Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"

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(updated Blaxter lab genomes)
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'''01 July 2015: The Blaxter lab, with support from [http://genomics.ed.ac.uk Edinburgh Genomics], has sequenced 18 further species and launched the ''Caenorhabditis Genomes Project'', see http://caenorhabditis.bio.ed.ac.uk/'''
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01 Sep 2016 The Blaxter lab website has moved to http://caenorhabditis.org/
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'''
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01 July 2015: The Blaxter lab, with support from [http://genomics.ed.ac.uk Edinburgh Genomics], has sequenced 18 further species and launched the ''Caenorhabditis Genomes Project'', see http://caenorhabditis.bio.ed.ac.uk/'''
 
There is a BLAST server for the new genome data in [http://bang.bio.ed.ac.uk:4567/ Edinburgh] and the new raw and preliminary assemblies can be downloaded from [ftp://bang.bio.ed.ac.uk/caenorhabditis/ the Blaxter lab FTP site].
 
There is a BLAST server for the new genome data in [http://bang.bio.ed.ac.uk:4567/ Edinburgh] and the new raw and preliminary assemblies can be downloaded from [ftp://bang.bio.ed.ac.uk/caenorhabditis/ the Blaxter lab FTP site].
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! Species name !! species number !! Reference strain !! Reproduction !! Collector !! Location !! Date !! Isolated by !! Phylogenetic affiliation !! Geographic distribution and available isolates (lab) !! Inbred strain !! Genome project see the Blaxter lab project page http://nematodes.org/genomes/index_caenorhabditis.html
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! Species name !! species number !! Reference strain !! Reproduction !! Collector !! Location !! Date !! Isolated by !! Phylogenetic affiliation !! Geographic distribution and available isolates (lab) !! Inbred strain !! Genome project see the Blaxter lab project page http://caenorhabditis.org/
 
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| '''''angaria''''' || 3 || PS1010 || F/M ||  || ||1990 || || ''Drosophilae'' super-group, ''Angaria'' group || 3 isolates from Florida USA || - ||  Mortazavi et al. 2010 Genome Research, '''@Wormbase'''
 
| '''''angaria''''' || 3 || PS1010 || F/M ||  || ||1990 || || ''Drosophilae'' super-group, ''Angaria'' group || 3 isolates from Florida USA || - ||  Mortazavi et al. 2010 Genome Research, '''@Wormbase'''
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| '''''japonica''''' || # ||  || F/M|| || || ||  || ''Elegans'' super-group, ''Japonica'' group|| isolates from Japan (Yoshiga/Cutter) || DF5080 || Wash U, '''@Wormbase'''
 
| '''''japonica''''' || # ||  || F/M|| || || ||  || ''Elegans'' super-group, ''Japonica'' group|| isolates from Japan (Yoshiga/Cutter) || DF5080 || Wash U, '''@Wormbase'''
 
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| '''''plicata''''' || # || SB355 || F/M ||  ||  ||  ||  ||  ||  ||  || Blaxter, preliminary assembly available. High proportion of bacterial DNA. To be reprepared in Felix lab.
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| '''''plicata''''' || # || SB355 || F/M ||  ||  ||  ||  ||  ||  ||  || Blaxter, preliminary assembly available. High proportion of bacterial DNA. Has been reprepared in Felix lab.
 
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| '''''remanei''''' || # ||  || F/M  ||  ||  ||  ||  || ''Elegans'' group|| USA/Canada, Europe, Japan, Taiwan, 100s of isolates || PB4641, PX356, PX349 || Wash U, '''@Wormbase'''; PX strains sequenced and assembled (ms in review, Phillips/Cutter labs); approx 35 wild isolates sequenced
 
| '''''remanei''''' || # ||  || F/M  ||  ||  ||  ||  || ''Elegans'' group|| USA/Canada, Europe, Japan, Taiwan, 100s of isolates || PB4641, PX356, PX349 || Wash U, '''@Wormbase'''; PX strains sequenced and assembled (ms in review, Phillips/Cutter labs); approx 35 wild isolates sequenced
 
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| '''sp. 1''' || 1 || SB341 || F/M || J. Raschka  || Berlin, Germany  || 2001  || W. Sudhaus  || base of ''Caenorhabditis'' || A second isolate from Norway (Félix) || JU1667  ||  Blaxter preliminary assembly http://nematodes.org/genomes/caenorhabditis_sp1/ ||   
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| '''sp. 1''' || 1 || SB341 || F/M || J. Raschka  || Berlin, Germany  || 2001  || W. Sudhaus  || base of ''Caenorhabditis'' || A second isolate from Norway (Félix) || JU1667  ||  Blaxter assembly v1  '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp1_v1/Info/Index''' ||   
 
