Difference between revisions of "LIST OF AVAILABLE CAENORHABDITIS SPECIES and the state of their genome projects"
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| '''sp. 5''' || JU727|| 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 | | '''sp. 5''' || JU727|| 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 | ||
|- | |- | ||
| − | | '''sp. 6 | + | | '''''portoensis''''' (ex-sp. 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 || |
|- | |- | ||
| − | | '''sp. 7 | + | | '''''afra''''' (ex-sp. 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 |
|- | |- | ||
| '''sp. 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) || || | | '''sp. 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) || || | ||
|- | |- | ||
| − | | '''sp. 9 | + | |'''''nigoni''''' (ex-sp. 9) || JU1325 || F/M || M.-A. Félix || Trivandrum Zoo, Kerala, India || 21 Dec 2007 || M.-A. Félix || ''Briggsae'' subgroup || Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) || JU1422 || (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer |
|- | |- | ||
| − | | '''sp. 10 | + | |'''''doughertyi''''' (ex-sp. 10)|| JU1323 || F/M || M.-A. Félix || Angela Spice Garden, Kerala, India || 27 Dec 2007 || M.-A. Félix || ''Brenneri'' subgroup || 6 isolates from South India || JU1771 || formerly sp. 10 |
|- | |- | ||
| − | | '''sp. 11 | + | | '''''tropicalis''''' (ex-sp. 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 |
|- | |- | ||
| − | | '''sp. 12 | + | | '''''castelli''''' (ex-sp. 12) || JU1426 || F/M || P. Châtelet || Nouragues Forest, French Guiana || May 2008 || M.-A. Félix || ''Angaria'' group || 2 isolates from French Guiana || JU1956 || |
|- | |- | ||
| − | | '''sp. 13 | + | | '''''virilis ''''' (ex-sp. 13) || JU1528 || F/M || M.-A. Félix || Orsay apple orchard || 9 Sep 2008 || M.-A. Félix || ''Drosophilae'' super group || A few isolates, all from Orsay, France || JU1968 || |
|- | |- | ||
| − | | '''sp. 14 | + | | '''''imperialis''''' (ex-sp. 14) || EG5716 || F/M || D. Ailion || Moorea, French Polynesia || 24 Jul 2009 || M. Ailion || ''Japonica'' group || also Polynesia, Guadeloupe (Félix, Braendle) || EG5942-EG5947 || |
|- | |- | ||
| − | | '''sp. 15 | + | | '''''kamaaina''''' (sp. 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 |
|- | |- | ||
| − | | '''sp. 16 | + | | '''''wallacei ''''' (ex-sp. 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 || Félix/Blaxter preliminary assembly available-ask us |
|- | |- | ||
| − | | '''sp. 17 | + | | '''''nouraguensis ''''' (ex-sp. 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 || planning Ailion |
|- | |- | ||
| − | | '''sp. 18 | + | | '''''macrosperma ''''' (ex-sp. 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 || |
|- | |- | ||
| − | | '''sp. 19 | + | | '''''yunquensis ''''' (ex-sp. 19) || EG6142 ||F/M || S. Dalton || El Yunque, Puerto Rico || 28 Mar 2010 || S. Dalton, M. Ailion || ''Japonica'' group || Puerto Rico || || |
|- | |- | ||
| − | | '''sp. 20 | + | | '''''guadeloupensis ''''' (ex-sp. 20)|| NIC113 || F/M || C. Braendle || Soufrière Forest trail, Guadeloupe || Mar 2010 || C. Braendle || ''Drosophilae'' supergroup || Guadeloupe || planned Braendle || |
|- | |- | ||
