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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.
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− | | |
− | '''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.
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− | | |
− | '''Tier III''' - No curation by WormBase. We will set up the genome on WormBase with any gene structures that the authors of this genome have predicted.
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− | | |
− | '''Tier IV''' - No curation by WormBase. Only transcriptome information provided by the authors and no coherent genome.
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− | | |
− | '''Tier V''' - No curation by WormBase. Only genome information provided by the authors and no coherent transcriptome.
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− | | |
− | === Genome ===
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− | | |
− | 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.
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− | | |
− | === Gene ===
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− | | |
− | The '''Genes''' column in the table indicates whether gene structures have been added to WormBase.
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− | | |
− | === Assembly ===
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− | | |
− | Which lab did the assembly.
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− | The sequence coverage.
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− | The Supercontig N50.
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− | And anything else that we know about it.
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− | | |
− | | |
− | | |
− | === The current genomes ===
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− | | |
− | {| class="wikitable" border="1"
| |
− | |-
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− | ! Clade
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− | ! Species
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− | ! NCBI Taxon
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− | ! Tier
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− | ! Genome
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− | ! Genes
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− | ! Assembly
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− | ! Comments
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− | | |
− | |-bgcolor="#FFFF99"
| |
− | | V
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− | | [[Caenorhabditis briggsae|''Caenorhabditis briggsae''<br>strain AF16]]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6238 6238]
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− | | II
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− | | [http://www.wormbase.org/db/gb2/gbrowse/c_briggsae/ 108419768 bp]
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− | | Yes
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− | | WashU
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− | | First added in WS132<br>[Sept 2010] New assembly from Erich Haag being worked on.<br>[Feb 2011] updated in WS224
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | ''Caenorhabditis species 9''<br>strain JU1422
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870437 870437]
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− | | V
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− | | 204396809 bp
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− | |
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− | | WashU<br>Supercontigs: 7636<br>N50: 196652
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− | | 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.
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | ''Caenorhabditis species 5''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=497829 497829]
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− | | V
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− | |
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− | |
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− | | WashU
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− | | First added in WS226
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | [[Caenorhabditis remanei|''Caenorhabditis remanei'']]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=31234 31234]
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− | | II
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− | | [http://www.wormbase.org/db/gb2/gbrowse/c_remanei/ 145500347 bp]
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− | | Yes
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− | | WashU<br>Coverage: 9.2x<br>Supercontigs: 3670<br>N50: 461060
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− | | First added in WS185
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | ''Caenorhabditis species 11''<br>strain JU1373
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=886184 886184]
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− | | III
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− | | 79321433 bp
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− | | Yes
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− | | WashU<br>Coverage: 19.1<br>Supercontigs: 665<br>N50: 20921866
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− | | First added in WS226<br>Replaced genes by RNAseq-based gene set in WS227.
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | [[Caenorhabditis brenneri|''Caenorhabditis brenneri'']]<br>(species 4)
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=135651 135651]
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− | | II
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− | | [http://www.wormbase.org/db/gb2/gbrowse/c_brenneri/ 190421492 bp]
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− | | Yes
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− | | WashU<br>Coverage: 9.5<br>Supercontigs: 3305<br>N50: 368319
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− | | 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+
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− | | |
− | |-bgcolor="#FFFF33"
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− | | V
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− | | [[Caenorhabditis elegans|'''''Caenorhabditis elegans''<br>strain Bristol N2''']]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
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− | | I
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− | | [http://www.wormbase.org/db/gb2/gbrowse/c_elegans/ 100272276 bp]
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− | | Yes
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− | | WashU/Sanger<br>Coverage: 6x
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− | | First added in WS1
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | ''Caenorhabditis species 7''<br>strain JU1286
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=870436 870436]
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− | | V
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− | |
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− | |
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− | | WashU
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− | | First added in WS226.<br>'''WARNING''' the genome sequence contains contaminations
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | [[Caenorhabditis japonica|''Caenorhabditis japonica''<br>strain DF5080]]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=281687 281687]
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− | | II
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− | | [http://www.wormbase.org/db/gb2/gbrowse/c_japonica/ 166565019 bp]
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− | | Yes
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− | | WashU<br>Coverage: 22x<br>Supercontigs: 18817<br>N50: 94149
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− | | First added in WS195<br>[Jan 2011] New/improved assembly is being worked on at WashU.<br>[Oct 2011] new assembly in WS227
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | [[Caenorhabditis angaria|''Caenorhabditis angaria''<br>strain PS1010]]<br>(species 3)
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96668 96668]
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− | | III
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− | | [http://www.wormbase.org/db/gb2/gbrowse/c_angaria/ 79761545 bp]
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− | | Yes
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− | | CalTech<br>Supercontigs: 33559<br>N50: 9453
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− | | First added in WS218<br>[Jan 2011] This species now has an official name of '''C. angaria'''
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | [[Haemonchus contortus|''Haemonchus contortus'']]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6289 6289]
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− | | III
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− | | [http://www.wormbase.org/db/gb2/gbrowse/h_contortus/ 297975349 bp]
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− | | Yes
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− | | Sanger<br>Supercontigs: 59707<br>N50: 13338
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− | | First added in WS209.