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| '''sp. 2''' || 2 || DF5070 || F/M  || S. Wirth  || Corsica, France ||  Oct 2001 || W. Sudhaus  || ''Drosophilae'' group, sister of ''C. drosophilae''  ||  1 single isolate || ||  
 
| '''sp. 2''' || 2 || DF5070 || F/M  || S. Wirth  || Corsica, France ||  Oct 2001 || W. Sudhaus  || ''Drosophilae'' group, sister of ''C. drosophilae''  ||  1 single isolate || ||  
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| '''''portoensis''''' || 6 || EG4788 || F/M ||  M. Ailion, A.-J.  Rodrigues || Amares, Portugal || 28 Mar 2007  || M. Ailion  || ''Drosophilae'' super group  ||  Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) || EG5626  ||  sent to Blaxter
 
| '''''portoensis''''' || 6 || EG4788 || F/M ||  M. Ailion, A.-J.  Rodrigues || Amares, Portugal || 28 Mar 2007  || M. Ailion  || ''Drosophilae'' super group  ||  Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) || EG5626  ||  sent to Blaxter
 
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| '''''afra''''' || 7 || JU1199 || F/M || M. Herrmann  || Begoro, Ghana  || Jun 2007  || M.-A. Félix  || ''Japonica'' group  ||  2 isolates from West Africa (Félix) || JU1286  || Wash U CONTAMINATED WITH SP. 9 www.nematodes.org/nematodegenomes/index.php/959_Nematode_Genomes
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| '''''afra''''' || 7 || JU1199 || F/M || M. Herrmann  || Begoro, Ghana  || Jun 2007  || M.-A. Félix  || ''Japonica'' group  ||  2 isolates from West Africa (Félix) || JU1286  || Wash U CONTAMINATED. Resequenced by Blaxter, assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_afra_v1/Info/Index'''
 
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| '''sp. 8''' || 8 || QX1182 || F/M || M. Rockman || Backyard of 93 Mercer St., Jersey City, NJ, USA || 28 Jul 2007 ||  M. Rockman || ''Angaria'' group|| Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman)  || ongoing using TGM13 (K. Kiontke)  ||  
 
| '''sp. 8''' || 8 || QX1182 || F/M || M. Rockman || Backyard of 93 Mercer St., Jersey City, NJ, USA || 28 Jul 2007 ||  M. Rockman || ''Angaria'' group|| Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman)  || ongoing using TGM13 (K. Kiontke)  ||  
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|'''''nigoni''''' || 9 || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India  || 21 Dec 2007 || M.-A. Félix  || ''Briggsae'' subgroup, sister of ''briggsae''  || Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue)  || JU1422 || (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer
 
|'''''nigoni''''' || 9 || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India  || 21 Dec 2007 || M.-A. Félix  || ''Briggsae'' subgroup, sister of ''briggsae''  || Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue)  || JU1422 || (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer
 
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|'''''doughertyi''''' || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India  || 27 Dec 2007  || M.-A. Félix  ||  ''Brenneri'' subgroup ||  6 isolates from South India || JU1771  || Blaxter, sequenced, preliminary assembly available;  RNA seq for JU1328 & JU1333 http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis
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|'''''doughertyi''''' || 10 || JU1333 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India  || 27 Dec 2007  || M.-A. Félix  ||  ''Brenneri'' subgroup ||  6 isolates from South India || JU1771  || Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11002, preliminary assembly available;  RNA seq for JU1328 & JU1333
 
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| '''''tropicalis''''' || 11 || JU1373 || '''H/M''' || V. Robert, L. Sablé ||  Saint-Benoît, La Réunion ||  Jan 2008 ||  M.-A. Félix || ''Brenneri'' subgroup || Common in tropical regions (not so far on the African continent, one in Asia) || N.A. || Wash U, '''@Wormbase'''
 
| '''''tropicalis''''' || 11 || JU1373 || '''H/M''' || V. Robert, L. Sablé ||  Saint-Benoît, La Réunion ||  Jan 2008 ||  M.-A. Félix || ''Brenneri'' subgroup || Common in tropical regions (not so far on the African continent, one in Asia) || N.A. || Wash U, '''@Wormbase'''
 
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| '''''castelli''''' || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || ''Angaria'' group || Several isolates from French Guiana (Félix, Braendle, Cutter) || JU1956  || Blaxter, sequenced
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| '''''castelli''''' || 12 || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || ''Angaria'' group || Several isolates from French Guiana (Félix, Braendle, Cutter) || JU1956  || Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11356
 