| '''sp. 21''' || NIC134 || F/M || C. Gimond || Island of Sainte Marie, Madagascar || Dec 2010 || C. Braendle || base of ''Caenorhabditis'' || Also Polynesia and Thailand (Félix) || planned Braendle || | | '''sp. 21''' || NIC134 || F/M || C. Gimond || Island of Sainte Marie, Madagascar || Dec 2010 || C. Braendle || base of ''Caenorhabditis'' || Also Polynesia and Thailand (Félix) || planned Braendle || | ||
|- | |- | ||
| − | | '''sp. 23 | + | | '''''latens ''''' (ex-sp. 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''' || QG555 || F/M || A. Paaby || Santa Barbara, USA || July 2011 || A. Paaby || ''Angaria'' group, sister of sp. 8 || 1 isolate from California and 3 from Panama (Rockman) || || | | '''sp. 24''' || QG555 || F/M || A. Paaby || Santa Barbara, USA || July 2011 || A. Paaby || ''Angaria'' group, sister of sp. 8 || 1 isolate from California and 3 from Panama (Rockman) || || | ||
Revision as of 09:56, 12 April 2014
| Species | Reference strain | Reproduction | Collector | Location | Date | Isolated by | Phylogenetic affiliation | Geographic distribution and available isolates (lab) | Inbred strain | Genome project | |
|---|---|---|---|---|---|---|---|---|---|---|---|
| angaria | PS1010 | F/M | 1990 | Drosophilae super-group, Angaria group | 3 isolates from Florida USA | - | formerly C. sp. 3; Mortazavi et al. 2010 Genome Research, @Wormbase | ||||
| brenneri | F/M | Elegans group | tropical, ~30 isolates (Felix, Cutter, Braendle) | PB2801 | Wash U, @Wormbase | ||||||
| briggsae | AF16 | H/M | Elegans group | world-wide distribution, 100s of isolates | N.A. | Stein et al. 2003 PLoS Biology, @Wormbase | |||||
| drosophilae | DF5077 | F/M | Drosophilae group | ||||||||
| 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 | |||||||||
| remanei | F/M | Elegans group | USA/Canada, Europe, Japan, Taiwan, 100s of isolates | PB4641 | Wash U,@Wormbase | ||||||
| sp. 1 | SB341 | F/M | S. Wirth | Berlin, Germany | 2000? | W. Sudhaus | base of Caenorhabditis | 1 single isolate | JU1667 | Félix/Blaxter preliminary assembly available-ask us | |
| sp. 2 | DF5070 | F/M | S. Wirth | Corsica, France | Oct 2001 | W. Sudhaus | Drosophilae group, sister of C. drosophilae | 1 single isolate | |||
| sp. 5 | JU727 | 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 (ex-sp. 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 | ||
| afra (ex-sp. 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 | |
| sp. 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) | |||
| nigoni (ex-sp. 9) | JU1325 | F/M | M.-A. Félix | Trivandrum Zoo, Kerala, India | 21 Dec 2007 | M.-A. Félix | Briggsae subgroup | Various wet tropical places from Yucatan to Singapore (Ailion, Félix, Inoue) | JU1422 | (Wash U: contaminated genomic, cDNAs OK) Resequenced by Barbara Meyer | |
| doughertyi (ex-sp. 10) | JU1323 | F/M | M.-A. Félix | Angela Spice Garden, Kerala, India | 27 Dec 2007 | M.-A. Félix | Brenneri subgroup | 6 isolates from South India | JU1771 | formerly sp. 10 | |
| tropicalis (ex-sp. 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 (ex-sp. 12) | JU1426 | F/M | P. Châtelet | Nouragues Forest, French Guiana | May 2008 | M.-A. Félix | Angaria group | 2 isolates from French Guiana | JU1956 | ||
| virilis (ex-sp. 13) | JU1528 | F/M | M.-A. Félix | Orsay apple orchard | 9 Sep 2008 | M.-A. Félix | Drosophilae super group | A few isolates, all from Orsay, France | JU1968 | ||