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | [[Heterorhabditis bacteriophora|''Heterorhabditis bacteriophora''<br>strain M31e]]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=37862 37862]
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− | | V
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− | | 76974349 bp
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− | |
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− | | WashU<br>Coverage: 26.1<br>Supercontigs: 1240<br>N50: 312328
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− | | First added in WS229<br>[Jan 2011] Submitted to GenBank - Accession: EF043402<br>[Sep 2011] Gene set and Annotations are being worked on.
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | [[Pristionchus pacificus|''Pristionchus pacificus''<br>strain PS312]]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=54126 54126]
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− | | II
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− | | [http://www.wormbase.org/db/gb2/gbrowse/p_pacificus/ 172773083 bp]
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− | | Yes
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− | | WashU/MPI<br>Coverage: 8.92<br>Supercontigs: 18083<br>N50: 1244534
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− | | First added in WS194<br>[16 December 2010] Updated to the newest assembly and geneset in WS221
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− | | |
− | |-bgcolor="#FFFF99"
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− | | V
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− | | ''Steinernema carpocapsae''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34508 34508]
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− | | III
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− | | 230 Mb
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− | |
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− | | [http://www.langebio.cinvestav.mx/ LANGEBIO] / CalTech
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− | | [May 2011] Being assembled.
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− | | |
− | |-bgcolor="#99FF99"
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− | | IV
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− | | [[Meloidogyne incognita|''Meloidogyne incognita'']]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6306 6306]
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− | | III
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− | | [http://www.wormbase.org/db/gb2/gbrowse/m_incognita/ 82095019 bp]
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− | |
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− | | [http://www.inra.fr/meloidogyne_incognita/genomic_resources INRA]<br>Supercontigs: 9538<br>N50: 83000
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− | | 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.