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| '''''virilis ''''' || 13 || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008  || M.-A. Félix || ''Drosophilae'' super group || Several isolates from two locations in France || JU1968 || Blaxter, preliminary assembly available
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| '''''virilis ''''' || 13 || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008  || M.-A. Félix || ''Drosophilae'' super group || Several isolates from two locations in France || JU1968 || Blaxter assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_virilis_v1/Info/Index'''
 
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| '''''imperialis''''' || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia  || 24 Jul 2009  ||  M. Ailion || ''Japonica'' group || also Polynesia, Guadeloupe (Félix, Braendle)  || EG5942-EG5947 || sent to Blaxter
 
| '''''imperialis''''' || 14 || EG5716 || F/M || D. Ailion || Moorea, French Polynesia  || 24 Jul 2009  ||  M. Ailion || ''Japonica'' group || also Polynesia, Guadeloupe (Félix, Braendle)  || EG5942-EG5947 || sent to Blaxter
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| '''''kamaaina''''' ||15 || QG122 || F/M || M. Rockman  || Near Hanalei Bay, Kauai, Hawaii, USA || 2 Aug 2009 ||  M. Rockman || ''Elegans'' super group || Kauai and Maui, 2 isolates || QG2076, QG2077 || under assembly, Rockman
 
| '''''kamaaina''''' ||15 || QG122 || F/M || M. Rockman  || Near Hanalei Bay, Kauai, Hawaii, USA || 2 Aug 2009 ||  M. Rockman || ''Elegans'' super group || Kauai and Maui, 2 isolates || QG2076, QG2077 || under assembly, Rockman
 
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| '''''wallacei ''''' || 16 || JU1873 || F/M || J.-B. Pénigault || Sanda Center, Bali, Indonesia || 11 Nov 2009 || J.-B. Pénigault || ''Brenneri'' subgroup  || 2 isolates from Indonesia (Félix) || JU1898 || Blaxter preliminary assembly available
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| '''''wallacei ''''' || 16 || JU1873 || F/M || J.-B. Pénigault || Sanda Center, Bali, Indonesia || 11 Nov 2009 || J.-B. Pénigault || ''Brenneri'' subgroup  || 2 isolates from Indonesia (Félix) || JU1898 || Blaxter preliminary assembly available, Erich Schwarz PacBio
 
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| '''''nouraguensis ''''' || 17 || JU1825 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 21 Nov 2009 || C. Braendle, M.-A. Félix || ''Japonica'' group ||  Many isolates from French Guiana || JU2079 || Blaxter, preliminary assembly available; additional strains sequenced also
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| '''''nouraguensis ''''' || 17 || JU1825 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 21 Nov 2009 || C. Braendle, M.-A. Félix || ''Japonica'' group ||  Many isolates from French Guiana || JU2079 || Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB10884, preliminary assembly available ; additional strains sequenced also
 
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| '''''macrosperma ''''' (ex-sp. 18) || 18 || JU1857 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 23 Nov 2009 || C. Braendle, M.-A. Félix || ''Japonica'' group  || A few isolates from Nouragues, French Guiana  || JU2083  || Blaxter, preliminary assembly available
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| '''''macrosperma ''''' || 18 || JU1857 || F/M || C. Braendle, M.-A. Félix || Nouragues Forest, French Guiana || 23 Nov 2009 || C. Braendle, M.-A. Félix || ''Japonica'' group  || A few isolates from Nouragues, French Guiana  || JU2083  || Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB10887, preliminary assembly available
 
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|  '''''yunquensis ''''' || 19 || EG6142 ||F/M || S. Dalton  || El Yunque, Puerto Rico || 28 Mar 2010  || S. Dalton, M. Ailion || ''Japonica'' group  ||  Puerto Rico ||  XZ1517-XZ1520 ||  sent to Blaxter
 
|  '''''yunquensis ''''' || 19 || EG6142 ||F/M || S. Dalton  || El Yunque, Puerto Rico || 28 Mar 2010  || S. Dalton, M. Ailion || ''Japonica'' group  ||  Puerto Rico ||  XZ1517-XZ1520 ||  sent to Blaxter
 
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|  '''''guadeloupensis ''''' || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010  || C. Braendle || ''Drosophilae'' supergroup || Guadeloupe ||  ||  Blaxter, preliminary assembly available
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|  '''''guadeloupensis ''''' || 20 || NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010  || C. Braendle || ''Drosophilae'' supergroup || Guadeloupe ||  ||  Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11393, preliminary assembly available
 