| imperialis (ex-sp. 14) | EG5716 | F/M | D. Ailion | Moorea, French Polynesia | 24 Jul 2009 | M. Ailion | Japonica group | also Polynesia, Guadeloupe (Félix, Braendle) | EG5942-EG5947 | ||
| kamaaina (sp. 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 (ex-sp. 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 | Félix/Blaxter preliminary assembly available-ask us | |
| nouraguensis (ex-sp. 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 | planning Ailion | |
| macrosperma (ex-sp. 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 | ||
| yunquensis (ex-sp. 19) | EG6142 | F/M | S. Dalton | El Yunque, Puerto Rico | 28 Mar 2010 | S. Dalton, M. Ailion | Japonica group | Puerto Rico | |||
| guadeloupensis (ex-sp. 20) | NIC113 | F/M | C. Braendle | Soufrière Forest trail, Guadeloupe | Mar 2010 | C. Braendle | Drosophilae supergroup | Guadeloupe | planned Braendle | ||
| sp. 21 | NIC134 | F/M | C. Gimond | Island of Sainte Marie, Madagascar | Dec 2010 | C. Braendle | base of Caenorhabditis | Also Polynesia and Thailand (Félix) | planned Braendle | ||
| latens (ex-sp. 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 | QG555 | F/M | A. Paaby | Santa Barbara, USA | July 2011 | A. Paaby | Angaria group, sister of sp. 8 | 1 isolate from California and 3 from Panama (Rockman) | |||
| sp. 25 | ZF1222 | F/M | A. Seah, T. Inoue | Singapore | 3 Sep 2011 | T. Inoue | Japonica group | 2 isolates from Singapore | ongoing (Inoue) | ||
| sp. 26 | JU2161 | F/M | M.-A. Félix | Zanzibar, Tanzania | 9 Mar 2012 | M.-A. Félix | Briggsae subgroup, sister of sp. 5 | 5 isolates from Zanzibar | JU2190 | ||
| sp. 27 | QX2263 | F/M | Buenos Aires, Argentina | 2 Mar 2012 | E. Andersen | Drosophilae supergroup, sister of sp. 6 | Argentina | ||||
| sp. 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 | QG704 | F/M | M. Rockman | Barro Colorado Island, Panama | 25 Apr 2012 | M. Rockman | Japonica group, sister of sp. 17 | many isofemale lines from Panama | QG2082, QG2083 | planning Ailion, under assembly, Rockman | |
| sp. 30 | DF5152 | F/M | Gallon Jug, Belize | 15 Nov 2012 | K. Kiontke | Drosophilae subgroup | 4 isofemale lines from Belize | ||||
| sp. 31 | JU2469 | F/M | L. Frézal | Madre de Dios, Peru | Jan 2013 | L. Frézal | Drosophilae super group | 2 isolates from Peru | JU2585 | ||
| sp. 32 | SB454 | F/M | East Africa? | Feb 2013 | W. Sudhaus | Japonica group, sister of sp. 7 | 1 isolate, from the gut of the millipede Archispirostreptus gigas | ||||
| sp. 33 | BRC20065 | F/M | J. Wang | Taiwan | 24 May 2012 | J. Wang | Briggsae subgroup | 1 isolate from Taiwan | BRC20066 | ||
| sp. 34 | NK74SC | F/M | N. Kanzaki | Japan | May 2013 | N. Kanzaki | likely Drosophilae super group | 1 isolate from Japan. Associated with fig wasps and Ficus septica | |||
| sp. 35 | no designation yet | F/M | Indonesia | Aug 2013 | N. Kanzaki | 2 Isolates from Indonesia, associated with Ficus hispida | |||||
| sp. 36 | NK02NV | F/M | N. Kanzaki | Japan | Apr 2013 | N. Kanzaki | 1 isolate from Japan. Associated with the weevil Niphades variegatus | ||||
Species numbers are assigned by Karin Kiontke, NYU.
Published phylogeny:
Kiontke et al. 2011 BMC Evolutionary Biology 11: 339.
Updated phylogeny: http://wormtails.bio.nyu.edu/RhabditinaDB_Images/GenusTrees/CaenorhabditisTree.png
