Difference between revisions of "WormBase Genomes"

From WormBaseWiki
Jump to navigationJump to search
 
(103 intermediate revisions by 3 users not shown)
Line 1: Line 1:
 
== 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
 
 
I think that this page is a correct statement of our intentions.
 
 
 
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.
 
 
 
 
 
=== 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 indicates whether the genome has been added to WormBase.
 
 
 
=== Gene ===
 
 
 
The '''Genes''' column in the table indicates whether gene structures have been added to WormBase.
 
 
 
=== The genome status ===
 
 
 
{| class="wikitable" border="1"
 
|-
 
!  Species
 
!  NCBI TaxonID
 
!  Tier
 
!  Genome
 
!  Genes
 
!  Origin
 
!  Comments
 
|-
 
| [[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/ Yes]
 
| Yes
 
| WashU
 
| [Sept 2010] New assembly from Erich Haag being worked on.
 
|-
 
| [[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/ Yes]
 
| Yes
 
| WashU
 
|
 
|-
 
| [[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/ Yes]
 
| Yes
 
| WashU
 
| [Jan 2011] The current assembly contains quite a bit of heterozygosity
 
|-bgcolor="#00D7D7"
 
| [[Caenorhabditis elegans|''Caenorhabditis elegans strain 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/ Yes]
 
| Yes
 
| WashU/Sanger
 
|
 
|-
 
| Caenorhabditis elegans strain DR1035
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
 
| III
 
|
 
|
 
| Mark Blaxter
 
| status unclear
 
|-
 
| [[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/ Yes]
 
| Yes
 
| WashU
 
| [Jan 2011] New/improved assembly is being worked on at WashU
 
|-
 
| Caenorhabditis drosophilae
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96641 96641]
 
| III
 
|
 
|
 
| WashU
 
| [Sept 2010] being assembled
 
|-
 
| [[Caenorhabditis angaria|''Caenorhabditis angaria'']] (species 3 strain PS1010)
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96668 96668]
 
| III
 
| Yes
 
| Yes
 
| CalTech
 
| Added to WormBase in release WS218.<br>[Jan 2011] This species now has an official name of '''C. angaria'''
 
|-
 
| Caenorhabditis species 7 strain JU1286
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870436 870436]
 
| V
 
|
 
|
 
| WashU
 
|  released in WS226
 
|-
 
| Caenorhabditis species 9 strain JU1422
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
 
| V
 
|
 
|
 
| WashU
 
|  released in WS226
 
|-
 
| Caenorhabditis species 11 strain JU1373
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=886184 886184]
 
| V
 
|
 
|
 
| WashU
 
|  released in WS226
 
|-
 
| [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=37862 37862]
 
| V
 
|
 
|
 
| WashU
 
|
 
|-
 
| [[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/ Yes]
 
| Yes
 
| WashU/MPI
 
| [16 December 2010] Updated to the newest assembly and geneset in WS221
 
|-
 
| [[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/ Yes]
 
| Yes
 
| Sanger
 
| Added to WormBase in release WS209.
 
|-
 
| [[Strongyloides ratti|''Strongyloides ratti'']]
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34506 34506]
 
| III
 
|
 
|
 
| Sanger
 
| [Jan 2011] draft assembly in GenBank, released in WS226
 
|-
 
| [[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/ Yes]
 
| Yes
 
| NCSU hapla.org
 
| Added to WormBase in release WS204.
 
|-
 
| [[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/ Yes]
 
|
 
| INRA
 
| Added to WormBase in release WS205. Genes are not yet available.
 
|-
 
| [[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/ Yes]
 
| 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
 
|-
 
| Onchocerca volvulus
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-
 
| Ascaris suum
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6253 6253]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-
 
| Globodera pallida
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36090 36090]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-
 
| Nippostrongylus brasiliensis
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27835 27835]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-
 
| Strongyloides ransomi
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=553534 553534]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-
 
| Teladorsagia circumcincta
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-
 
| Trichuris muris
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=70415 70415]
 
| III
 
|
 
|
 
| Sanger
 
|
 
|-
 
| Trichinella spiralis
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6334 6334]
 
| III
 
|
 
|
 
| WashU
 
| [Sept 2010] Being assembled. [Feb 2011] published in Nature. [Mar 2011] will be in WS225
 
|-
 
| Steinernema carpocapsae
 
| [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
 
|
 
|
 
|
 
| Laboratorio Nacional de Genómica para la Biodiversidad / CalTech
 
| [May 2011] Being assembled.
 
|}
 
 
 
== 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]), the correct guide tree would be:
 
<pre>
 
((((((((C.elegans,(((C.briggsae, C.sp9), C.remanei),(C.sp11, C.brenneri))),(C.sp7, C.japonica)), C.angaria), (H.contortus,H.bacteriophora)), P.pacificus),((M.incognita, M.hapla), S.ratti)), B.malayi), T.spiralis);
 
</pre>
 
[[File:treeprint2.png]]
 
  
 
== See also ==
 
== See also ==

Latest revision as of 15:07, 14 January 2016