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| '''sp. 21''' || 21 || NIC134 || F/M || C. Gimond || Island of Sainte Marie, Madagascar || Dec 2010 || C. Braendle || base of ''Caenorhabditis'' || Also Polynesia, Thailand and Caribbean (Félix) || NIC534 || Blaxter, preliminary assembly available
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| '''sp. 21''' || 21 || NIC134 || F/M || C. Gimond || Island of Sainte Marie, Madagascar || Dec 2010 || C. Braendle || base of ''Caenorhabditis'' || Also Polynesia, Thailand and Caribbean (Félix) || NIC534 || Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12595/, preliminary assembly available
 
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|  '''''latens ''''' || 23 || VX88 || F/M || G.-X. Wang  || Jiufeng Village, Wuhan City, Hubei Province, China || 27 Oct 2009 || G.-X. Wang || ''Briggsae'' subgroup, sister of ''C. remanei'' || Several isolates from China (Cutter) || PX534, PX573, PX574, PX580 || under assembly, Cutter/Phillips
 
|  '''''latens ''''' || 23 || VX88 || F/M || G.-X. Wang  || Jiufeng Village, Wuhan City, Hubei Province, China || 27 Oct 2009 || G.-X. Wang || ''Briggsae'' subgroup, sister of ''C. remanei'' || Several isolates from China (Cutter) || PX534, PX573, PX574, PX580 || under assembly, Cutter/Phillips
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| '''sp. 25''' || 25 || ZF1222 || F/M || A. Seah, T. Inoue  || Singapore || 3 Sep 2011  || T. Inoue || ''Japonica'' group  || 2 isolates from Singapore || ongoing (Inoue)  ||   
 
| '''sp. 25''' || 25 || ZF1222 || F/M || A. Seah, T. Inoue  || Singapore || 3 Sep 2011  || T. Inoue || ''Japonica'' group  || 2 isolates from Singapore || ongoing (Inoue)  ||   
 
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| '''sp. 26''' || 26 || JU2161 || F/M || M.-A. Félix || Zanzibar, Tanzania || 9 Mar 2012  || M.-A. Félix || ''Briggsae'' subgroup, close relative of ''C. sinica'' || 5 isolates from Zanzibar || JU2190 || Blaxter, preliminary assembly available
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| '''sp. 26''' || 26 || JU2161 || F/M || M.-A. Félix || Zanzibar, Tanzania || 9 Mar 2012  || M.-A. Félix || ''Briggsae'' subgroup, close relative of ''C. sinica'' || 5 isolates from Zanzibar || JU2190 || Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12596/, preliminary assembly available
 
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| '''sp. 27''' || 27 || QX2263 || F/M || || Buenos Aires, Argentina  || 2 Mar 2012  || E. Andersen  || ''Drosophilae'' supergroup, sister of ''portoensis''  ||  Argentina ||  ||   
 
| '''sp. 27''' || 27 || QX2263 || F/M || || Buenos Aires, Argentina  || 2 Mar 2012  || E. Andersen  || ''Drosophilae'' supergroup, sister of ''portoensis''  ||  Argentina ||  ||   
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|  '''sp. 30''' || 30 || DF5152  ||  F/M  ||  ||  Gallon Jug, Belize  || 15 Nov 2012 || K. Kiontke  || ''Drosophilae'' subgroup  || 4 isofemale lines from Belize  || ongoing (K. Kiontke)  ||   
 
|  '''sp. 30''' || 30 || DF5152  ||  F/M  ||  ||  Gallon Jug, Belize  || 15 Nov 2012 || K. Kiontke  || ''Drosophilae'' subgroup  || 4 isofemale lines from Belize  || ongoing (K. Kiontke)  ||   
 
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|| '''sp. 31''' || 31 || JU2469 ||  F/M  ||  ||  Madre de Dios, Peru || Jan 2013  || L. Frézal  || ''Drosophilae'' super group ||  2 isolates from Peru  || JU2585 || Blaxter, preliminary assembly available  ||   
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|| '''sp. 31''' || 31 || JU2469 ||  F/M  ||  ||  Madre de Dios, Peru || Jan 2013  || L. Frézal  || ''Drosophilae'' super group ||  2 isolates from Peru  || JU2585 || Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12600/, preliminary assembly available  ||   
 
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| '''sp. 32''' || 32 || SB454 || F/M ||  || East Africa? || Feb 2013  || W. Sudhaus || ''Japonica'' group, sister of ''afra''  ||  1 isolate, from the gut of the millipede ''Archispirostreptus gigas'' || JU2788 ||  Blaxter, preliminary assembly available
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| '''sp. 32''' || 32 || SB454 || F/M ||  || East Africa? || Feb 2013  || W. Sudhaus || ''Japonica'' group, sister of ''afra''  ||  1 isolate, from the gut of the millipede ''Archispirostreptus gigas'' || JU2788 ||  Blaxter assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp32_v1/Info/Index'''
 
