes
 
| WashU
 
| [Sept 2010] New assembly from Erich Haag being worked on. [Feb 2011] updated in WS224
 
|-bgcolor="#FFFF99"
 
| V
 
| ''Caenorhabditis species 9''<br>strain JU1422
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
 
| V
 
| 204396809 bp
 
|
 
| WashU
 
|  released in WS226. '''WARNING''' the genome sequence contains contaminations
 
|-bgcolor="#FFFF99"
 
| V
 
| ''Caenorhabditis species 5''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=? ?]
 
| V
 
|
 
|
 
| WashU
 
|  released in WS226.
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis remanei|''Caenorhabditis remanei'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=31234 31234]
 
| II
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_remanei/ 145500347 bp]
 
| Yes
 
| WashU
 
|
 
|-bgcolor="#FFFF99"
 
| V
 
| ''Caenorhabditis species 11''<br>strain JU1373
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=886184 886184]
 
| III
 
| 79321433 bp
 
| Yes
 
| WashU
 
|  genome and deNovo gene set released in WS226.<br>Replaced by RNAseq based gene set in WS227.
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis brenneri|''Caenorhabditis brenneri'']]<br>species 4
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135651 135651]
 
| II
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_brenneri/ 190421492 bp]
 
| Yes
 
| WashU
 
| [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]
 
| I
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ 100272276 bp]
 
| Yes
 
| WashU/Sanger
 
|
 
|-bgcolor="#FFFF99"
 
| V
 
| ''Caenorhabditis species 7''<br>strain JU1286
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870436 870436]
 
| V
 
|
 
|
 
| WashU
 
|  released in WS226.<br>'''WARNING''' the genome sequence contains contaminations
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Caenorhabditis japonica|''Caenorhabditis japonica'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=281687 281687]
 
| II
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_japonica/ 166565019 bp]
 
| Yes
 
| WashU
 
| [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>species 3 strain PS1010
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96668 96668]
 
| III
 
| [http://www.wormbase.org/db/gb2/gbrowse/c_angaria/ 79761545 bp]
 
| Yes
 
| CalTech
 
| Added to WormBase in release 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]
 
| III
 
| [http://www.wormbase.org/db/gb2/gbrowse/h_contortus/ 297975349 bp]
 
| Yes
 
| Sanger
 
| Added to WormBase in release WS209.
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=37862 37862]
 
| V
 
| 76974349 bp
 
|
 
| WashU
 
|  [Jan 2011] Submitted to GenBank - Accession: EF043402<br>[Sep 2011] Gene set and Annotations are being worked on.<br>[Nov 2011] on WormBase as of WS229
 
|-bgcolor="#FFFF99"
 
| V
 
| [[Pristionchus pacificus|''Pristionchus pacificus'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=54126 54126]
 
| II
 
| [http://www.wormbase.org/db/gb2/gbrowse/p_pacificus/ 172773083 bp]
 
| Yes
 
| WashU/MPI
 
| [16 December 2010] Updated to the newest assembly and geneset in WS221
 
|-bgcolor="#FFFF99"
 
| V
 
| ''Steinernema carpocapsae''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
 
| III
 
| 230 Mb
 
|
 
| [http://www.langebio.cinvestav.mx/ LANGEBIO] / CalTech
 
| [May 2011] Being assembled.
 
|-bgcolor="#99FF99"
 
| IV
 
| [[Meloidogyne incognita|''Meloidogyne incognita'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6306 6306]
 
| III
 
| [http://www.wormbase.org/db/gb2/gbrowse/m_incognita/ 82095019 bp]
 
|
 
| INRA
 
| Added to WormBase in release WS205.<br>Genes are not yet available.
 
|-bgcolor="#99FF99"
 
| IV
 
| [[Meloidogyne hapla|''Meloidogyne hapla'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6305 6305]
 
| III
 
| [http://www.wormbase.org/db/gb2/gbrowse/m_hapla/ 53017507 bp]
 
| Yes
 
| NCSU hapla.org
 
| Added to WormBase in release WS204.
 
|-bgcolor="#99FF99"
 
| IV
 
| [[Strongyloides ratti|''Strongyloides ratti'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34506 34506]
 
| III
 
| 52638471 bp
 
|
 
| Sanger
 
| [Jan 2011] draft assembly in GenBank, released in WS226
 
|-bgcolor="#99FF99"
 
| IV
 
| ''Bursaphelenchus xylophilus''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6326 6326]
 
| III
 
| 74561461 bp
 
| Yes
 
| Sanger
 
| [Sept 2011] published in PLOS Pathogens<br>[Nov 2011] added to WormBase in WS229
 
|-bgcolor="#FF9900"
 
| III
 
| ''Ascaris suum''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6253 6253]
 
| III
 
| [http://www.wormbase.org/db/gb2/gbrowse/a_suum/ 272782664 bp]
 
| Yes
 
| Davis
 
| [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'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6279 6279]
 
| III
 
| [http://www.wormbase.org/db/gb2/gbrowse/b_malayi/ 95814443 bp]
 
| Yes
 
| TIGR -> WashU/Sanger
 
| [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''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6334 6334]
 
| III
 
| [http://www.wormbase.org/db/gb2/gbrowse/t_spiralis/ 56779425 bp]
 
| Yes
 
| WashU
 
| [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] added to WormBase in WS225
 
|}
 
 
 
 
 
 
 
=== Genomes coming soon ===
 
 
 
{| class="wikitable" border="1"
 
|-
 
!  Clade
 
!  Species
 
!  NCBI Taxon
 
!  Tier
 
!  Genome
 
!  Genes
 
!  Origin
 
!  Comments
 
|-bgcolor="#CC9999"
 
| V
 
| ''Caenorhabditis drosophilae''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96641 96641]
 
| III
 
|
 
|
 
| WashU
 
| [Sept 2010] being assembled
 
|-bgcolor="#CC9999"
 
| V
 
| ''Caenorhabditis elegans''<br>strain DR1035
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
 
| III
 
| 100 Mb
 
|
 
| Mark Blaxter
 
| status unclear
 
|-bgcolor="#CC9999"
 
|
 
| ''Onchocerca volvulus''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-bgcolor="#CC9999"
 
|
 
| ''Globodera pallida''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36090 36090]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-bgcolor="#CC9999"
 
|
 
| ''Nippostrongylus brasiliensis''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27835 27835]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-bgcolor="#CC9999"
 
|
 
| ''Strongyloides ransomi''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=553534 553534]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-bgcolor="#CC9999"
 
|
 
| ''Teladorsagia circumcincta''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-bgcolor="#CC9999"
 
|
 
| ''Trichuris muris''
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=70415 70415]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|}
 
 
 
 
 
 
 
 
 
 
 
 
 
 
 
== 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