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− | | |
− | |-bgcolor="#99FF99"
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− | | IV
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− | | [[Meloidogyne hapla|''Meloidogyne hapla'']]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6305 6305]
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− | | III
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− | | [http://www.wormbase.org/db/gb2/gbrowse/m_hapla/ 53017507 bp]
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− | | Yes
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− | | NCSU hapla.org<br>Supercontigs: 3452<br>84000
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− | | First added in WS204
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− | | |
− | |-bgcolor="#99FF99"
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− | | IV
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− | | [[Strongyloides ratti|''Strongyloides ratti''<br>natural isolate]]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=34506 34506]
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− | | III
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− | | 52638471 bp
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− | |
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− | | Sanger<br>Coverage: 70x<br>Supercontigs: 2184<br>N50: 359029
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− | | [Jan 2011] draft assembly in GenBank<br>First added in WS226
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− | | |
− | |-bgcolor="#99FF99"
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− | | IV
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− | | ''Bursaphelenchus xylophilus''<br>strain Ka4C1
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6326 6326]
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− | | III
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− | | 74561461 bp
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− | | Yes
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− | | Sanger<br>Coverage: 13x<br>Supercontigs: 5527<br>N50: 1158000
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− | | [Sept 2011] published in PLOS Pathogens<br>[Nov 2011] First added in WS229
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− | | |
− | |-bgcolor="#FF9900"
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− | | III
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− | | ''Ascaris suum''<br>natural isolate
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6253 6253]
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− | | III
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− | | [http://www.wormbase.org/db/gb2/gbrowse/a_suum/ 272782664 bp]
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− | | Yes
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− | | Davis<br>Coverage: 70x<br>Supercontig: 29831<br>N50: 407899
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− | | First added in WS229<br>[Oct 2011] integrated the Davis genome without a reference gene set.<br>[Nov 2011] added a reference gene set
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− | | |
− | |-bgcolor="#FF9900"
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− | | III
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− | | [[Brugia malayi|''Brugia malayi''<br>natural isolate]]
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6279 6279]
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− | | III
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− | | [http://www.wormbase.org/db/gb2/gbrowse/b_malayi/ 95814443 bp]
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− | | Yes
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− | | TIGR -> WashU/Sanger<br>Supercontigs: 27210<br>N50: 37841
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− | | 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
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− | | |
− | |-bgcolor="#33FFFF"
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− | | I
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− | | ''Trichinella spiralis''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6334 6334]
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− | | III
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− | | [http://www.wormbase.org/db/gb2/gbrowse/t_spiralis/ 56779425 bp]
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− | | Yes
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− | | WashU<br>Supercontigs: 6863<br>N50: 3383625
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− | | [Sept 2010] Being assembled.<br>[Feb 2011] published in Nature.<br>[Mar 2011] First added in WS225
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− | |}
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− | | |
− | === Genomes coming soon ===
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− | | |
− | {| class="wikitable" border="1"
| |
− | |-
| |
− | ! Clade
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− | ! Species
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− | ! NCBI Taxon
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− | ! Tier
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− | ! Genome
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− | ! Genes
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− | ! Assembly
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− | ! Comments
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− | | |
− | |-bgcolor="#CC9999"
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− | | V
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− | | ''Caenorhabditis drosophilae''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=96641 96641]
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− | | III
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− | |
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− | |
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− | | WashU
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− | | [Sept 2010] being assembled
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− | | |
− | |-bgcolor="#CC9999"
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− | | V
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− | | ''Caenorhabditis elegans''<br>strain DR1035
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6239 6239]
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− | | III
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− | | 100 Mb
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− | |
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− | | Mark Blaxter
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− | | status unclear
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− | | |
− | |-bgcolor="#CC9999"
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− | |
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− | | ''Onchocerca volvulus''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=6282 6282]
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− | | III
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− | |
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− | |
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− | | Sanger
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− | |
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− | | |
− | |-bgcolor="#CC9999"
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− | |
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− | | ''Globodera pallida''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=36090 36090]
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− | | III
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− | |
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− | |
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− | | Sanger
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− | |
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− | | |
− | |-bgcolor="#CC9999"
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− | |
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− | | ''Nippostrongylus brasiliensis''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=27835 27835]
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− | | III
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− | |
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− | |
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− | | Sanger
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− | |
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− | | |
− | |-bgcolor="#CC9999"
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− | |
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− | | ''Strongyloides ransomi''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=553534 553534]
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− | | III
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− | |
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− | |
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− | | Sanger
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− | |
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− | | |
− | |-bgcolor="#CC9999"
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− | |
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− | | ''Teladorsagia circumcincta''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=45464 45464]
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− | | III
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− | |
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− | |
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− | | Sanger
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− | |
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− | | |
− | |-bgcolor="#CC9999"
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− | |
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− | | ''Trichuris muris''
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− | | [http://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=70415 70415]
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− | | III
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− | |
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− | |
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− | | Sanger
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− | |
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− | |}
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− | | |
− | | |
− | | |
− | | |
− | | |
− | | |
− | | |
− | == Phylogeny ==
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− | | |
− | 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>
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− | ((((((((((((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 == |