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| '''sp. 33''' || 33 || BRC20065 ||F/M || J. Wang || Taiwan || 24 May 2012 || J. Wang ||  ''Briggsae'' subgroup || 1 isolate from Taiwan  || BRC20066 || planned by J. Wang  
 
| '''sp. 33''' || 33 || BRC20065 ||F/M || J. Wang || Taiwan || 24 May 2012 || J. Wang ||  ''Briggsae'' subgroup || 1 isolate from Taiwan  || BRC20066 || planned by J. Wang  
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| '''sp. 37''' || 37 || NIC394  || F/M  || C. Braendle, A. Cutter, R. Jovelin, N. Callemeyn  ||  Nouragues National Reserve, French Guiana ||  18 Apr 2013 || C. Braendle  || ''Angaria'' group  || 1 isolate from French Guiana  ||  ||   
 
| '''sp. 37''' || 37 || NIC394  || F/M  || C. Braendle, A. Cutter, R. Jovelin, N. Callemeyn  ||  Nouragues National Reserve, French Guiana ||  18 Apr 2013 || C. Braendle  || ''Angaria'' group  || 1 isolate from French Guiana  ||  ||   
 
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| '''sp. 38''' || 38 || JU2745  || F/M  || F. Besnard  ||  Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard  || ''Angaria'' group  || 1 isolate from Guadeloupe  || JU2809 ||  Blaxter, preliminary assembly available
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| '''sp. 38''' || 38 || JU2745  || F/M  || F. Besnard  ||  Guadeloupe (Basse Terre) || 09 June 2014 || F. Besnard  || ''Angaria'' group  || 1 isolate from Guadeloupe  || JU2809 ||  Blaxter assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp38_v1/Info/Index'''
 
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| '''sp. 39''' || 39 || NIC564  || F/M  || C. Braendle ||  Dominica || 13 May 2014 || C. Braendle  || ''Japonica'' group  || 1 isolate from Dominique  ||  || Blaxter, sequenced  
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| '''sp. 39''' || 39 || NIC564  || F/M  || C. Braendle ||  Dominica || 13 May 2014 || C. Braendle  || ''Japonica'' group  || 1 isolate from Dominique  ||  || Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12602/
 
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| '''sp. 40''' || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014  || L. Frézal || ''Briggsae'' subgroup, close relative of ''C. sinica''  || 5 isolates from Australia, in fresh or rotting figs || JU2818 || Blaxter, preliminary assembly available
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| '''sp. 40''' || 40 || JU2774 || F/M || J.-B. Pénigault || Danbulla, Australia || 08 August 2014  || L. Frézal || ''Briggsae'' subgroup, close relative of ''C. sinica''  || 5 isolates from Australia, in fresh or rotting figs || JU2818 || Blaxter assembly v1 '''http://ensembl.caenorhabditis.org/Caenorhabditis_sp40_v1/Info/Index'''
 
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| '''sp. 41''' || 41 || BRC20276 || F/M || || Salomon Islands || October 2014  || J. Wang || ''Briggsae'' subgroup, sister species of C. sp. 40  || 2 isolates from Salomon Islands ||  ||
 
| '''sp. 41''' || 41 || BRC20276 || F/M || || Salomon Islands || October 2014  || J. Wang || ''Briggsae'' subgroup, sister species of C. sp. 40  || 2 isolates from Salomon Islands ||  ||
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| '''sp. 42''' || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014  || C. Braendle ||  ''Drosophilae'' super group  || one isolate from French Guiana ||  ||  
 
| '''sp. 42''' || 42 || NIC1040 || F/M || C. Braendle/A. Cutter || Nouragues Forest, French Guiana || August 2014  || C. Braendle ||  ''Drosophilae'' super group  || one isolate from French Guiana ||  ||  
 
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| '''sp. 43''' || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014  || C. Braendle || ''Drosophilae'' super group  || 2 isolates from Mexico; in orange berries ||  || Blaxter, preliminary assembly available
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| '''sp. 43''' || 43 || NIC1070 || F/M || C. Gosse || Chichén Itzá, Yucatán, Mexico || 17 October 2014  || C. Braendle || ''Drosophilae'' super group  || 2 isolates from Mexico; in orange berries ||  ||  
 
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| '''sp. 44''' || 44 || BRC20300 || F/M ||  || Shihting mountain near Taipei City, Taiwan || Dec 2014  || J. Wang || sister species of ''C. brenneri''  || one isolate from Taiwan; in flowers ||  ||  
 
| '''sp. 44''' || 44 || BRC20300 || F/M ||  || Shihting mountain near Taipei City, Taiwan || Dec 2014  || J. Wang || sister species of ''C. brenneri''  || one isolate from Taiwan; in flowers ||  ||  

Revision as of 18:22, 18 September 2016

01 Sep 2016 The Blaxter lab website has moved to http://caenorhabditis.org/ 01 July 2015: The Blaxter lab, with support from Edinburgh Genomics, has sequenced 18 further species and launched the Caenorhabditis Genomes Project, see http://caenorhabditis.bio.ed.ac.uk/ There is a BLAST server for the new genome data in Edinburgh and the new raw and preliminary assemblies can be downloaded from the Blaxter lab FTP site.
Species name species number Reference strain Reproduction Collector Location Date Isolated by Phylogenetic affiliation Geographic distribution and available isolates (lab) Inbred strain Genome project see the Blaxter lab project page http://caenorhabditis.org/
angaria 3 PS1010 F/M 1990 Drosophilae super-group, Angaria group 3 isolates from Florida USA - Mortazavi et al. 2010 Genome Research, @Wormbase
brenneri 4 F/M Elegans group tropical, ~30 isolates (Felix, Cutter, Braendle) PB2801, VX223-225, VX227 Wash U, @Wormbase; VX strains sequenced but not yet assembled (Cutter lab); RNA seq for 10 isolates http://www.ncbi.nlm.nih.gov/sra/?term=SRP042651+Caenorhabditis
briggsae # AF16 H/M Elegans group world-wide distribution, 100s of isolates N.A. Stein et al. 2003 PLoS Biology, @Wormbase; 37 wild isolates sequenced 30x (Cutter lab)
drosophilae # DF5077 F/M Drosophilae group rotting saguaro cactus in Arizona, a few isolates DF5112
elegans # N2 H/M Elegans group world-wide (mostly temperate) distribution, 100s of isolates N.A. C. elegans Sequencing Consortium 1998 Science, @Wormbase
japonica # F/M Elegans super-group, Japonica group isolates from Japan (Yoshiga/Cutter) DF5080 Wash U, @Wormbase
plicata # SB355 F/M Blaxter, preliminary assembly available. High proportion of bacterial DNA. Has been reprepared in Felix lab.
remanei # F/M Elegans group USA/Canada, Europe, Japan, Taiwan, 100s of isolates PB4641, PX356, PX349 Wash U, @Wormbase; PX strains sequenced and assembled (ms in review, Phillips/Cutter labs); approx 35 wild isolates sequenced
sp. 1 1 SB341 F/M J. Raschka Berlin, Germany 2001 W. Sudhaus base of Caenorhabditis A second isolate from Norway (Félix) JU1667 Blaxter assembly v1 http://ensembl.caenorhabditis.org/Caenorhabditis_sp1_v1/Info/Index
sp. 2 2 DF5070 F/M S. Wirth Corsica, France Oct 2001 W. Sudhaus Drosophilae group, sister of C. drosophilae 1 single isolate
sinica 5 F/M M.-A. Félix Chengyang, Guangxi, China 6 May 2005 M.-A. Félix Briggsae subgroup Isolates from China, Vietnam (Cutter, Ailion, Félix) JU800 Cutter/Blaxter, @Wormbase
portoensis 6 EG4788 F/M M. Ailion, A.-J. Rodrigues Amares, Portugal 28 Mar 2007 M. Ailion Drosophilae super group Portugal, Spain, France, Ireland (Ailion, Félix, Braendle) EG5626 sent to Blaxter
afra 7 JU1199 F/M M. Herrmann Begoro, Ghana Jun 2007 M.-A. Félix Japonica group 2 isolates from West Africa (Félix) JU1286 Wash U CONTAMINATED. Resequenced by Blaxter, assembly v1 http://ensembl.caenorhabditis.org/Caenorhabditis_afra_v1/Info/Index
sp. 8 8 QX1182 F/M M. Rockman Backyard of 93 Mercer St., Jersey City, NJ, USA 28 Jul 2007 M. Rockman Angaria group Isolates from USA (Fitch), Europe (Braendle, Félix), Canada (Rockman) ongoing using TGM13 (K. Kiontke)
nigoni 9 JU1325 F/M M.-A. Félix Trivandrum Zoo, Kerala, India 21 Dec 2007 M.-A. Félix Briggsae subgroup, sister of briggsae Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) JU1422 (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer
doughertyi 10 JU1333 F/M M.-A. Félix Angela Spice Garden, Kerala, India 27 Dec 2007 M.-A. Félix Brenneri subgroup 6 isolates from South India JU1771 Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11002, preliminary assembly available; RNA seq for JU1328 & JU1333
tropicalis 11 JU1373 H/M V. Robert, L. Sablé Saint-Benoît, La Réunion Jan 2008 M.-A. Félix Brenneri subgroup Common in tropical regions (not so far on the African continent, one in Asia) N.A. Wash U, @Wormbase
castelli 12 JU1426 F/M P. Châtelet Nouragues Forest, French Guiana May 2008 M.-A. Félix Angaria group Several isolates from French Guiana (Félix, Braendle, Cutter) JU1956 Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11356
virilis 13 JU1528 F/M M.-A. Félix Orsay apple orchard 9 Sep 2008 M.-A. Félix Drosophilae super group Several isolates from two locations in France JU1968 Blaxter assembly v1 http://ensembl.caenorhabditis.org/Caenorhabditis_virilis_v1/Info/Index
imperialis 14 EG5716 F/M D. Ailion Moorea, French Polynesia 24 Jul 2009 M. Ailion Japonica group also Polynesia, Guadeloupe (Félix, Braendle) EG5942-EG5947 sent to Blaxter
kamaaina 15 QG122 F/M M. Rockman Near Hanalei Bay, Kauai, Hawaii, USA 2 Aug 2009 M. Rockman Elegans super group Kauai and Maui, 2 isolates QG2076, QG2077 under assembly, Rockman
wallacei 16 JU1873 F/M J.-B. Pénigault Sanda Center, Bali, Indonesia 11 Nov 2009 J.-B. Pénigault Brenneri subgroup 2 isolates from Indonesia (Félix) JU1898 Blaxter preliminary assembly available, Erich Schwarz PacBio
nouraguensis 17 JU1825 F/M C. Braendle, M.-A. Félix Nouragues Forest, French Guiana 21 Nov 2009 C. Braendle, M.-A. Félix Japonica group Many isolates from French Guiana JU2079 Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB10884, preliminary assembly available ; additional strains sequenced also
macrosperma 18 JU1857 F/M C. Braendle, M.-A. Félix Nouragues Forest, French Guiana 23 Nov 2009 C. Braendle, M.-A. Félix Japonica group A few isolates from Nouragues, French Guiana JU2083 Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB10887, preliminary assembly available
yunquensis 19 EG6142 F/M S. Dalton El Yunque, Puerto Rico 28 Mar 2010 S. Dalton, M. Ailion Japonica group Puerto Rico XZ1517-XZ1520 sent to Blaxter
guadeloupensis 20 NIC113 F/M C. Braendle Soufrière Forest trail, Guadeloupe Mar 2010 C. Braendle Drosophilae supergroup Guadeloupe Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB11393, preliminary assembly available
sp. 21 21 NIC134 F/M C. Gimond Island of Sainte Marie, Madagascar Dec 2010 C. Braendle base of Caenorhabditis Also Polynesia, Thailand and Caribbean (Félix) NIC534 Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12595/, preliminary assembly available
latens 23 VX88 F/M G.-X. Wang Jiufeng Village, Wuhan City, Hubei Province, China 27 Oct 2009 G.-X. Wang Briggsae subgroup, sister of C. remanei Several isolates from China (Cutter) PX534, PX573, PX574, PX580 under assembly, Cutter/Phillips
sp. 24 24 QG555 F/M A. Paaby Santa Barbara, USA July 2011 A. Paaby Angaria group, sister of sp. 8 Isolates from California, Panama, Mexico (Rockman, Félix)
sp. 25 25 ZF1222 F/M A. Seah, T. Inoue Singapore 3 Sep 2011 T. Inoue Japonica group 2 isolates from Singapore ongoing (Inoue)
sp. 26 26 JU2161 F/M M.-A. Félix Zanzibar, Tanzania 9 Mar 2012 M.-A. Félix Briggsae subgroup, close relative of C. sinica 5 isolates from Zanzibar JU2190 Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12596/, preliminary assembly available
sp. 27 27 QX2263 F/M Buenos Aires, Argentina 2 Mar 2012 E. Andersen Drosophilae supergroup, sister of portoensis Argentina
sp. 28 28 QG702 F/M M. Rockman Barro Colorado Island, Panama 23 Apr 2012 M. Rockman Japonica group several isofemale lines from Panama QG2080, QG2081 under assembly, Rockman
sp. 29 29 QG704 F/M M. Rockman Barro Colorado Island, Panama 25 Apr 2012 M. Rockman Japonica group, sister of nouraguensis many isofemale lines from Panama QG2082, QG2083 under assembly, Rockman
sp. 30 30 DF5152 F/M Gallon Jug, Belize 15 Nov 2012 K. Kiontke Drosophilae subgroup 4 isofemale lines from Belize ongoing (K. Kiontke)
sp. 31 31 JU2469 F/M Madre de Dios, Peru Jan 2013 L. Frézal Drosophilae super group 2 isolates from Peru JU2585 Blaxter https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12600/, preliminary assembly available
sp. 32 32 SB454 F/M East Africa? Feb 2013 W. Sudhaus Japonica group, sister of afra 1 isolate, from the gut of the millipede Archispirostreptus gigas JU2788 Blaxter assembly v1 http://ensembl.caenorhabditis.org/Caenorhabditis_sp32_v1/Info/Index
sp. 33 33 BRC20065 F/M J. Wang Taiwan 24 May 2012 J. Wang Briggsae subgroup 1 isolate from Taiwan BRC20066 planned by J. Wang
sp. 34 34 NK74SC F/M N. Kanzaki Ishigaki Island, Japan May 2013 N. Kanzaki Elegans supergroup, with C. sp. 35 sister of C. elegans 1 isolate from Japan. Associated with fig wasps and Ficus septica started by N. Kanzaki and collaborators
sp. 35 35 DF5171 F/M Banda Ache, Indonesia Aug 2013 N. Kanzaki Elegans supergroup, with C. sp. 34 sister of C. elegans 2 Isolates from Indonesia, associated with Ficus hispida
sp. 36 36 NK02NV F/M N. Kanzaki Tokyo, Japan Apr 2013 N. Kanzaki Japonica group 1 isolate from Japan. Associated with the weevil Niphades variegatus
sp. 37 37 NIC394 F/M C. Braendle, A. Cutter, R. Jovelin, N. Callemeyn Nouragues National Reserve, French Guiana 18 Apr 2013 C. Braendle Angaria group 1 isolate from French Guiana
sp. 38 38 JU2745 F/M F. Besnard Guadeloupe (Basse Terre) 09 June 2014 F. Besnard Angaria group 1 isolate from Guadeloupe JU2809 Blaxter assembly v1 http://ensembl.caenorhabditis.org/Caenorhabditis_sp38_v1/Info/Index
sp. 39 39 NIC564 F/M C. Braendle Dominica 13 May 2014 C. Braendle Japonica group 1 isolate from Dominique Blaxter, sequenced https://www.ncbi.nlm.nih.gov/bioproject/PRJEB12602/
sp. 40 40 JU2774 F/M J.-B. Pénigault Danbulla, Australia 08 August 2014 L. Frézal Briggsae subgroup, close relative of C. sinica 5 isolates from Australia, in fresh or rotting figs JU2818 Blaxter assembly v1 http://ensembl.caenorhabditis.org/Caenorhabditis_sp40_v1/Info/Index
sp. 41 41 BRC20276 F/M Salomon Islands October 2014 J. Wang Briggsae subgroup, sister species of C. sp. 40 2 isolates from Salomon Islands
sp. 42 42 NIC1040 F/M C. Braendle/A. Cutter Nouragues Forest, French Guiana August 2014 C. Braendle Drosophilae super group one isolate from French Guiana
sp. 43 43 NIC1070 F/M C. Gosse Chichén Itzá, Yucatán, Mexico 17 October 2014 C. Braendle Drosophilae super group 2 isolates from Mexico; in orange berries
sp. 44 44 BRC20300 F/M Shihting mountain near Taipei City, Taiwan Dec 2014 J. Wang sister species of C. brenneri one isolate from Taiwan; in flowers
sp. 45 45 NIC759 F/M C. Braendle Sylvania, Dominica 16 May 2014 C. Braendle sister species of C. guadeloupensis one isolate from Dominica; in Cecropia fruit
sp. 46 46 NIC1120 F/M C. Braendle Macchu Picchu, Aguas Calientes, Peru 7 April 2015 C. Braendle Japonica group one isolate from Peru
sp. 47 47 NIC1127 F/M C. Braendle Tambopata region, Amazon, Peru 7 April 2015 C. Braendle Angaria group one isolate from Peru
sp. 48 48 BRC20359 F/M J. Wang Khao Yai National park, Thailand 4 May 2015 J. Wang sister of C. brenneri? one isolate from Thailand
sp. 49 49 BRC20376 F/M J. Wang? Solomon Islands ? J. Wang? Japonica group? one isolate Solomon Islands
sp. 50 50 BRC20387 F/M Dai near Taipei City, Taiwan 18 October 2015 J. Wang Elegans supergroup two isolates from Taiwan


Species numbers are assigned by Karin Kiontke, NYU.

Published phylogeny, up to sp. 21:

  • Kiontke et al. 2011 BMC Evolutionary Biology 11: 339.

Published phylogeny from Kiontke et al. 2011 with species names from Félix, Braendle & Cutter 2014

Updated phylogeny, up to sp. 32: http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png

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